# Data.download(force=True)
Data
Setup
from katlas.data import *
Kinase Dataset
We will go through how to load kinase information data and phosphorylation sites data.
Datasets used in this study can be accessed through Data
Data
Data ()
A class for fetching various datasets.
You can change it to local path if you want:
=Path('katlas_dataset') Data.DATASET_DIR
Data.download
Data.download (download_dir=None, force=False, verbose=True)
Download dataset zip and extract them in tmp folder if dataset_dir is not given.
Type | Default | Details | |
---|---|---|---|
download_dir | NoneType | None | dest directory of downloaded folder |
force | bool | False | if force, will overwrite the current dataset folder |
verbose | bool | True | print existing dataset folder |
For the first time download or to update data folder:
=True) Data.download(force
Data.read_file
Data.read_file (rel_path)
*Load a CSV or Parquet file from the local dataset folder.
Automatically infers file type from the filename extension. Renames ‘Unnamed: 0’ column to ‘kinase’ if present.*
'kinase_info.csv') Data.read_file(
kinase | ID_coral | uniprot | gene | modi_group | group | family | subfamily_coral | subfamily | in_pspa_st | in_pspa_tyr | in_pspa | in_cddm | kd_ID | active_D1_D2 | active_kd_ID | pspa_ID | pseudo | pspa_category_small | pspa_category_big | cddm_big | cddm_small | length | human_uniprot_sequence | kinasecom_domain | nucleus | cytosol | cytoskeleton | plasma membrane | mitochondrion | Golgi apparatus | endoplasmic reticulum | vesicle | centrosome | aggresome | main_location | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | AAK1 | AAK1 | Q2M2I8 | AAK1 | Other | Other | NAK | NaN | NAK | 1 | 0 | 1 | 0 | Q2M2I8_AAK1_HUMAN_KD1 | 1.0 | Q2M2I8_AAK1_HUMAN_KD1 | AAK1 | 0 | Nak | Nak | NaN | NaN | 961 | MKKFFDSRREQGGSGLGSGSSGGGGSTSGLGSGYIGRVFGIGRQQV... | VTVDEVLAEGGFAIVFLVRTSNGMKCALKRMFVNNEHDLQVCKREI... | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
1 | AATK | LMR1 | Q6ZMQ8 | AATK | TK | TK | Lmr | NaN | Lmr | 0 | 0 | 0 | 0 | Q6ZMQ8_LMTK1_HUMAN_KD1 | 1.0 | Q6ZMQ8_LMTK1_HUMAN_KD1 | NaN | 0 | NaN | NaN | NaN | NaN | 1374 | MSSSFFNPSFAFSSHFDPDGAPLSELSWPSSLAVVAVSFSGLFAVI... | LLYLKEIGRGWFGKVFLGEVNSGISSAQVVVKELQASASVQEQMQF... | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
521 | ZAK | ZAK | Q9NYL2 | MAP3K20 | TKL | TKL | MLK | ZAK | ZAK | 1 | 0 | 1 | 1 | Q9NYL2_M3K20_HUMAN_KD1 | 1.0 | Q9NYL2_M3K20_HUMAN_KD1 | ZAK | 0 | Map3k | Map3k | 2.0 | 9.0 | 800 | MSSLGASFVQIKFDDLQFFENCGGGSFGSVYRAKWISQDKEVAVKK... | LQFFENCGGGSFGSVYRAKWISQDKEVAVKKLLKIEKEAEILSVLS... | 5.0 | 5.0 | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | nucleus |
522 | ZAP70 | ZAP70 | P43403 | ZAP70 | TK | TK | Syk | NaN | Syk | 0 | 1 | 1 | 1 | P43403_ZAP70_HUMAN_KD1 | 1.0 | P43403_ZAP70_HUMAN_KD1 | ZAP70 | 0 | Syk and fak | Syk and fak | 1.0 | 3.0 | 619 | MPDPAAHLPFFYGSISRAEAEEHLKLAGMADGLFLLRQCLRSLGGY... | LIADIELGCGNFGSVRQGVYRMRKKQIDVAIKVLKQGTEKADTEEM... | 3.0 | 5.0 | NaN | 2.0 | NaN | NaN | NaN | NaN | NaN | NaN | cytosol |
523 rows × 36 columns
Kinase info
Data.get_kinase_info
Data.get_kinase_info ()
Get information of 523 human kinases on kinome tree. Group, family, and subfamily classifications are sourced from Coral; full protein sequences are retrieved using UniProt IDs; kinase domain sequences are obtained from KinaseDomain.com; and cellular localization data is extracted from published literature.
Data.get_kinase_info()
kinase | ID_coral | uniprot | gene | modi_group | group | family | subfamily_coral | subfamily | in_pspa_st | in_pspa_tyr | in_pspa | in_cddm | kd_ID | active_D1_D2 | active_kd_ID | pspa_ID | pseudo | pspa_category_small | pspa_category_big | cddm_big | cddm_small | length | human_uniprot_sequence | kinasecom_domain | nucleus | cytosol | cytoskeleton | plasma membrane | mitochondrion | Golgi apparatus | endoplasmic reticulum | vesicle | centrosome | aggresome | main_location | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | AAK1 | AAK1 | Q2M2I8 | AAK1 | Other | Other | NAK | NaN | NAK | 1 | 0 | 1 | 0 | Q2M2I8_AAK1_HUMAN_KD1 | 1.0 | Q2M2I8_AAK1_HUMAN_KD1 | AAK1 | 0 | Nak | Nak | NaN | NaN | 961 | MKKFFDSRREQGGSGLGSGSSGGGGSTSGLGSGYIGRVFGIGRQQV... | VTVDEVLAEGGFAIVFLVRTSNGMKCALKRMFVNNEHDLQVCKREI... | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
1 | AATK | LMR1 | Q6ZMQ8 | AATK | TK | TK | Lmr | NaN | Lmr | 0 | 0 | 0 | 0 | Q6ZMQ8_LMTK1_HUMAN_KD1 | 1.0 | Q6ZMQ8_LMTK1_HUMAN_KD1 | NaN | 0 | NaN | NaN | NaN | NaN | 1374 | MSSSFFNPSFAFSSHFDPDGAPLSELSWPSSLAVVAVSFSGLFAVI... | LLYLKEIGRGWFGKVFLGEVNSGISSAQVVVKELQASASVQEQMQF... | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
521 | ZAK | ZAK | Q9NYL2 | MAP3K20 | TKL | TKL | MLK | ZAK | ZAK | 1 | 0 | 1 | 1 | Q9NYL2_M3K20_HUMAN_KD1 | 1.0 | Q9NYL2_M3K20_HUMAN_KD1 | ZAK | 0 | Map3k | Map3k | 2.0 | 9.0 | 800 | MSSLGASFVQIKFDDLQFFENCGGGSFGSVYRAKWISQDKEVAVKK... | LQFFENCGGGSFGSVYRAKWISQDKEVAVKKLLKIEKEAEILSVLS... | 5.0 | 5.0 | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | nucleus |
522 | ZAP70 | ZAP70 | P43403 | ZAP70 | TK | TK | Syk | NaN | Syk | 0 | 1 | 1 | 1 | P43403_ZAP70_HUMAN_KD1 | 1.0 | P43403_ZAP70_HUMAN_KD1 | ZAP70 | 0 | Syk and fak | Syk and fak | 1.0 | 3.0 | 619 | MPDPAAHLPFFYGSISRAEAEEHLKLAGMADGLFLLRQCLRSLGGY... | LIADIELGCGNFGSVRQGVYRMRKKQIDVAIKVLKQGTEKADTEEM... | 3.0 | 5.0 | NaN | 2.0 | NaN | NaN | NaN | NaN | NaN | NaN | cytosol |
523 rows × 36 columns
Data.get_kinase_uniprot
Data.get_kinase_uniprot ()
Get information of 672 uniprot human kinases, which were retrieved from UniProt by filtering all human protein entries using the keyword ‘kinase’. It includes additional pseudokinases and lipid kinases.
Data.get_kinase_uniprot()
Entry | Entry Name | Protein names | Gene Names | uniprot_keyword_kinase | on_tree | Organism | Keywords | Sequence | |
---|---|---|---|---|---|---|---|---|---|
0 | A2RU49 | HYKK_HUMAN | Hydroxylysine kinase (5-hydroxy-L-lysine kinas... | HYKK AGPHD1 | 1 | 0 | Homo sapiens (Human) | Alternative splicing;Cytoplasm;Kinase;Proteomi... | MSSGNYQQSEALSKPTFSEEQASALVESVFGLKVSKVRPLPSYDDQ... |
1 | A4D2B8 | PM2P1_HUMAN | Putative postmeiotic segregation increased 2-l... | PMS2P1 PMS2L1 PMS2L13 PMS2L6 PMS2L8 PMS3 PMS8 ... | 1 | 0 | Homo sapiens (Human) | Alternative splicing;Kinase;Reference proteome... | MVTMCGGHRPENFLHQVLTEFGEELAGEGKSEVGGGAPRSYLQVAS... |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
670 | Q8NCB2 | CAMKV_HUMAN | CaM kinase-like vesicle-associated protein | CAMKV | 0 | 1 | Homo sapiens (Human) | Alternative splicing;Calmodulin-binding;Cell m... | MPFGCVTLGDKKNYNQPSEVTDRYDLGQVIKTEEFCEIFRAKDKTT... |
671 | Q8IV63 | VRK3_HUMAN | Serine/threonine-protein kinase VRK3 (EC 2.7.1... | VRK3 | 0 | 1 | Homo sapiens (Human) | 3D-structure;Alternative splicing;Cytoplasm;Nu... | MISFCPDCGKSIQAAFKFCPYCGNSLPVEEHVGSQTFVNPHVSSFQ... |
672 rows × 9 columns
Data.get_kd_uniprot
Data.get_kd_uniprot ()
Kinase domains extracted from UniProt database.
Data.get_kd_uniprot()
kd_ID | Uniprot | Entry Name | Protein names | Gene Names | Gene Names (primary) | Organism | kd_note | kd_evidence | kd_start | kd_end | kd_seq | Domain [FT] | Domain [CC] | Region | Motif | Protein families | Reactome | ComplexPortal | Subcellular location [CC] | Gene Ontology (biological process) | Tissue specificity | Interacts with | Subunit structure | Function [CC] | Activity regulation | full_seq | D1 | D2 | D3 | N1 | active_D1_D2 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | A0A075F7E9_LERK1_ORYSI_KD1 | A0A075F7E9 | LERK1_ORYSI | G-type lectin S-receptor-like serine/threonine... | LECRK1 LECRK OsI_14840 | LECRK1 | Oryza sativa subsp. indica (Rice) | Protein kinase | ECO:0000255|PROSITE-ProRule:PRU00159 | 523 | 797 | AGFHEILGAGASGVVYKGQLEDELKTNIAVKTIHKLQPETEKEFMV... | DOMAIN 22..149; /note="Bulb-type lectin"; /evi... | None | None | None | Protein kinase superfamily, Ser/Thr protein ki... | None | None | SUBCELLULAR LOCATION: Membrane {ECO:0000255}; ... | defense response [GO:0006952]; response to oth... | TISSUE SPECIFICITY: Expressed in plumules, rad... | None | SUBUNIT: Interacts (via kinase domain) with AD... | FUNCTION: Involved in innate immunity. Require... | None | MVALLLFPMLLQLLSPTCAQTQKNITLGSTLAPQGPASSWLSPSGD... | 1 | 1 | 1 | 1 | 1 |
1 | A0A078BQP2_GCY25_CAEEL_KD1 | A0A078BQP2 | GCY25_CAEEL | Receptor-type guanylate cyclase gcy-25 (EC 4.6... | gcy-25 Y105C5B.2 | gcy-25 | Caenorhabditis elegans | Protein kinase | ECO:0000255|PROSITE-ProRule:PRU00159 | 464 | 749 | RVSTISTARASYSSIFSGNVAEHAIVNKQKVSVKRHVQRRAITFSR... | DOMAIN 464..749; /note="Protein kinase"; /evid... | DOMAIN: The protein kinase domain is predicted... | None | None | Adenylyl cyclase class-4/guanylyl cyclase family | R-CEL-2514859; | None | SUBCELLULAR LOCATION: Cell membrane {ECO:00003... | cGMP biosynthetic process [GO:0006182]; intrac... | TISSUE SPECIFICITY: Expressed in AQR, PQR and ... | None | None | FUNCTION: Guanylate cyclase involved in the pr... | None | MLLLLLLLKISTFVDSFQIGHLEFENSNETRILEICMKNAGSWRDH... | 0 | 0 | 1 | 0 | 0 |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
5534 | X5M5N0_WNK_CAEEL_KD1 | X5M5N0 | WNK_CAEEL | Serine/threonine-protein kinase WNK (EC 2.7.11... | wnk-1 C46C2.1 | wnk-1 | Caenorhabditis elegans | Protein kinase | ECO:0000255|PROSITE-ProRule:PRU00159 | 334 | 596 | LKFDEELGRGSFKTVFRGLDTETGVAVAWCELQESKLNKTERQRFR... | DOMAIN 334..596; /note="Protein kinase"; /evid... | DOMAIN: Disordered regions undergo liquid-liqu... | None | None | Protein kinase superfamily, Ser/Thr protein ki... | None | None | SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|U... | cell volume homeostasis [GO:0006884]; cellular... | TISSUE SPECIFICITY: Expressed in pharynx, nerv... | G5EEN4 | SUBUNIT: Interacts with gck-3 (via C-terminus)... | FUNCTION: Serine/threonine-protein kinase comp... | ACTIVITY REGULATION: Activated in response to ... | MPDSITNGGRPPAPPSSVSSTTASTTGNFGTRRRLVNRIKKVDELH... | 1 | 1 | 1 | 1 | 1 |
5535 | X5M8U1_GCY17_CAEEL_KD1 | X5M8U1 | GCY17_CAEEL | Receptor-type guanylate cyclase gcy-17 (EC 4.6... | gcy-17 W03F11.2 | gcy-17 | Caenorhabditis elegans | Protein kinase | ECO:0000255|PROSITE-ProRule:PRU00159 | 535 | 824 | EASQRSFASGPSTSTKLTVESRTETTRFIFYIYQVRNNEVVAANKH... | DOMAIN 535..824; /note="Protein kinase"; /evid... | DOMAIN: The protein kinase domain is predicted... | None | None | Adenylyl cyclase class-4/guanylyl cyclase family | R-CEL-2514859; | None | SUBCELLULAR LOCATION: Cell membrane {ECO:00003... | cGMP biosynthetic process [GO:0006182]; intrac... | TISSUE SPECIFICITY: Expressed in PHA sensory n... | None | None | FUNCTION: Guanylate cyclase involved in the pr... | None | MLFLRLFIFTPFLILANCQARRTIKVGLLFVQNVSSLQVGIGYRTS... | 0 | 1 | 1 | 0 | 0 |
5536 rows × 32 columns
PSPA data
get_pspa_tyr_norm
get_pspa_tyr_norm ()
Get PSPA normalized data of tyrosine kinase.
Data.get_pspa_tyr_norm()
-5P | -5G | -5A | -5C | -5S | -5T | -5V | -5I | -5L | -5M | -5F | -5Y | -5W | -5H | -5K | -5R | -5Q | -5N | -5D | -5E | -5s | -5t | -5y | -4P | -4G | -4A | -4C | -4S | -4T | -4V | -4I | -4L | -4M | -4F | -4Y | -4W | -4H | -4K | -4R | -4Q | -4N | -4D | -4E | -4s | -4t | -4y | -3P | -3G | -3A | -3C | ... | 4A | 4C | 4S | 4T | 4V | 4I | 4L | 4M | 4F | 4Y | 4W | 4H | 4K | 4R | 4Q | 4N | 4D | 4E | 4s | 4t | 4y | 5P | 5G | 5A | 5C | 5S | 5T | 5V | 5I | 5L | 5M | 5F | 5Y | 5W | 5H | 5K | 5R | 5Q | 5N | 5D | 5E | 5s | 5t | 5y | 0S | 0T | 0Y | 0s | 0t | 0y | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
kinase | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ABL1 | 0.0668 | 0.0689 | 0.0646 | 0.0520 | 0.0564 | 0.0539 | 0.0485 | 0.0448 | 0.0520 | 0.0536 | 0.0454 | 0.0454 | 0.0283 | 0.0597 | 0.0600 | 0.0662 | 0.0594 | 0.0606 | 0.0575 | 0.0535 | 0.0507 | 0.0507 | 0.0658 | 0.0680 | 0.0758 | 0.0687 | 0.0518 | 0.0478 | 0.0442 | 0.0561 | 0.0443 | 0.0547 | 0.0491 | 0.0390 | 0.0390 | 0.0345 | 0.0496 | 0.0485 | 0.0530 | 0.0655 | 0.0502 | 0.0667 | 0.0843 | 0.0618 | 0.0618 | 0.0925 | 0.0634 | 0.0642 | 0.0568 | 0.0527 | ... | 0.0526 | 0.0584 | 0.0563 | 0.0522 | 0.0514 | 0.0429 | 0.0510 | 0.0664 | 0.0645 | 0.0645 | 0.0600 | 0.0647 | 0.0647 | 0.0757 | 0.0607 | 0.0499 | 0.0322 | 0.0342 | 0.0217 | 0.0217 | 0.0306 | 0.0769 | 0.0707 | 0.0624 | 0.0493 | 0.0591 | 0.0661 | 0.0553 | 0.0378 | 0.0548 | 0.0603 | 0.0392 | 0.0392 | 0.0413 | 0.0613 | 0.0652 | 0.0756 | 0.0526 | 0.0512 | 0.0362 | 0.0339 | 0.0254 | 0.0254 | 0.0337 | 0 | 0 | 1 | 0 | 0 | 1 |
TNK2 | 0.0679 | 0.0818 | 0.0627 | 0.0617 | 0.0529 | 0.0528 | 0.0419 | 0.0463 | 0.0437 | 0.0453 | 0.0539 | 0.0539 | 0.0598 | 0.0583 | 0.0624 | 0.0727 | 0.0537 | 0.0553 | 0.0451 | 0.0435 | 0.0430 | 0.0430 | 0.0555 | 0.0723 | 0.0682 | 0.0665 | 0.0567 | 0.0458 | 0.0423 | 0.0436 | 0.0426 | 0.0433 | 0.0495 | 0.0584 | 0.0584 | 0.0697 | 0.0556 | 0.0664 | 0.0757 | 0.0647 | 0.0532 | 0.0409 | 0.0413 | 0.0398 | 0.0398 | 0.0493 | 0.0755 | 0.0653 | 0.0572 | 0.0544 | ... | 0.0580 | 0.0648 | 0.0670 | 0.0571 | 0.0470 | 0.0493 | 0.0412 | 0.0568 | 0.0516 | 0.0516 | 0.0499 | 0.0559 | 0.0430 | 0.0553 | 0.0485 | 0.0502 | 0.0416 | 0.0464 | 0.0452 | 0.0452 | 0.0533 | 0.0644 | 0.0599 | 0.0609 | 0.0629 | 0.0564 | 0.0634 | 0.0527 | 0.0502 | 0.0641 | 0.0539 | 0.0679 | 0.0679 | 0.0680 | 0.0499 | 0.0385 | 0.0302 | 0.0531 | 0.0465 | 0.0630 | 0.0572 | 0.0364 | 0.0364 | 0.0572 | 0 | 0 | 1 | 0 | 0 | 1 |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
YES1 | 0.0677 | 0.0571 | 0.0537 | 0.0530 | 0.0527 | 0.0505 | 0.0435 | 0.0375 | 0.0400 | 0.0463 | 0.0478 | 0.0478 | 0.0419 | 0.0564 | 0.0681 | 0.0647 | 0.0610 | 0.0752 | 0.0748 | 0.0610 | 0.0652 | 0.0652 | 0.0668 | 0.0625 | 0.0695 | 0.0524 | 0.0530 | 0.0470 | 0.0404 | 0.0476 | 0.0416 | 0.0528 | 0.0529 | 0.0406 | 0.0406 | 0.0424 | 0.0566 | 0.0549 | 0.0561 | 0.0607 | 0.0559 | 0.0786 | 0.0875 | 0.0596 | 0.0596 | 0.0705 | 0.0564 | 0.0580 | 0.0456 | 0.0572 | ... | 0.0464 | 0.0747 | 0.0521 | 0.0561 | 0.0468 | 0.0452 | 0.0481 | 0.0716 | 0.0689 | 0.0689 | 0.0619 | 0.0623 | 0.0587 | 0.0757 | 0.0652 | 0.0499 | 0.0421 | 0.0492 | 0.0371 | 0.0371 | 0.0467 | 0.0762 | 0.0532 | 0.0533 | 0.0610 | 0.0596 | 0.0558 | 0.0416 | 0.0375 | 0.0467 | 0.0518 | 0.0627 | 0.0627 | 0.0456 | 0.0593 | 0.0662 | 0.0840 | 0.0559 | 0.0604 | 0.0422 | 0.0482 | 0.0374 | 0.0374 | 0.0411 | 0 | 0 | 1 | 0 | 0 | 1 |
ZAP70 | 0.0602 | 0.0880 | 0.0623 | 0.0496 | 0.0471 | 0.0514 | 0.0465 | 0.0380 | 0.0307 | 0.0526 | 0.0479 | 0.0479 | 0.0347 | 0.0641 | 0.0471 | 0.0452 | 0.0492 | 0.0703 | 0.0870 | 0.0777 | 0.1622 | 0.1622 | 0.1208 | 0.0977 | 0.0792 | 0.0865 | 0.0556 | 0.0487 | 0.0367 | 0.0375 | 0.0312 | 0.0317 | 0.0344 | 0.0274 | 0.0274 | 0.0347 | 0.0474 | 0.0338 | 0.0380 | 0.0571 | 0.0457 | 0.0929 | 0.1392 | 0.1432 | 0.1432 | 0.1685 | 0.0588 | 0.0610 | 0.0537 | 0.0581 | ... | 0.0491 | 0.0520 | 0.0583 | 0.0530 | 0.0504 | 0.0304 | 0.0424 | 0.0554 | 0.0393 | 0.0393 | 0.0539 | 0.0671 | 0.0562 | 0.0557 | 0.0712 | 0.0406 | 0.0597 | 0.0558 | 0.0440 | 0.0440 | 0.0318 | 0.1269 | 0.0904 | 0.0737 | 0.0457 | 0.0638 | 0.0692 | 0.0343 | 0.0235 | 0.0305 | 0.0461 | 0.0343 | 0.0343 | 0.0344 | 0.0484 | 0.0477 | 0.0290 | 0.0520 | 0.0537 | 0.0709 | 0.0710 | 0.0862 | 0.0862 | 0.0605 | 0 | 0 | 1 | 0 | 0 | 1 |
93 rows × 236 columns
get_pspa_st_norm
get_pspa_st_norm ()
Get PSPA normalized data of serine/threonine kinase.
Data.get_pspa_st_norm()
-5P | -5G | -5A | -5C | -5S | -5T | -5V | -5I | -5L | -5M | -5F | -5Y | -5W | -5H | -5K | -5R | -5Q | -5N | -5D | -5E | -5s | -5t | -5y | -4P | -4G | -4A | -4C | -4S | -4T | -4V | -4I | -4L | -4M | -4F | -4Y | -4W | -4H | -4K | -4R | -4Q | -4N | -4D | -4E | -4s | -4t | -4y | -3P | -3G | -3A | -3C | ... | 3A | 3C | 3S | 3T | 3V | 3I | 3L | 3M | 3F | 3Y | 3W | 3H | 3K | 3R | 3Q | 3N | 3D | 3E | 3s | 3t | 3y | 4P | 4G | 4A | 4C | 4S | 4T | 4V | 4I | 4L | 4M | 4F | 4Y | 4W | 4H | 4K | 4R | 4Q | 4N | 4D | 4E | 4s | 4t | 4y | 0s | 0t | 0y | 0S | 0T | 0Y | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
kinase | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AAK1 | 0.0720 | 0.0245 | 0.0284 | 0.0456 | 0.0425 | 0.0425 | 0.0951 | 0.1554 | 0.0993 | 0.0864 | 0.0425 | 0.0952 | 0.0315 | 0.0331 | 0.0262 | 0.0956 | 0.0560 | 0.0275 | 0.0160 | 0.0153 | 0.0201 | 0.0201 | 0.0611 | 0.0534 | 0.0642 | 0.0706 | 0.0560 | 0.0619 | 0.0619 | 0.0619 | 0.0621 | 0.0742 | 0.0693 | 0.0520 | 0.0534 | 0.0403 | 0.0514 | 0.0809 | 0.0715 | 0.0627 | 0.0429 | 0.0332 | 0.0560 | 0.0332 | 0.0332 | 0.0339 | 0.1084 | 0.0512 | 0.1119 | 0.0655 | ... | 0.0582 | 0.0742 | 0.0582 | 0.0582 | 0.0610 | 0.0388 | 0.0489 | 0.0437 | 0.0430 | 0.0533 | 0.0481 | 0.0674 | 0.0739 | 0.0901 | 0.0623 | 0.0735 | 0.0405 | 0.0371 | 0.0335 | 0.0335 | 0.0359 | 0.0628 | 0.0702 | 0.0646 | 0.0603 | 0.0560 | 0.0560 | 0.0422 | 0.0415 | 0.0461 | 0.0464 | 0.0523 | 0.0521 | 0.0826 | 0.0560 | 0.0831 | 0.0928 | 0.0635 | 0.0592 | 0.0389 | 0.0457 | 0.0251 | 0.0251 | 0.0270 | 0.1013 | 1.0 | 0.0 | 0.1013 | 1.0 | 0.0 |
ACVR2A | 0.0415 | 0.0481 | 0.0584 | 0.0489 | 0.0578 | 0.0578 | 0.0598 | 0.0625 | 0.0596 | 0.0521 | 0.0600 | 0.0578 | 0.0803 | 0.0570 | 0.0510 | 0.0475 | 0.0430 | 0.0536 | 0.0888 | 0.0789 | 0.0783 | 0.0783 | 0.0760 | 0.0466 | 0.0549 | 0.0555 | 0.0551 | 0.0549 | 0.0549 | 0.0543 | 0.0526 | 0.0520 | 0.0576 | 0.0619 | 0.0586 | 0.0754 | 0.0551 | 0.0406 | 0.0457 | 0.0482 | 0.0501 | 0.1040 | 0.0869 | 0.0809 | 0.0809 | 0.0681 | 0.0502 | 0.0653 | 0.0537 | 0.0588 | ... | 0.0529 | 0.0481 | 0.0590 | 0.0590 | 0.0567 | 0.0554 | 0.0612 | 0.0589 | 0.0644 | 0.0654 | 0.0635 | 0.0590 | 0.0462 | 0.0387 | 0.0499 | 0.0524 | 0.0622 | 0.0870 | 0.0519 | 0.0519 | 0.0815 | 0.0758 | 0.0544 | 0.0498 | 0.0517 | 0.0563 | 0.0563 | 0.0516 | 0.0563 | 0.0512 | 0.0662 | 0.0523 | 0.0579 | 0.0800 | 0.0573 | 0.0527 | 0.0491 | 0.0616 | 0.0556 | 0.0640 | 0.0640 | 0.0703 | 0.0703 | 0.0589 | 0.9833 | 1.0 | 0.0 | 0.9833 | 1.0 | 0.0 |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
YSK4 | 0.0593 | 0.0728 | 0.0744 | 0.0734 | 0.0597 | 0.0597 | 0.0517 | 0.0400 | 0.0433 | 0.0512 | 0.0636 | 0.0600 | 0.0755 | 0.0664 | 0.0525 | 0.0597 | 0.0481 | 0.0616 | 0.0692 | 0.0508 | 0.0703 | 0.0703 | 0.0474 | 0.0622 | 0.0683 | 0.0618 | 0.0652 | 0.0618 | 0.0618 | 0.0477 | 0.0412 | 0.0519 | 0.0570 | 0.0610 | 0.0620 | 0.0714 | 0.0626 | 0.0491 | 0.0523 | 0.0551 | 0.0649 | 0.0671 | 0.0645 | 0.0663 | 0.0663 | 0.0534 | 0.0561 | 0.0683 | 0.0571 | 0.0636 | ... | 0.0531 | 0.0545 | 0.0578 | 0.0578 | 0.0540 | 0.0436 | 0.0481 | 0.0473 | 0.0573 | 0.0578 | 0.0625 | 0.0645 | 0.0774 | 0.0697 | 0.0580 | 0.0720 | 0.0471 | 0.0450 | 0.0642 | 0.0642 | 0.0397 | 0.0790 | 0.0721 | 0.0573 | 0.0557 | 0.0573 | 0.0573 | 0.0445 | 0.0471 | 0.0481 | 0.0507 | 0.0461 | 0.0493 | 0.0539 | 0.0657 | 0.0814 | 0.0618 | 0.0741 | 0.0620 | 0.0585 | 0.0484 | 0.0634 | 0.0634 | 0.0389 | 0.7907 | 1.0 | 0.0 | 0.7907 | 1.0 | 0.0 |
ZAK | 0.0604 | 0.0641 | 0.0659 | 0.0631 | 0.0597 | 0.0597 | 0.0454 | 0.0431 | 0.0477 | 0.0484 | 0.0544 | 0.0597 | 0.0673 | 0.0650 | 0.0815 | 0.0669 | 0.0538 | 0.0653 | 0.0591 | 0.0520 | 0.0716 | 0.0716 | 0.0611 | 0.0627 | 0.0682 | 0.0537 | 0.0621 | 0.0627 | 0.0627 | 0.0447 | 0.0423 | 0.0433 | 0.0500 | 0.0526 | 0.0564 | 0.0630 | 0.0663 | 0.0634 | 0.0653 | 0.0548 | 0.0701 | 0.0759 | 0.0673 | 0.0703 | 0.0703 | 0.0469 | 0.0723 | 0.0694 | 0.0593 | 0.0680 | ... | 0.0489 | 0.0588 | 0.0582 | 0.0582 | 0.0579 | 0.0636 | 0.0630 | 0.0572 | 0.0652 | 0.0710 | 0.0738 | 0.0664 | 0.0851 | 0.0833 | 0.0527 | 0.0484 | 0.0281 | 0.0319 | 0.0459 | 0.0459 | 0.0423 | 0.0684 | 0.0623 | 0.0561 | 0.0519 | 0.0556 | 0.0556 | 0.0406 | 0.0429 | 0.0395 | 0.0481 | 0.0424 | 0.0526 | 0.0698 | 0.0672 | 0.1207 | 0.1012 | 0.0614 | 0.0556 | 0.0342 | 0.0370 | 0.0390 | 0.0390 | 0.0408 | 0.6135 | 1.0 | 0.0 | 0.6135 | 1.0 | 0.0 |
303 rows × 213 columns
get_pspa_all_norm
get_pspa_all_norm ()
Get PSPA normalized data of serine/threonine and tyrosine kinases.
Data.get_pspa_all_norm()
-5P | -5G | -5A | -5C | -5S | -5T | -5V | -5I | -5L | -5M | -5F | -5Y | -5W | -5H | -5K | -5R | -5Q | -5N | -5D | -5E | -5s | -5t | -5y | -4P | -4G | -4A | -4C | -4S | -4T | -4V | -4I | -4L | -4M | -4F | -4Y | -4W | -4H | -4K | -4R | -4Q | -4N | -4D | -4E | -4s | -4t | -4y | -3P | -3G | -3A | -3C | ... | 4A | 4C | 4S | 4T | 4V | 4I | 4L | 4M | 4F | 4Y | 4W | 4H | 4K | 4R | 4Q | 4N | 4D | 4E | 4s | 4t | 4y | 0s | 0t | 0y | 0S | 0T | 0Y | 5P | 5G | 5A | 5C | 5S | 5T | 5V | 5I | 5L | 5M | 5F | 5Y | 5W | 5H | 5K | 5R | 5Q | 5N | 5D | 5E | 5s | 5t | 5y | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
kinase | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AAK1 | 0.0720 | 0.0245 | 0.0284 | 0.0456 | 0.0425 | 0.0425 | 0.0951 | 0.1554 | 0.0993 | 0.0864 | 0.0425 | 0.0952 | 0.0315 | 0.0331 | 0.0262 | 0.0956 | 0.0560 | 0.0275 | 0.0160 | 0.0153 | 0.0201 | 0.0201 | 0.0611 | 0.0534 | 0.0642 | 0.0706 | 0.0560 | 0.0619 | 0.0619 | 0.0619 | 0.0621 | 0.0742 | 0.0693 | 0.0520 | 0.0534 | 0.0403 | 0.0514 | 0.0809 | 0.0715 | 0.0627 | 0.0429 | 0.0332 | 0.0560 | 0.0332 | 0.0332 | 0.0339 | 0.1084 | 0.0512 | 0.1119 | 0.0655 | ... | 0.0646 | 0.0603 | 0.0560 | 0.0560 | 0.0422 | 0.0415 | 0.0461 | 0.0464 | 0.0523 | 0.0521 | 0.0826 | 0.0560 | 0.0831 | 0.0928 | 0.0635 | 0.0592 | 0.0389 | 0.0457 | 0.0251 | 0.0251 | 0.0270 | 0.1013 | 1.0 | 0.0 | 0.1013 | 1.0 | 0.0 | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
ACVR2A | 0.0415 | 0.0481 | 0.0584 | 0.0489 | 0.0578 | 0.0578 | 0.0598 | 0.0625 | 0.0596 | 0.0521 | 0.0600 | 0.0578 | 0.0803 | 0.0570 | 0.0510 | 0.0475 | 0.0430 | 0.0536 | 0.0888 | 0.0789 | 0.0783 | 0.0783 | 0.0760 | 0.0466 | 0.0549 | 0.0555 | 0.0551 | 0.0549 | 0.0549 | 0.0543 | 0.0526 | 0.0520 | 0.0576 | 0.0619 | 0.0586 | 0.0754 | 0.0551 | 0.0406 | 0.0457 | 0.0482 | 0.0501 | 0.1040 | 0.0869 | 0.0809 | 0.0809 | 0.0681 | 0.0502 | 0.0653 | 0.0537 | 0.0588 | ... | 0.0498 | 0.0517 | 0.0563 | 0.0563 | 0.0516 | 0.0563 | 0.0512 | 0.0662 | 0.0523 | 0.0579 | 0.0800 | 0.0573 | 0.0527 | 0.0491 | 0.0616 | 0.0556 | 0.0640 | 0.0640 | 0.0703 | 0.0703 | 0.0589 | 0.9833 | 1.0 | 0.0 | 0.9833 | 1.0 | 0.0 | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
YES1 | 0.0677 | 0.0571 | 0.0537 | 0.0530 | 0.0527 | 0.0505 | 0.0435 | 0.0375 | 0.0400 | 0.0463 | 0.0478 | 0.0478 | 0.0419 | 0.0564 | 0.0681 | 0.0647 | 0.0610 | 0.0752 | 0.0748 | 0.0610 | 0.0652 | 0.0652 | 0.0668 | 0.0625 | 0.0695 | 0.0524 | 0.0530 | 0.0470 | 0.0404 | 0.0476 | 0.0416 | 0.0528 | 0.0529 | 0.0406 | 0.0406 | 0.0424 | 0.0566 | 0.0549 | 0.0561 | 0.0607 | 0.0559 | 0.0786 | 0.0875 | 0.0596 | 0.0596 | 0.0705 | 0.0564 | 0.0580 | 0.0456 | 0.0572 | ... | 0.0464 | 0.0747 | 0.0521 | 0.0561 | 0.0468 | 0.0452 | 0.0481 | 0.0716 | 0.0689 | 0.0689 | 0.0619 | 0.0623 | 0.0587 | 0.0757 | 0.0652 | 0.0499 | 0.0421 | 0.0492 | 0.0371 | 0.0371 | 0.0467 | 0.0000 | 0.0 | 1.0 | 0.0000 | 0.0 | 1.0 | 0.0762 | 0.0532 | 0.0533 | 0.0610 | 0.0596 | 0.0558 | 0.0416 | 0.0375 | 0.0467 | 0.0518 | 0.0627 | 0.0627 | 0.0456 | 0.0593 | 0.0662 | 0.084 | 0.0559 | 0.0604 | 0.0422 | 0.0482 | 0.0374 | 0.0374 | 0.0411 |
ZAP70 | 0.0602 | 0.0880 | 0.0623 | 0.0496 | 0.0471 | 0.0514 | 0.0465 | 0.0380 | 0.0307 | 0.0526 | 0.0479 | 0.0479 | 0.0347 | 0.0641 | 0.0471 | 0.0452 | 0.0492 | 0.0703 | 0.0870 | 0.0777 | 0.1622 | 0.1622 | 0.1208 | 0.0977 | 0.0792 | 0.0865 | 0.0556 | 0.0487 | 0.0367 | 0.0375 | 0.0312 | 0.0317 | 0.0344 | 0.0274 | 0.0274 | 0.0347 | 0.0474 | 0.0338 | 0.0380 | 0.0571 | 0.0457 | 0.0929 | 0.1392 | 0.1432 | 0.1432 | 0.1685 | 0.0588 | 0.0610 | 0.0537 | 0.0581 | ... | 0.0491 | 0.0520 | 0.0583 | 0.0530 | 0.0504 | 0.0304 | 0.0424 | 0.0554 | 0.0393 | 0.0393 | 0.0539 | 0.0671 | 0.0562 | 0.0557 | 0.0712 | 0.0406 | 0.0597 | 0.0558 | 0.0440 | 0.0440 | 0.0318 | 0.0000 | 0.0 | 1.0 | 0.0000 | 0.0 | 1.0 | 0.1269 | 0.0904 | 0.0737 | 0.0457 | 0.0638 | 0.0692 | 0.0343 | 0.0235 | 0.0305 | 0.0461 | 0.0343 | 0.0343 | 0.0344 | 0.0484 | 0.0477 | 0.029 | 0.0520 | 0.0537 | 0.0709 | 0.0710 | 0.0862 | 0.0862 | 0.0605 |
396 rows × 236 columns
get_pspa_all_scale
get_pspa_all_scale ()
Get PSPA (-5 to +4) scaled data from PSPA normalized data. Each position (including both pS/pT and pS=pT) are normalized to 1.
Data.get_pspa_all_scale()
-5P | -5G | -5A | -5C | -5S | -5T | -5V | -5I | -5L | -5M | -5F | -5Y | -5W | -5H | -5K | -5R | -5Q | -5N | -5D | -5E | -5pS | -5pT | -5pY | -4P | -4G | -4A | -4C | -4S | -4T | -4V | -4I | -4L | -4M | -4F | -4Y | -4W | -4H | -4K | -4R | -4Q | -4N | -4D | -4E | -4pS | -4pT | -4pY | -3P | -3G | -3A | -3C | ... | 2E | 2pS | 2pT | 2pY | 3P | 3G | 3A | 3C | 3S | 3T | 3V | 3I | 3L | 3M | 3F | 3Y | 3W | 3H | 3K | 3R | 3Q | 3N | 3D | 3E | 3pS | 3pT | 3pY | 4P | 4G | 4A | 4C | 4S | 4T | 4V | 4I | 4L | 4M | 4F | 4Y | 4W | 4H | 4K | 4R | 4Q | 4N | 4D | 4E | 4pS | 4pT | 4pY | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
kinase | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AAK1 | 0.05845 | 0.01989 | 0.02305 | 0.03702 | 0.03450 | 0.03450 | 0.07720 | 0.12615 | 0.08061 | 0.07014 | 0.03450 | 0.07728 | 0.02557 | 0.02687 | 0.02127 | 0.07760 | 0.04546 | 0.02232 | 0.01299 | 0.01242 | 0.01632 | 0.01632 | 0.04960 | 0.04172 | 0.05015 | 0.05515 | 0.04375 | 0.04836 | 0.04836 | 0.04836 | 0.04851 | 0.05796 | 0.05414 | 0.04062 | 0.04172 | 0.03148 | 0.04015 | 0.06320 | 0.05586 | 0.04898 | 0.03351 | 0.02594 | 0.04375 | 0.02594 | 0.02594 | 0.02648 | 0.08610 | 0.04067 | 0.08888 | 0.05203 | ... | 0.04025 | 0.03142 | 0.03142 | 0.03149 | 0.05264 | 0.07135 | 0.04499 | 0.05735 | 0.04499 | 0.04499 | 0.04715 | 0.02999 | 0.03780 | 0.03378 | 0.03324 | 0.04120 | 0.03718 | 0.05210 | 0.05712 | 0.06965 | 0.04816 | 0.05681 | 0.03131 | 0.02868 | 0.02589 | 0.02589 | 0.02775 | 0.05026 | 0.05618 | 0.05170 | 0.04826 | 0.04482 | 0.04482 | 0.03377 | 0.03321 | 0.03689 | 0.03713 | 0.04186 | 0.04170 | 0.06611 | 0.04482 | 0.06651 | 0.07427 | 0.05082 | 0.04738 | 0.03113 | 0.03657 | 0.02009 | 0.02009 | 0.02161 |
ACVR2A | 0.02971 | 0.03443 | 0.04180 | 0.03500 | 0.04137 | 0.04137 | 0.04281 | 0.04474 | 0.04266 | 0.03729 | 0.04295 | 0.04137 | 0.05748 | 0.04080 | 0.03651 | 0.03400 | 0.03078 | 0.03837 | 0.06356 | 0.05648 | 0.05605 | 0.05605 | 0.05440 | 0.03341 | 0.03936 | 0.03979 | 0.03950 | 0.03936 | 0.03936 | 0.03893 | 0.03771 | 0.03728 | 0.04130 | 0.04438 | 0.04201 | 0.05406 | 0.03950 | 0.02911 | 0.03276 | 0.03456 | 0.03592 | 0.07456 | 0.06230 | 0.05800 | 0.05800 | 0.04882 | 0.03345 | 0.04351 | 0.03578 | 0.03918 | ... | 0.04447 | 0.04786 | 0.04786 | 0.03799 | 0.04958 | 0.04381 | 0.03914 | 0.03559 | 0.04366 | 0.04366 | 0.04196 | 0.04099 | 0.04529 | 0.04358 | 0.04765 | 0.04839 | 0.04699 | 0.04366 | 0.03419 | 0.02864 | 0.03692 | 0.03877 | 0.04603 | 0.06438 | 0.03840 | 0.03840 | 0.06031 | 0.05559 | 0.03989 | 0.03652 | 0.03791 | 0.04129 | 0.04129 | 0.03784 | 0.04129 | 0.03755 | 0.04855 | 0.03835 | 0.04246 | 0.05867 | 0.04202 | 0.03865 | 0.03601 | 0.04517 | 0.04077 | 0.04693 | 0.04693 | 0.05155 | 0.05155 | 0.04319 |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
YES1 | 0.05216 | 0.04399 | 0.04137 | 0.04084 | 0.04060 | 0.03891 | 0.03352 | 0.02889 | 0.03082 | 0.03567 | 0.03683 | 0.03683 | 0.03228 | 0.04345 | 0.05247 | 0.04985 | 0.04700 | 0.05794 | 0.05763 | 0.04700 | 0.05023 | 0.05023 | 0.05147 | 0.04870 | 0.05416 | 0.04083 | 0.04130 | 0.03662 | 0.03148 | 0.03709 | 0.03242 | 0.04114 | 0.04122 | 0.03164 | 0.03164 | 0.03304 | 0.04411 | 0.04278 | 0.04372 | 0.04730 | 0.04356 | 0.06125 | 0.06818 | 0.04644 | 0.04644 | 0.05494 | 0.04363 | 0.04486 | 0.03527 | 0.04425 | ... | 0.05324 | 0.05535 | 0.05535 | 0.05174 | 0.02228 | 0.02870 | 0.02669 | 0.03458 | 0.02886 | 0.03899 | 0.05880 | 0.06545 | 0.06259 | 0.04333 | 0.12155 | 0.12155 | 0.07172 | 0.04309 | 0.02375 | 0.03923 | 0.02576 | 0.02824 | 0.02120 | 0.02352 | 0.02135 | 0.02135 | 0.02739 | 0.03449 | 0.04429 | 0.03670 | 0.05908 | 0.04121 | 0.04437 | 0.03702 | 0.03575 | 0.03804 | 0.05663 | 0.05450 | 0.05450 | 0.04896 | 0.04928 | 0.04643 | 0.05988 | 0.05157 | 0.03947 | 0.03330 | 0.03891 | 0.02934 | 0.02934 | 0.03694 |
ZAP70 | 0.03902 | 0.05704 | 0.04038 | 0.03215 | 0.03053 | 0.03332 | 0.03014 | 0.02463 | 0.01990 | 0.03410 | 0.03105 | 0.03105 | 0.02249 | 0.04155 | 0.03053 | 0.02930 | 0.03189 | 0.04557 | 0.05639 | 0.05037 | 0.10514 | 0.10514 | 0.07830 | 0.06354 | 0.05151 | 0.05625 | 0.03616 | 0.03167 | 0.02387 | 0.02439 | 0.02029 | 0.02062 | 0.02237 | 0.01782 | 0.01782 | 0.02257 | 0.03083 | 0.02198 | 0.02471 | 0.03713 | 0.02972 | 0.06041 | 0.09052 | 0.09313 | 0.09313 | 0.10958 | 0.03211 | 0.03331 | 0.02933 | 0.03173 | ... | 0.04035 | 0.08151 | 0.08151 | 0.09746 | 0.12355 | 0.03982 | 0.04552 | 0.04723 | 0.05148 | 0.03701 | 0.07326 | 0.05267 | 0.04518 | 0.09377 | 0.04374 | 0.04374 | 0.07471 | 0.04476 | 0.01838 | 0.02042 | 0.02961 | 0.02357 | 0.02051 | 0.01293 | 0.01719 | 0.01719 | 0.02374 | 0.08125 | 0.05210 | 0.04054 | 0.04294 | 0.04814 | 0.04376 | 0.04162 | 0.02510 | 0.03501 | 0.04574 | 0.03245 | 0.03245 | 0.04450 | 0.05540 | 0.04640 | 0.04599 | 0.05879 | 0.03352 | 0.04929 | 0.04607 | 0.03633 | 0.03633 | 0.02626 |
396 rows × 230 columns
get_pspa_st_pct
get_pspa_st_pct ()
Get PSPA reference score to calculate percentile for serine/threonine kinases.
Data.get_pspa_st_pct()
kinase | AAK1 | ACVR2A | ACVR2B | AKT1 | AKT2 | AKT3 | ALK2 | ALK4 | ALPHAK3 | AMPKA1 | AMPKA2 | ANKRD3 | ASK1 | ATM | ATR | AURA | AURB | AURC | BCKDK | BIKE | BMPR1A | BMPR1B | BMPR2 | BRAF | BRSK1 | BRSK2 | BUB1 | CAMK1A | CAMK1B | CAMK1D | CAMK1G | CAMK2A | CAMK2B | CAMK2D | CAMK2G | CAMK4 | CAMKK1 | CAMKK2 | CAMLCK | CDC7 | CDK1 | CDK10 | CDK12 | CDK13 | CDK14 | CDK16 | CDK17 | CDK18 | CDK19 | CDK2 | ... | RIPK1 | RIPK2 | RIPK3 | ROCK1 | ROCK2 | RSK2 | RSK3 | RSK4 | SBK | SGK1 | SGK3 | SIK | SKMLCK | SLK | SMG1 | SMMLCK | SNRK | SRPK1 | SRPK2 | SRPK3 | SSTK | STK33 | STLK3 | TAK1 | TAO1 | TAO2 | TAO3 | TBK1 | TGFBR1 | TGFBR2 | TLK1 | TLK2 | TNIK | TSSK1 | TSSK2 | TTBK1 | TTBK2 | TTK | ULK1 | ULK2 | VRK1 | VRK2 | WNK1 | WNK3 | WNK4 | YANK2 | YANK3 | YSK1 | YSK4 | ZAK |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | -10.960 | -0.581 | 0.329 | -3.891 | -3.591 | -5.312 | 0.814 | -0.559 | -0.933 | -2.607 | -3.167 | -0.764 | -6.366 | 2.533 | 0.010 | -1.164 | -4.296 | -4.302 | 1.695 | -7.684 | 1.713 | 1.965 | 0.183 | 0.018 | -0.379 | -3.219 | -9.801 | -3.750 | 0.149 | -0.610 | -2.746 | 4.377 | 4.940 | 0.902 | 2.957 | -2.297 | -3.196 | -3.469 | -1.716 | -0.232 | -1.378 | -9.497 | -5.727 | -4.521 | -8.698 | -7.186 | -5.666 | -5.802 | -4.029 | -4.039 | ... | -3.605 | -5.763 | -5.047 | -6.065 | -4.406 | -1.298 | -3.001 | -0.837 | -2.256 | -3.190 | -3.763 | -0.262 | -0.226 | -3.190 | -1.971 | -3.519 | -4.495 | -3.007 | -2.348 | -3.560 | -4.580 | -6.610 | -6.038 | -1.211 | -4.498 | -2.911 | 0.463 | -1.287 | 0.680 | -3.707 | 1.479 | 3.406 | -3.950 | -2.172 | -2.109 | -7.773 | -4.765 | -5.262 | -3.549 | -2.822 | -4.682 | -2.854 | -1.669 | -1.527 | -2.965 | -2.877 | -1.792 | -6.283 | -1.715 | -3.204 |
1 | -6.788 | -0.166 | 0.307 | -5.886 | -4.786 | -6.576 | 1.561 | -0.865 | -3.399 | -3.261 | -3.464 | -4.366 | -7.176 | 0.019 | -0.697 | -1.581 | -4.628 | -4.533 | -1.092 | -5.161 | 1.202 | 1.525 | -0.386 | -3.377 | -1.858 | -3.819 | -5.141 | -5.537 | -1.294 | -3.311 | -5.862 | -0.315 | 0.517 | -0.535 | 0.877 | -3.692 | -1.182 | -1.239 | -1.285 | 2.578 | -4.304 | -7.431 | -4.146 | -3.498 | -6.062 | -5.981 | -5.925 | -5.136 | -4.122 | -3.122 | ... | -2.358 | -5.160 | -3.075 | -7.793 | -6.160 | -1.518 | -2.279 | -2.877 | -2.437 | -5.513 | -6.566 | -4.297 | -0.846 | -7.367 | 1.751 | -4.481 | -5.585 | -4.549 | -5.719 | -5.101 | -2.420 | -6.698 | -8.190 | -4.619 | -8.130 | -4.908 | -5.247 | -1.650 | 1.537 | -4.228 | -5.881 | -4.427 | -7.145 | -2.825 | -0.935 | -4.638 | -3.624 | -9.189 | -4.698 | -3.656 | -5.670 | -2.817 | -4.071 | -3.394 | -5.097 | -1.874 | -1.480 | -8.709 | -3.708 | -6.093 |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
89782 | -3.753 | 1.451 | 1.883 | -5.583 | -5.253 | -7.164 | 1.226 | -0.399 | 3.341 | -5.932 | -7.009 | -1.346 | -1.257 | -1.930 | -1.086 | -5.300 | -6.268 | -6.415 | -6.027 | -2.674 | 2.403 | 3.097 | 0.315 | 0.331 | -8.989 | -9.727 | -0.962 | -6.574 | -2.149 | -5.753 | -6.502 | -3.379 | -3.798 | -4.577 | -2.381 | -5.040 | -0.197 | -0.772 | -1.802 | -0.784 | -1.720 | -6.366 | -3.784 | -2.870 | -4.482 | -2.392 | -2.803 | -2.889 | -3.985 | -2.087 | ... | -5.479 | -5.107 | -5.028 | -4.316 | -3.410 | -4.957 | -5.244 | -5.152 | -5.324 | -5.636 | -5.262 | -5.684 | -3.825 | -1.824 | -3.824 | -4.159 | -6.882 | -4.014 | -4.454 | -3.755 | -8.207 | -5.581 | -2.655 | 1.240 | -2.303 | -0.338 | 0.146 | -3.978 | 0.138 | -3.302 | -3.075 | -1.497 | -1.209 | -6.844 | -5.322 | -4.496 | -2.852 | -1.356 | -3.828 | -3.049 | -1.930 | -1.420 | -5.949 | -4.854 | -5.401 | -1.853 | -2.068 | -2.824 | -0.340 | -1.326 |
89783 | -1.540 | -2.180 | -2.014 | -2.416 | -0.592 | -1.364 | -3.320 | -0.826 | -4.438 | -1.393 | -2.058 | -2.101 | -2.838 | -3.597 | -0.664 | -4.098 | -1.564 | -2.006 | -5.130 | -2.428 | -3.192 | -2.013 | -0.868 | -2.795 | -5.958 | -6.211 | -0.309 | -1.495 | 0.020 | -1.378 | -1.652 | -2.380 | -3.275 | -3.026 | -2.647 | -1.958 | -5.024 | -3.868 | 0.578 | -2.915 | -3.348 | -4.227 | -5.020 | -5.209 | -1.570 | -2.480 | -2.677 | -2.574 | -5.737 | -5.213 | ... | -1.942 | -6.158 | -0.930 | -1.559 | -0.154 | 0.361 | -0.754 | -0.276 | -3.035 | -1.083 | -0.965 | -3.652 | 1.355 | -0.824 | -3.360 | -0.030 | -5.503 | -2.102 | -4.456 | -3.284 | -2.001 | -3.563 | -4.212 | -4.696 | -4.132 | -2.436 | -2.292 | -3.454 | -2.188 | -2.436 | -2.339 | -1.988 | -1.042 | -0.358 | -0.074 | -2.837 | -1.059 | 0.434 | -5.814 | -4.250 | -1.979 | -0.661 | -2.586 | -4.076 | -2.832 | -0.575 | -0.859 | -2.415 | -2.999 | -2.550 |
89784 rows × 303 columns
get_pspa_tyr_pct
get_pspa_tyr_pct ()
Get PSPA reference score to calculate percentile for tyrosine kinases.
Data.get_pspa_tyr_pct()
kinase | ABL1 | TNK2 | ALK | ABL2 | AXL | BLK | BMPR2_TYR | PTK6 | BTK | CSF1R | CSK | MATK | DDR1 | DDR2 | EGFR | EPHA1 | EPHA2 | EPHA3 | EPHA4 | EPHA5 | EPHA6 | EPHA7 | EPHA8 | EPHB1 | EPHB2 | EPHB3 | EPHB4 | BMX | PTK2 | FER | FES | FGFR1 | FGFR2 | FGFR3 | FGFR4 | FGR | FLT3 | FRK | FYN | HCK | ERBB2 | ERBB4 | IGF1R | INSR | INSRR | ITK | JAK1 | JAK2 | JAK3 | KIT | LCK | LIMK1_TYR | LIMK2_TYR | LTK | LYN | MERTK | MET | MAP2K4_TYR | MAP2K6_TYR | MAP2K7_TYR | MST1R | MUSK | PKMYT1_TYR | NEK10_TYR | PDGFRA | PDGFRB | PDHK1_TYR | PDHK3_TYR | PDHK4_TYR | PINK1_TYR | PTK2B | RET | ROS1 | SRC | SRMS | SYK | TEC | TESK1_TYR | TEK | TNK1 | TNNI3K_TYR | NTRK1 | NTRK2 | NTRK3 | TXK | TYK2 | TYRO3 | FLT1 | KDR | FLT4 | WEE1_TYR | YES1 | ZAP70 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | -0.709617 | -3.624831 | -2.136338 | -0.022776 | -0.737589 | 2.345905 | 0.504821 | 2.417165 | -0.121611 | -1.205218 | 1.576014 | 1.917812 | -2.449589 | -3.806540 | 1.005984 | -2.925415 | -0.609664 | -1.256237 | 0.491093 | 0.494654 | -1.348782 | -1.938472 | 0.221994 | -0.805070 | 1.130282 | 0.111910 | -0.253774 | 0.221683 | 2.233854 | 2.295975 | -0.025152 | -1.738376 | -0.986921 | -0.375908 | 1.631896 | 2.154664 | -1.214864 | -1.185009 | 6.124421 | 1.940066 | -1.020647 | -0.292182 | 0.761946 | -0.992736 | -0.599703 | 0.298515 | -4.146873 | -2.339013 | -2.479359 | -1.082389 | 1.758755 | -3.027934 | -3.701494 | -0.480120 | 1.346726 | 1.124192 | -1.205155 | -0.094138 | 1.031112 | -0.287930 | -2.589829 | -3.379800 | -1.341062 | -3.607123 | -4.385381 | -1.978546 | 1.390759 | 0.259191 | 0.378106 | -0.094980 | 0.908537 | -0.618981 | -2.562691 | 4.377146 | 1.855049 | 2.017083 | -0.572871 | -2.295149 | -2.833113 | -3.811383 | -6.262204 | 0.683287 | -0.626250 | -0.368491 | 1.187208 | -1.601712 | -1.143748 | -0.891566 | -1.888643 | -1.758264 | -1.610344 | 4.545175 | 0.280174 |
1 | 0.986158 | -1.645273 | -1.183920 | 0.553010 | -1.098784 | -1.245678 | -0.276461 | -0.156496 | -1.322652 | -0.684989 | 0.447463 | 0.054841 | -0.295641 | -2.374194 | 0.261968 | -0.444003 | 0.620075 | -0.918899 | -0.266802 | -1.466189 | 0.181707 | -0.884474 | -0.829816 | -1.039152 | -1.332577 | -1.553626 | -1.557679 | -1.041167 | -1.465569 | -0.573358 | -1.402839 | -1.119166 | -0.006615 | -0.690700 | 0.057757 | -1.329587 | -0.752020 | -1.421231 | -1.119607 | -0.361730 | -0.067540 | -1.488971 | -1.959423 | -1.198227 | -1.250944 | -1.559043 | -1.742221 | -0.297813 | -0.737524 | 0.101179 | -0.785122 | -0.803239 | -0.227134 | -0.226996 | -1.061925 | -0.749321 | -0.324825 | 0.101380 | -0.753605 | -0.186826 | -0.078232 | -1.533730 | -0.949200 | 1.335091 | -0.953302 | -1.471499 | -0.039170 | 0.376709 | -0.653393 | -0.690604 | -0.187336 | 0.372630 | -1.753648 | -0.822064 | 0.291210 | -1.380433 | -0.652058 | -0.974885 | -2.822036 | -1.223497 | -2.903235 | -0.909811 | -1.158577 | -0.777541 | -0.385554 | -0.624216 | -0.737089 | -0.315447 | -1.293708 | -1.182827 | -1.891533 | -0.456570 | -2.465316 |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
7313 | 0.737694 | -0.477689 | -0.646850 | 0.928066 | 0.187149 | -1.000041 | -0.283551 | -3.053869 | -0.750475 | 0.132043 | 0.069439 | 0.778468 | -0.572751 | -0.877774 | 0.279656 | -1.905299 | -2.542936 | -0.629488 | -1.433432 | -1.319311 | -0.959149 | -1.904233 | -1.836303 | -0.665941 | -0.500875 | -1.140260 | -0.324883 | -0.138589 | -1.634647 | -1.463951 | -2.856428 | 1.338733 | 1.308337 | 1.210296 | 0.236992 | -1.117447 | 0.508686 | -1.152320 | -0.680328 | -1.311162 | -1.278938 | -0.529947 | -0.707274 | -0.296606 | 0.170371 | -0.406315 | 0.053109 | -0.184986 | 1.285550 | -1.175831 | -0.657466 | -0.059045 | -0.307151 | -0.027580 | -1.925899 | 0.415170 | 0.535199 | -0.446664 | 0.591918 | 0.316993 | 0.457042 | 0.960955 | -1.222173 | 0.783990 | -0.043431 | 1.226039 | 0.035492 | 0.102904 | 0.600526 | 0.732808 | -1.478030 | 1.261671 | 0.460373 | -1.074805 | -1.293450 | -1.402257 | -0.780591 | -0.107376 | -0.479018 | 1.326369 | -1.912418 | -0.017800 | 0.585871 | -0.122134 | -1.275022 | -0.020350 | 0.483620 | -0.060204 | 1.378042 | 0.573273 | -2.383657 | -0.246005 | 1.174693 |
7314 | 2.115113 | 0.153795 | 0.356357 | 1.846239 | -0.856035 | -0.422296 | -0.985140 | 0.554181 | 0.381133 | -1.666383 | -0.728353 | -0.254733 | -0.999583 | 0.117162 | -1.622541 | -1.882815 | -3.830351 | -1.601071 | -1.750483 | -2.748548 | -0.900263 | -1.661417 | -2.349142 | -0.825704 | -1.211989 | -1.668258 | -0.242232 | 0.727625 | -2.099673 | 0.240011 | -0.659603 | -1.569382 | -1.979445 | -2.605414 | -1.726131 | 0.175403 | -2.030979 | -0.537023 | -0.303194 | -0.134410 | -1.497615 | -2.364148 | -3.279693 | -1.919277 | -2.157962 | 0.598978 | -0.792918 | -0.965011 | -1.728287 | -1.616595 | -0.084054 | -0.968384 | -0.373329 | -0.234884 | -1.088861 | -1.129566 | -0.358743 | 0.154190 | -0.787745 | -0.482053 | -1.581810 | -1.865008 | -0.707663 | -0.049274 | -1.190498 | -1.403224 | -0.849104 | -0.212996 | -0.159123 | -0.885066 | 0.447393 | -0.121666 | -0.543588 | 0.170109 | 0.044321 | -1.576300 | 1.325049 | -1.122959 | -2.962076 | -0.786136 | -1.090242 | -1.402034 | -1.365117 | -1.670434 | 1.684176 | -0.508297 | -0.304215 | -2.045909 | -1.629804 | -2.227050 | -2.294855 | 0.428825 | -1.789086 |
7315 rows × 93 columns
get_num_dict
get_num_dict ()
Get a dictionary mapping kinase to number of random amino acids in PSPA.
list(Data.get_num_dict().items())[:5]
[('SYK', 18), ('PTK2', 18), ('ZAP70', 18), ('ERBB2', 18), ('CSK', 18)]
CDDM data
Data.get_ks_unique
Data.get_ks_unique ()
Get kinase substrate dataset with unique sub site ID.
Data.get_ks_unique()
sub_site | num_kin | bin | sub_genes | site_seq | source_combine | acceptor | O00141_SGK1 | O00238_BMPR1B | O00311_CDC7 | O00329_PIK3CD | O00418_EEF2K | O00443_PIK3C2A | O00444_PLK4 | O00506_STK25 | O14578_CIT | O14730_RIOK3 | O14733_MAP2K7 | O14757_CHEK1 | O14874_BCKDK | O14920_IKBKB | O14936_CASK | O14965_AURKA | O14976_GAK | O15021_MAST4 | O15075_DCLK1 | O15111_CHUK | O15146_MUSK | O15264_MAPK13 | O15530_PDPK1 | O43283_MAP3K13 | O43293_DAPK3 | O43318_MAP3K7 | O43353_RIPK2 | O43683_BUB1 | O43781_DYRK3 | O60285_NUAK1 | O60331_PIP5K1C | O60566_BUB1B | O60674_JAK2 | O60885_BRD4 | O75116_ROCK2 | O75385_ULK1 | O75460_ERN1 | O75582_RPS6KA5 | O75676_RPS6KA4 | O75716_STK16 | O75914_PAK3 | O76039_CDKL5 | O94768_STK17B | ... | Q9HBY8_SGK2 | Q9HC98_NEK6 | Q9HCP0_CSNK1G1 | Q9NQU5_PAK6 | Q9NR20_DYRK4 | Q9NRA0_SPHK2 | Q9NRM7_LATS2 | Q9NSY1_BMP2K | Q9NWZ3_IRAK4 | Q9NYA1_SPHK1 | Q9NYL2_MAP3K20 | Q9NYV4_CDK12 | Q9NYY3_PLK2 | Q9NZJ5_EIF2AK3 | Q9P0L2_MARK1 | Q9P1W9_PIM2 | Q9P286_PAK5 | Q9P289_STK26 | Q9P2K8_EIF2AK4 | Q9UBE8_NLK | Q9UBS0_RPS6KB2 | Q9UEE5_STK17A | Q9UEW8_STK39 | Q9UF33_EPHA6 | Q9UHD2_TBK1 | Q9UIG0_BAZ1B | Q9UIK4_DAPK2 | Q9UK32_RPS6KA6 | Q9UKE5_TNIK | Q9UKI8_TLK1 | Q9UL54_TAOK2 | Q9UM73_ALK | Q9UPE1_SRPK3 | Q9UPZ9_CILK1 | Q9UQ07_MOK | Q9UQ88_CDK11A | Q9UQB9_AURKC | Q9UQM7_CAMK2A | Q9Y243_AKT3 | Q9Y2H1_STK38L | Q9Y2K2_SIK3 | Q9Y2U5_MAP3K2 | Q9Y3S1_WNK2 | Q9Y463_DYRK1B | Q9Y4K4_MAP4K5 | Q9Y572_RIPK3 | Q9Y5S2_CDC42BPB | Q9Y6E0_STK24 | Q9Y6M4_CSNK1G3 | Q9Y6R4_MAP3K4 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | A0A2R8Y4L2_S158 | 1 | 1 | HNRNPA1L3 HNRNPA1P48 | TDRGSGKKRGFAFVTFDDHDsVDKIVIQKYHTVNGHNCEVR | Sugiyama | S | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
1 | A0A2R8Y4L2_S22 | 3 | 2~10 | HNRNPA1L3 HNRNPA1P48 | SKSEsPKEPEQLRKLFIGGLsFEtTDESLRSHFEQWGTLTD | Sugiyama | S | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
29809 | Q9Y6Y9_Y131 | 1 | 1 | LY96 ESOP1 MD2 | ETVNTTISFSFKGIKFSKGKyKCVVEAISGSPEEMLFCLEF | Non-Sugiyama | Y | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
29810 | Q9Y6Y9_Y22 | 1 | 1 | LY96 ESOP1 MD2 | LPFLFFSTLFSSIFTEAQKQyWVCNSSDASISYTYCDKMQY | Non-Sugiyama | Y | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
29811 rows × 462 columns
Data.get_ks_dataset
Data.get_ks_dataset (add_kinase_info=True)
Get kinase–substrate dataset collected from public resources, with the option of enriching with kinase info.
Data.get_ks_dataset()
kin_sub_site | kinase_uniprot | substrate_uniprot | site | source | substrate_genes | substrate_phosphoseq | position | site_seq | sub_site | substrate_sequence | kinase_on_tree | kinase_genes | kinase_group | kinase_family | kinase_subfamily | kinase_pspa_big | kinase_pspa_small | kinase_coral_ID | kinase_protein | num_kin | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | O00141_A4FU28_S140 | O00141 | A4FU28 | S140 | Sugiyama | CTAGE9 | MEEPGATPQPYLGLVLEELGRVVAALPESMRPDENPYGFPSELVVC... | 140 | AAAEEARSLEATCEKLSRsNsELEDEILCLEKDLKEEKSKH | A4FU28_S140 | MEEPGATPQPYLGLVLEELGRVVAALPESMRPDENPYGFPSELVVC... | 1 | SGK1 SGK | AGC | SGK | SGK | Basophilic | Akt/rock | SGK1 | SGK1 | 22 |
1 | O00141_O00141_S252 | O00141 | O00141 | S252 | Sugiyama | SGK1 SGK | MTVKTEAAKGTLTYSRMRGMVAILIAFMKQRRMGLNDFIQKIANNS... | 252 | SQGHIVLTDFGLCKENIEHNsTtstFCGtPEyLAPEVLHKQ | O00141_S252 | MTVKTEAAKGTLTYSRMRGMVAILIAFMKQRRMGLNDFIQKIANNS... | 1 | SGK1 SGK | AGC | SGK | SGK | Basophilic | Akt/rock | SGK1 | SGK1 | 1 |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
187064 | Q9Y6R4_Q9Y6R4_T1494 | Q9Y6R4 | Q9Y6R4 | T1494 | SIGNOR|EPSD|PSP | MAP3K4 KIAA0213 MAPKKK4 MEKK4 MTK1 | MREAAAALVPPPAFAVTPAAAMEEPPPPPPPPPPPPEPETESEPEC... | 1494 | SGLIKLGDFGCSVKLKNNAQtMPGEVNSTLGTAAYMAPEVI | Q9Y6R4_T1494 | MREAAAALVPPPAFAVTPAAAMEEPPPPPPPPPPPPEPETESEPEC... | 1 | MAP3K4 KIAA0213 MAPKKK4 MEKK4 MTK1 | STE | STE11 | STE11 | NaN | NaN | MAP3K4 | MAP3K4 | 1 |
187065 | Q9Y6R4_Q9Y6R4_Y1328 | Q9Y6R4 | Q9Y6R4 | Y1328 | Sugiyama | MAP3K4 KIAA0213 MAPKKK4 MEKK4 MTK1 | MREAAAALVPPPAFAVTPAAAMEEPPPPPPPPPPPPEPETESEPEC... | 1328 | RYREMRRKNIIGQVCDtPKSyDNVMHVGLRKVTFKWQRGNK | Q9Y6R4_Y1328 | MREAAAALVPPPAFAVTPAAAMEEPPPPPPPPPPPPEPETESEPEC... | 1 | MAP3K4 KIAA0213 MAPKKK4 MEKK4 MTK1 | STE | STE11 | STE11 | NaN | NaN | MAP3K4 | MAP3K4 | 1 |
187066 rows × 21 columns
get_ks_background
get_ks_background ()
Get kinase substrate dataset with unique sub site ID.
Data.get_ks_background()
-20P | -20G | -20A | -20C | -20S | -20T | -20V | -20I | -20L | -20M | -20F | -20Y | -20W | -20H | -20K | -20R | -20Q | -20N | -20D | -20E | -20s | -20t | -20y | -19P | -19G | -19A | -19C | -19S | -19T | -19V | -19I | -19L | -19M | -19F | -19Y | -19W | -19H | -19K | -19R | -19Q | -19N | -19D | -19E | -19s | -19t | -19y | -18P | -18G | -18A | -18C | ... | 18E | 18s | 18t | 18y | 19P | 19G | 19A | 19C | 19S | 19T | 19V | 19I | 19L | 19M | 19F | 19Y | 19W | 19H | 19K | 19R | 19Q | 19N | 19D | 19E | 19s | 19t | 19y | 20P | 20G | 20A | 20C | 20S | 20T | 20V | 20I | 20L | 20M | 20F | 20Y | 20W | 20H | 20K | 20R | 20Q | 20N | 20D | 20E | 20s | 20t | 20y | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
index | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ks_S | 0.074296 | 0.068105 | 0.075925 | 0.014664 | 0.053246 | 0.038517 | 0.051290 | 0.040342 | 0.078989 | 0.020269 | 0.028806 | 0.016228 | 0.008081 | 0.023266 | 0.068952 | 0.056765 | 0.046728 | 0.036301 | 0.053506 | 0.082573 | 0.041645 | 0.015511 | 0.005996 | 0.067780 | 0.069925 | 0.072069 | 0.012867 | 0.056343 | 0.036392 | 0.049454 | 0.038472 | 0.084546 | 0.022550 | 0.025994 | 0.017611 | 0.008773 | 0.020665 | 0.066220 | 0.065181 | 0.048739 | 0.038991 | 0.052963 | 0.079218 | 0.042566 | 0.016246 | 0.006434 | 0.065772 | 0.069725 | 0.072771 | 0.012960 | ... | 0.082005 | 0.043003 | 0.014401 | 0.006134 | 0.068513 | 0.069249 | 0.073398 | 0.012980 | 0.056336 | 0.037803 | 0.050114 | 0.035996 | 0.080222 | 0.018801 | 0.030510 | 0.014720 | 0.009635 | 0.023752 | 0.071056 | 0.061087 | 0.046434 | 0.037535 | 0.053258 | 0.082363 | 0.044627 | 0.015656 | 0.005955 | 0.070061 | 0.067710 | 0.072412 | 0.015181 | 0.053469 | 0.036676 | 0.058910 | 0.037885 | 0.084906 | 0.018338 | 0.030093 | 0.017935 | 0.007926 | 0.021294 | 0.070330 | 0.059313 | 0.044200 | 0.036273 | 0.054880 | 0.077316 | 0.043461 | 0.014980 | 0.006449 |
ks_T | 0.061634 | 0.065896 | 0.074266 | 0.016436 | 0.043829 | 0.034394 | 0.059656 | 0.040177 | 0.089484 | 0.024806 | 0.033024 | 0.019175 | 0.010501 | 0.020088 | 0.072896 | 0.056460 | 0.042764 | 0.035002 | 0.065287 | 0.076548 | 0.028915 | 0.018566 | 0.010196 | 0.060989 | 0.072395 | 0.072395 | 0.013840 | 0.046388 | 0.036502 | 0.062662 | 0.040913 | 0.081217 | 0.024183 | 0.031787 | 0.016730 | 0.007452 | 0.019468 | 0.080152 | 0.059468 | 0.044715 | 0.034981 | 0.055057 | 0.083498 | 0.033916 | 0.015665 | 0.005627 | 0.063562 | 0.070692 | 0.069326 | 0.015777 | ... | 0.086112 | 0.037420 | 0.017222 | 0.011116 | 0.059683 | 0.067222 | 0.073033 | 0.012879 | 0.044605 | 0.034867 | 0.054343 | 0.043191 | 0.082142 | 0.017905 | 0.031255 | 0.018847 | 0.009267 | 0.021988 | 0.076174 | 0.065023 | 0.040364 | 0.043349 | 0.063295 | 0.081200 | 0.030470 | 0.019632 | 0.009267 | 0.063397 | 0.067497 | 0.066393 | 0.015140 | 0.047784 | 0.031698 | 0.053304 | 0.046838 | 0.080902 | 0.019871 | 0.035483 | 0.020659 | 0.010093 | 0.022394 | 0.075067 | 0.060558 | 0.045261 | 0.038007 | 0.058666 | 0.076644 | 0.035483 | 0.019871 | 0.008989 |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
human_ST_upper | 0.082791 | 0.066656 | 0.072951 | 0.012749 | 0.111414 | 0.054709 | 0.049589 | 0.032810 | 0.080030 | 0.019268 | 0.025079 | 0.019063 | 0.007013 | 0.022010 | 0.067710 | 0.062114 | 0.047611 | 0.033510 | 0.052219 | 0.080702 | 0.000000 | 0.000000 | 0.000000 | 0.082364 | 0.066437 | 0.073391 | 0.012502 | 0.112851 | 0.054252 | 0.050835 | 0.031845 | 0.078539 | 0.019614 | 0.024361 | 0.017966 | 0.006609 | 0.022350 | 0.067405 | 0.063942 | 0.048713 | 0.033838 | 0.051655 | 0.080531 | 0.000000 | 0.000000 | 0.000000 | 0.083261 | 0.066199 | 0.074920 | 0.013477 | ... | 0.081781 | 0.000000 | 0.000000 | 0.000000 | 0.081470 | 0.068046 | 0.070355 | 0.013078 | 0.113824 | 0.056426 | 0.049966 | 0.031747 | 0.078665 | 0.016032 | 0.025418 | 0.018332 | 0.006834 | 0.021884 | 0.066924 | 0.063147 | 0.048788 | 0.034962 | 0.052911 | 0.081189 | 0.000000 | 0.000000 | 0.000000 | 0.082942 | 0.067364 | 0.070982 | 0.012747 | 0.114370 | 0.054382 | 0.050436 | 0.032196 | 0.080711 | 0.016468 | 0.026638 | 0.018652 | 0.007058 | 0.021877 | 0.067252 | 0.064102 | 0.047521 | 0.032946 | 0.051795 | 0.079558 | 0.000000 | 0.000000 | 0.000000 |
human_STY_upper | 0.082206 | 0.066688 | 0.072961 | 0.012965 | 0.110244 | 0.054656 | 0.049733 | 0.033379 | 0.080515 | 0.019334 | 0.025206 | 0.020031 | 0.007049 | 0.022131 | 0.067141 | 0.062035 | 0.047677 | 0.033640 | 0.052120 | 0.080289 | 0.000000 | 0.000000 | 0.000000 | 0.081832 | 0.066727 | 0.073458 | 0.012827 | 0.111061 | 0.053752 | 0.050734 | 0.032307 | 0.078615 | 0.019802 | 0.024967 | 0.018880 | 0.006679 | 0.022410 | 0.067327 | 0.063718 | 0.048352 | 0.034185 | 0.051743 | 0.080624 | 0.000000 | 0.000000 | 0.000000 | 0.082377 | 0.066193 | 0.074272 | 0.013311 | ... | 0.081579 | 0.000000 | 0.000000 | 0.000000 | 0.080805 | 0.067923 | 0.070240 | 0.013196 | 0.112567 | 0.056073 | 0.050258 | 0.032331 | 0.079073 | 0.016362 | 0.025728 | 0.019064 | 0.006917 | 0.021705 | 0.066891 | 0.062991 | 0.048728 | 0.035155 | 0.052847 | 0.081146 | 0.000000 | 0.000000 | 0.000000 | 0.082350 | 0.067688 | 0.070582 | 0.012733 | 0.112743 | 0.054403 | 0.050360 | 0.032901 | 0.080631 | 0.016863 | 0.026965 | 0.019844 | 0.007094 | 0.021870 | 0.067153 | 0.063812 | 0.047677 | 0.032840 | 0.052027 | 0.079465 | 0.000000 | 0.000000 | 0.000000 |
20 rows × 943 columns
get_cddm
get_cddm ()
Get the CDDM dataset.
Data.get_cddm()
-20P | -20G | -20A | -20C | -20S | -20T | -20V | -20I | -20L | -20M | -20F | -20Y | -20W | -20H | -20K | -20R | -20Q | -20N | -20D | -20E | -20pS | -20pT | -20pY | -19P | -19G | -19A | -19C | -19S | -19T | -19V | -19I | -19L | -19M | -19F | -19Y | -19W | -19H | -19K | -19R | -19Q | -19N | -19D | -19E | -19pS | -19pT | -19pY | -18P | -18G | -18A | -18C | ... | 18E | 18pS | 18pT | 18pY | 19P | 19G | 19A | 19C | 19S | 19T | 19V | 19I | 19L | 19M | 19F | 19Y | 19W | 19H | 19K | 19R | 19Q | 19N | 19D | 19E | 19pS | 19pT | 19pY | 20P | 20G | 20A | 20C | 20S | 20T | 20V | 20I | 20L | 20M | 20F | 20Y | 20W | 20H | 20K | 20R | 20Q | 20N | 20D | 20E | 20pS | 20pT | 20pY | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
SRC | 0.054538 | 0.081380 | 0.060077 | 0.012356 | 0.036216 | 0.032382 | 0.055816 | 0.052407 | 0.083511 | 0.023434 | 0.031530 | 0.023008 | 0.005965 | 0.018747 | 0.082659 | 0.058372 | 0.051555 | 0.039625 | 0.059651 | 0.071155 | 0.022582 | 0.020452 | 0.022582 | 0.048428 | 0.075616 | 0.085387 | 0.017417 | 0.035684 | 0.029737 | 0.056500 | 0.052676 | 0.079864 | 0.024214 | 0.032285 | 0.019966 | 0.011895 | 0.019541 | 0.081563 | 0.061597 | 0.044605 | 0.036534 | 0.064146 | 0.071793 | 0.025064 | 0.012744 | 0.012744 | 0.054968 | 0.069345 | 0.066808 | 0.015222 | ... | 0.080938 | 0.030075 | 0.011057 | 0.010615 | 0.052375 | 0.071460 | 0.064359 | 0.017754 | 0.047048 | 0.035508 | 0.052375 | 0.050599 | 0.091434 | 0.024856 | 0.041278 | 0.015535 | 0.011096 | 0.015979 | 0.064802 | 0.066134 | 0.047048 | 0.035508 | 0.062583 | 0.074123 | 0.028407 | 0.011540 | 0.018198 | 0.05830 | 0.085447 | 0.064976 | 0.012906 | 0.041834 | 0.039163 | 0.043169 | 0.050734 | 0.074766 | 0.032488 | 0.040053 | 0.018692 | 0.008456 | 0.013351 | 0.076992 | 0.060970 | 0.037383 | 0.036938 | 0.052960 | 0.086337 | 0.025367 | 0.015576 | 0.023142 |
EPHA3 | 0.044276 | 0.088013 | 0.065335 | 0.008639 | 0.037797 | 0.036717 | 0.072354 | 0.048596 | 0.075594 | 0.026998 | 0.031317 | 0.022678 | 0.011339 | 0.021598 | 0.084233 | 0.059395 | 0.046436 | 0.036177 | 0.059935 | 0.064255 | 0.023758 | 0.018898 | 0.015659 | 0.047875 | 0.064551 | 0.087144 | 0.016138 | 0.031737 | 0.039806 | 0.051103 | 0.046799 | 0.080151 | 0.026358 | 0.035503 | 0.015600 | 0.010221 | 0.023669 | 0.090909 | 0.060785 | 0.042496 | 0.033889 | 0.067240 | 0.079613 | 0.020979 | 0.011296 | 0.016138 | 0.047696 | 0.060557 | 0.057878 | 0.018221 | ... | 0.076362 | 0.039304 | 0.017967 | 0.006738 | 0.050197 | 0.070502 | 0.067682 | 0.020305 | 0.029329 | 0.039481 | 0.053017 | 0.049069 | 0.095319 | 0.027637 | 0.038917 | 0.016920 | 0.011280 | 0.016920 | 0.071066 | 0.061478 | 0.039481 | 0.037225 | 0.062606 | 0.083474 | 0.029893 | 0.011844 | 0.016356 | 0.04918 | 0.084228 | 0.064443 | 0.017524 | 0.031656 | 0.038440 | 0.047484 | 0.062747 | 0.070661 | 0.031656 | 0.042962 | 0.017524 | 0.007914 | 0.014132 | 0.083098 | 0.059356 | 0.031091 | 0.033917 | 0.056529 | 0.100622 | 0.025438 | 0.013567 | 0.015828 |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
MAST2 | 0.046512 | 0.116279 | 0.069767 | 0.000000 | 0.023256 | 0.069767 | 0.069767 | 0.000000 | 0.046512 | 0.046512 | 0.023256 | 0.000000 | 0.000000 | 0.162791 | 0.023256 | 0.023256 | 0.023256 | 0.000000 | 0.046512 | 0.139535 | 0.023256 | 0.023256 | 0.023256 | 0.023256 | 0.162791 | 0.093023 | 0.000000 | 0.046512 | 0.046512 | 0.023256 | 0.046512 | 0.093023 | 0.000000 | 0.046512 | 0.046512 | 0.000000 | 0.093023 | 0.023256 | 0.046512 | 0.023256 | 0.000000 | 0.046512 | 0.116279 | 0.023256 | 0.000000 | 0.000000 | 0.023256 | 0.023256 | 0.093023 | 0.000000 | ... | 0.146341 | 0.000000 | 0.000000 | 0.000000 | 0.000000 | 0.048780 | 0.121951 | 0.024390 | 0.073171 | 0.048780 | 0.048780 | 0.024390 | 0.073171 | 0.000000 | 0.146341 | 0.000000 | 0.000000 | 0.000000 | 0.097561 | 0.048780 | 0.000000 | 0.048780 | 0.073171 | 0.073171 | 0.048780 | 0.000000 | 0.000000 | 0.00000 | 0.024390 | 0.048780 | 0.024390 | 0.024390 | 0.097561 | 0.170732 | 0.024390 | 0.048780 | 0.048780 | 0.024390 | 0.000000 | 0.073171 | 0.000000 | 0.048780 | 0.219512 | 0.000000 | 0.048780 | 0.024390 | 0.024390 | 0.024390 | 0.000000 | 0.000000 |
BRAF | 0.095238 | 0.071429 | 0.047619 | 0.000000 | 0.095238 | 0.047619 | 0.071429 | 0.000000 | 0.095238 | 0.047619 | 0.000000 | 0.000000 | 0.000000 | 0.023810 | 0.023810 | 0.071429 | 0.023810 | 0.023810 | 0.095238 | 0.095238 | 0.047619 | 0.000000 | 0.023810 | 0.071429 | 0.047619 | 0.023810 | 0.000000 | 0.000000 | 0.047619 | 0.000000 | 0.071429 | 0.047619 | 0.000000 | 0.023810 | 0.071429 | 0.000000 | 0.023810 | 0.095238 | 0.071429 | 0.000000 | 0.071429 | 0.023810 | 0.166667 | 0.119048 | 0.023810 | 0.000000 | 0.047619 | 0.071429 | 0.071429 | 0.000000 | ... | 0.025000 | 0.025000 | 0.025000 | 0.000000 | 0.025000 | 0.075000 | 0.025000 | 0.000000 | 0.125000 | 0.050000 | 0.050000 | 0.025000 | 0.050000 | 0.050000 | 0.000000 | 0.025000 | 0.000000 | 0.000000 | 0.075000 | 0.100000 | 0.025000 | 0.050000 | 0.050000 | 0.050000 | 0.100000 | 0.050000 | 0.000000 | 0.02500 | 0.075000 | 0.100000 | 0.000000 | 0.075000 | 0.100000 | 0.100000 | 0.050000 | 0.050000 | 0.000000 | 0.000000 | 0.000000 | 0.025000 | 0.000000 | 0.075000 | 0.075000 | 0.025000 | 0.025000 | 0.075000 | 0.075000 | 0.050000 | 0.000000 | 0.000000 |
328 rows × 943 columns
get_cddm_upper
get_cddm_upper ()
Get the CDDM dataset of all uppercase sequence.
Data.get_cddm_upper()
-20P | -20G | -20A | -20C | -20S | -20T | -20V | -20I | -20L | -20M | -20F | -20Y | -20W | -20H | -20K | -20R | -20Q | -20N | -20D | -20E | -20pS | -20pT | -20pY | -19P | -19G | -19A | -19C | -19S | -19T | -19V | -19I | -19L | -19M | -19F | -19Y | -19W | -19H | -19K | -19R | -19Q | -19N | -19D | -19E | -19pS | -19pT | -19pY | -18P | -18G | -18A | -18C | ... | 18E | 18pS | 18pT | 18pY | 19P | 19G | 19A | 19C | 19S | 19T | 19V | 19I | 19L | 19M | 19F | 19Y | 19W | 19H | 19K | 19R | 19Q | 19N | 19D | 19E | 19pS | 19pT | 19pY | 20P | 20G | 20A | 20C | 20S | 20T | 20V | 20I | 20L | 20M | 20F | 20Y | 20W | 20H | 20K | 20R | 20Q | 20N | 20D | 20E | 20pS | 20pT | 20pY | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
SRC | 0.054538 | 0.081380 | 0.060077 | 0.012356 | 0.058798 | 0.052833 | 0.055816 | 0.052407 | 0.083511 | 0.023434 | 0.031530 | 0.045590 | 0.005965 | 0.018747 | 0.082659 | 0.058372 | 0.051555 | 0.039625 | 0.059651 | 0.071155 | 0.0 | 0.0 | 0.0 | 0.048428 | 0.075616 | 0.085387 | 0.017417 | 0.060748 | 0.042481 | 0.056500 | 0.052676 | 0.079864 | 0.024214 | 0.032285 | 0.032710 | 0.011895 | 0.019541 | 0.081563 | 0.061597 | 0.044605 | 0.036534 | 0.064146 | 0.071793 | 0.0 | 0.0 | 0.0 | 0.054968 | 0.069345 | 0.066808 | 0.015222 | ... | 0.080938 | 0.0 | 0.0 | 0.0 | 0.052375 | 0.071460 | 0.064359 | 0.017754 | 0.075455 | 0.047048 | 0.052375 | 0.050599 | 0.091434 | 0.024856 | 0.041278 | 0.033733 | 0.011096 | 0.015979 | 0.064802 | 0.066134 | 0.047048 | 0.035508 | 0.062583 | 0.074123 | 0.0 | 0.0 | 0.0 | 0.05830 | 0.085447 | 0.064976 | 0.012906 | 0.067201 | 0.054740 | 0.043169 | 0.050734 | 0.074766 | 0.032488 | 0.040053 | 0.041834 | 0.008456 | 0.013351 | 0.076992 | 0.060970 | 0.037383 | 0.036938 | 0.052960 | 0.086337 | 0.0 | 0.0 | 0.0 |
EPHA3 | 0.044276 | 0.088013 | 0.065335 | 0.008639 | 0.061555 | 0.055616 | 0.072354 | 0.048596 | 0.075594 | 0.026998 | 0.031317 | 0.038337 | 0.011339 | 0.021598 | 0.084233 | 0.059395 | 0.046436 | 0.036177 | 0.059935 | 0.064255 | 0.0 | 0.0 | 0.0 | 0.047875 | 0.064551 | 0.087144 | 0.016138 | 0.052717 | 0.051103 | 0.051103 | 0.046799 | 0.080151 | 0.026358 | 0.035503 | 0.031737 | 0.010221 | 0.023669 | 0.090909 | 0.060785 | 0.042496 | 0.033889 | 0.067240 | 0.079613 | 0.0 | 0.0 | 0.0 | 0.047696 | 0.060557 | 0.057878 | 0.018221 | ... | 0.076362 | 0.0 | 0.0 | 0.0 | 0.050197 | 0.070502 | 0.067682 | 0.020305 | 0.059222 | 0.051325 | 0.053017 | 0.049069 | 0.095319 | 0.027637 | 0.038917 | 0.033277 | 0.011280 | 0.016920 | 0.071066 | 0.061478 | 0.039481 | 0.037225 | 0.062606 | 0.083474 | 0.0 | 0.0 | 0.0 | 0.04918 | 0.084228 | 0.064443 | 0.017524 | 0.057094 | 0.052007 | 0.047484 | 0.062747 | 0.070661 | 0.031656 | 0.042962 | 0.033352 | 0.007914 | 0.014132 | 0.083098 | 0.059356 | 0.031091 | 0.033917 | 0.056529 | 0.100622 | 0.0 | 0.0 | 0.0 |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
MAST2 | 0.046512 | 0.116279 | 0.069767 | 0.000000 | 0.046512 | 0.093023 | 0.069767 | 0.000000 | 0.046512 | 0.046512 | 0.023256 | 0.023256 | 0.000000 | 0.162791 | 0.023256 | 0.023256 | 0.023256 | 0.000000 | 0.046512 | 0.139535 | 0.0 | 0.0 | 0.0 | 0.023256 | 0.162791 | 0.093023 | 0.000000 | 0.069767 | 0.046512 | 0.023256 | 0.046512 | 0.093023 | 0.000000 | 0.046512 | 0.046512 | 0.000000 | 0.093023 | 0.023256 | 0.046512 | 0.023256 | 0.000000 | 0.046512 | 0.116279 | 0.0 | 0.0 | 0.0 | 0.023256 | 0.023256 | 0.093023 | 0.000000 | ... | 0.146341 | 0.0 | 0.0 | 0.0 | 0.000000 | 0.048780 | 0.121951 | 0.024390 | 0.121951 | 0.048780 | 0.048780 | 0.024390 | 0.073171 | 0.000000 | 0.146341 | 0.000000 | 0.000000 | 0.000000 | 0.097561 | 0.048780 | 0.000000 | 0.048780 | 0.073171 | 0.073171 | 0.0 | 0.0 | 0.0 | 0.00000 | 0.024390 | 0.048780 | 0.024390 | 0.048780 | 0.097561 | 0.170732 | 0.024390 | 0.048780 | 0.048780 | 0.024390 | 0.000000 | 0.073171 | 0.000000 | 0.048780 | 0.219512 | 0.000000 | 0.048780 | 0.024390 | 0.024390 | 0.0 | 0.0 | 0.0 |
BRAF | 0.095238 | 0.071429 | 0.047619 | 0.000000 | 0.142857 | 0.047619 | 0.071429 | 0.000000 | 0.095238 | 0.047619 | 0.000000 | 0.023810 | 0.000000 | 0.023810 | 0.023810 | 0.071429 | 0.023810 | 0.023810 | 0.095238 | 0.095238 | 0.0 | 0.0 | 0.0 | 0.071429 | 0.047619 | 0.023810 | 0.000000 | 0.119048 | 0.071429 | 0.000000 | 0.071429 | 0.047619 | 0.000000 | 0.023810 | 0.071429 | 0.000000 | 0.023810 | 0.095238 | 0.071429 | 0.000000 | 0.071429 | 0.023810 | 0.166667 | 0.0 | 0.0 | 0.0 | 0.047619 | 0.071429 | 0.071429 | 0.000000 | ... | 0.025000 | 0.0 | 0.0 | 0.0 | 0.025000 | 0.075000 | 0.025000 | 0.000000 | 0.225000 | 0.100000 | 0.050000 | 0.025000 | 0.050000 | 0.050000 | 0.000000 | 0.025000 | 0.000000 | 0.000000 | 0.075000 | 0.100000 | 0.025000 | 0.050000 | 0.050000 | 0.050000 | 0.0 | 0.0 | 0.0 | 0.02500 | 0.075000 | 0.100000 | 0.000000 | 0.125000 | 0.100000 | 0.100000 | 0.050000 | 0.050000 | 0.000000 | 0.000000 | 0.000000 | 0.025000 | 0.000000 | 0.075000 | 0.075000 | 0.025000 | 0.025000 | 0.075000 | 0.075000 | 0.0 | 0.0 | 0.0 |
328 rows × 943 columns
get_cddm_LO
get_cddm_LO ()
Get CDDM Log-odds data with ‘STY’ background.
Data.get_cddm_LO()
-20P | -20G | -20A | -20C | -20S | -20T | -20V | -20I | -20L | -20M | -20F | -20Y | -20W | -20H | -20K | -20R | -20Q | -20N | -20D | -20E | -20pS | -20pT | -20pY | -19P | -19G | -19A | -19C | -19S | -19T | -19V | -19I | -19L | -19M | -19F | -19Y | -19W | -19H | -19K | -19R | -19Q | -19N | -19D | -19E | -19pS | -19pT | -19pY | -18P | -18G | -18A | -18C | ... | 18E | 18pS | 18pT | 18pY | 19P | 19G | 19A | 19C | 19S | 19T | 19V | 19I | 19L | 19M | 19F | 19Y | 19W | 19H | 19K | 19R | 19Q | 19N | 19D | 19E | 19pS | 19pT | 19pY | 20P | 20G | 20A | 20C | 20S | 20T | 20V | 20I | 20L | 20M | 20F | 20Y | 20W | 20H | 20K | 20R | 20Q | 20N | 20D | 20E | 20pS | 20pT | 20pY | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
SRC | -0.298965 | 0.245926 | -0.306472 | -0.315249 | -0.436393 | -0.216885 | 0.039840 | 0.331979 | 0.006587 | 0.074104 | 0.026464 | 0.300781 | -0.484863 | -0.234235 | 0.238737 | 0.035866 | 0.173786 | 0.112172 | 0.062717 | -0.187118 | -0.598455 | 0.418275 | 1.228850 | -0.394990 | 0.116437 | 0.241674 | 0.270796 | -0.536063 | -0.295952 | 0.089650 | 0.359646 | -0.082026 | 0.078067 | 0.157708 | 0.196729 | 0.443758 | -0.096374 | 0.191619 | -0.036922 | -0.065461 | -0.093194 | 0.198348 | -0.149715 | -0.521873 | -0.217518 | 0.779107 | -0.209860 | 0.005564 | -0.061876 | 0.087346 | ... | -0.024870 | -0.295180 | -0.362786 | 0.382054 | -0.265140 | 0.085462 | -0.135241 | 0.341197 | -0.144617 | -0.081201 | -0.016493 | 0.302052 | 0.137508 | 0.404226 | 0.299088 | -0.066971 | 0.165626 | -0.468907 | -0.152143 | 0.097919 | 0.055576 | -0.162821 | 0.125989 | -0.139554 | -0.371114 | -0.369706 | 1.148641 | -0.219858 | 0.305918 | -0.086212 | -0.217325 | -0.300629 | 0.133833 | -0.379744 | 0.266731 | -0.143992 | 0.691717 | 0.259364 | -0.031653 | -0.018293 | -0.661728 | 0.104673 | 0.041005 | -0.236473 | -0.001987 | -0.082064 | 0.136414 | -0.538512 | 0.006337 | 1.268341 |
EPHA3 | -0.599679 | 0.358959 | -0.185427 | -0.831496 | -0.374767 | -0.035616 | 0.414240 | 0.223052 | -0.137106 | 0.278334 | 0.016725 | 0.279945 | 0.441832 | -0.030005 | 0.265960 | 0.060927 | 0.022921 | -0.019164 | 0.069583 | -0.334271 | -0.525210 | 0.304329 | 0.700644 | -0.411559 | -0.111818 | 0.271060 | 0.160722 | -0.705150 | 0.124806 | -0.055189 | 0.188981 | -0.076858 | 0.200475 | 0.294762 | -0.159291 | 0.224919 | 0.180083 | 0.348124 | -0.056065 | -0.135338 | -0.201591 | 0.266315 | -0.000554 | -0.778526 | -0.391503 | 1.119694 | -0.414603 | -0.189918 | -0.268878 | 0.346775 | ... | -0.108833 | 0.090914 | 0.337630 | -0.273672 | -0.326395 | 0.065984 | -0.062604 | 0.534849 | -0.826443 | 0.071809 | 0.001107 | 0.257761 | 0.197541 | 0.557236 | 0.214109 | 0.056291 | 0.189352 | -0.386287 | -0.019033 | -0.007411 | -0.197407 | -0.094701 | 0.126509 | 0.031850 | -0.297539 | -0.332173 | 0.994725 | -0.465271 | 0.285190 | -0.098081 | 0.223956 | -0.702797 | 0.106930 | -0.242274 | 0.573323 | -0.225459 | 0.654314 | 0.360504 | -0.124708 | -0.113799 | -0.579696 | 0.214783 | 0.002284 | -0.502364 | -0.125070 | 0.012040 | 0.357301 | -0.534483 | -0.192918 | 0.720322 |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
MAST2 | -0.528628 | 0.760762 | -0.090724 | -20.552054 | -1.075446 | 0.890487 | 0.361717 | -21.989358 | -0.837785 | 1.063081 | -0.412652 | -20.832929 | -19.671043 | 2.884025 | -1.590838 | -1.291829 | -0.974740 | -21.805810 | -0.296229 | 0.784477 | -0.556038 | 0.603650 | 1.271267 | -1.453246 | 1.222693 | 0.365256 | -20.461283 | -0.153747 | 0.349399 | -1.190998 | 0.180083 | 0.138019 | -21.129349 | 0.684414 | 1.416774 | -19.738124 | 2.154697 | -1.618709 | -0.442197 | -1.005072 | -21.893985 | -0.265423 | 0.545967 | -0.629882 | -20.498936 | -19.502311 | -1.450868 | -1.570628 | 0.415703 | -20.450380 | ... | 0.829586 | -21.815323 | -20.439323 | -19.635590 | -22.585576 | -0.465375 | 0.786858 | 0.799349 | 0.492504 | 0.376951 | -0.119057 | -0.750758 | -0.183951 | -20.840923 | 2.124971 | -20.634048 | -19.916025 | -21.076626 | 0.438112 | -0.341170 | -22.110138 | 0.295330 | 0.351480 | -0.158216 | 0.408965 | -20.507940 | -19.646705 | -22.694922 | -1.502811 | -0.499805 | 0.700926 | -1.078985 | 1.450633 | 1.603930 | -0.789927 | -0.760077 | 1.278125 | -0.456257 | -20.865612 | 3.094973 | -21.010260 | -0.553723 | 1.889130 | -22.070431 | 0.399205 | -1.200649 | -1.687266 | -0.595170 | -20.564588 | -19.873740 |
BRAF | 0.505319 | 0.057744 | -0.641739 | -20.552054 | 0.958501 | 0.339472 | 0.395665 | -21.989358 | 0.196162 | 1.097028 | -21.561812 | -20.832929 | -19.671043 | 0.110618 | -1.556891 | 0.327081 | -0.940792 | -0.622702 | 0.737718 | 0.233462 | 0.477909 | -20.545511 | 1.305214 | 0.165663 | -0.550715 | -1.600796 | -20.461283 | -22.302907 | 0.383346 | -22.340159 | 0.798993 | -0.828033 | -21.129349 | -0.281638 | 2.035683 | -19.738124 | 0.188645 | 0.415238 | 0.176712 | -22.154233 | 0.874085 | -1.231475 | 1.065341 | 1.725993 | 0.684172 | -19.502311 | -0.416921 | 0.048281 | 0.034613 | -20.450380 | ... | -1.719752 | -0.561825 | 0.814174 | -19.635590 | -1.332079 | 0.155211 | -1.499446 | -20.418525 | 1.265094 | 0.412575 | -0.083433 | -0.715134 | -0.733289 | 1.412574 | -21.677864 | 0.619449 | -19.916025 | -21.076626 | 0.058698 | 0.694454 | -0.856641 | 0.330954 | -0.197858 | -0.707554 | 1.444589 | 1.745557 | -19.646705 | -1.441424 | 0.117775 | 0.535819 | -20.516947 | 0.541601 | 1.486257 | 0.832199 | 0.245697 | -0.724453 | -20.939748 | -21.674130 | -20.865612 | 1.545635 | -21.010260 | 0.066864 | 0.339792 | -0.816934 | -0.565170 | 0.419937 | -0.066680 | 0.440454 | -20.564588 | -19.873740 |
328 rows × 943 columns
get_cddm_LO_upper
get_cddm_LO_upper ()
Get CDDM Log-odds data of all-uppercase sequence with ‘STY’ background.
Data.get_cddm_LO_upper()
-20P | -20G | -20A | -20C | -20S | -20T | -20V | -20I | -20L | -20M | -20F | -20Y | -20W | -20H | -20K | -20R | -20Q | -20N | -20D | -20E | -20pS | -20pT | -20pY | -19P | -19G | -19A | -19C | -19S | -19T | -19V | -19I | -19L | -19M | -19F | -19Y | -19W | -19H | -19K | -19R | -19Q | -19N | -19D | -19E | -19pS | -19pT | -19pY | -18P | -18G | -18A | -18C | ... | 18E | 18pS | 18pT | 18pY | 19P | 19G | 19A | 19C | 19S | 19T | 19V | 19I | 19L | 19M | 19F | 19Y | 19W | 19H | 19K | 19R | 19Q | 19N | 19D | 19E | 19pS | 19pT | 19pY | 20P | 20G | 20A | 20C | 20S | 20T | 20V | 20I | 20L | 20M | 20F | 20Y | 20W | 20H | 20K | 20R | 20Q | 20N | 20D | 20E | 20pS | 20pT | 20pY | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
SRC | -0.298965 | 0.245926 | -0.306472 | -0.315249 | -0.500805 | -0.002884 | 0.039840 | 0.331979 | 0.006587 | 0.074104 | 0.026464 | 0.687254 | -0.484863 | -0.234235 | 0.238737 | 0.035866 | 0.173786 | 0.112172 | 0.062717 | -0.187118 | 0.0 | 0.0 | 0.0 | -0.394990 | 0.116437 | 0.241674 | 0.270796 | -0.530225 | -0.272866 | 0.089650 | 0.359646 | -0.082026 | 0.078067 | 0.157708 | 0.396654 | 0.443758 | -0.096374 | 0.191619 | -0.036922 | -0.065461 | -0.093194 | 0.198348 | -0.149715 | 0.0 | 0.0 | 0.0 | -0.209860 | 0.005564 | -0.061876 | 0.087346 | ... | -0.024870 | 0.0 | 0.0 | 0.0 | -0.265140 | 0.085462 | -0.135241 | 0.341197 | -0.234110 | -0.157485 | -0.016493 | 0.302052 | 0.137508 | 0.404226 | 0.299088 | 0.462480 | 0.165626 | -0.468907 | -0.152143 | 0.097919 | 0.055576 | -0.162821 | 0.125989 | -0.139554 | 0.0 | 0.0 | 0.0 | -0.219858 | 0.305918 | -0.086212 | -0.217325 | -0.395092 | 0.096392 | -0.379744 | 0.266731 | -0.143992 | 0.691717 | 0.259364 | 0.542941 | -0.018293 | -0.661728 | 0.104673 | 0.041005 | -0.236473 | -0.001987 | -0.082064 | 0.136414 | 0.0 | 0.0 | 0.0 |
EPHA3 | -0.599679 | 0.358959 | -0.185427 | -0.831496 | -0.434706 | 0.071154 | 0.414240 | 0.223052 | -0.137106 | 0.278334 | 0.016725 | 0.437268 | 0.441832 | -0.030005 | 0.265960 | 0.060927 | 0.022921 | -0.019164 | 0.069583 | -0.334271 | 0.0 | 0.0 | 0.0 | -0.411559 | -0.111818 | 0.271060 | 0.160722 | -0.734799 | -0.006279 | -0.055189 | 0.188981 | -0.076858 | 0.200475 | 0.294762 | 0.353099 | 0.224919 | 0.180083 | 0.348124 | -0.056065 | -0.135338 | -0.201591 | 0.266315 | -0.000554 | 0.0 | 0.0 | 0.0 | -0.414603 | -0.189918 | -0.268878 | 0.346775 | ... | -0.108833 | 0.0 | 0.0 | 0.0 | -0.326395 | 0.065984 | -0.062604 | 0.534849 | -0.583601 | -0.031956 | 0.001107 | 0.257761 | 0.197541 | 0.557236 | 0.214109 | 0.442850 | 0.189352 | -0.386287 | -0.019033 | -0.007411 | -0.197407 | -0.094701 | 0.126509 | 0.031850 | 0.0 | 0.0 | 0.0 | -0.465271 | 0.285190 | -0.098081 | 0.223956 | -0.630220 | 0.022506 | -0.242274 | 0.573323 | -0.225459 | 0.654314 | 0.360504 | 0.216062 | -0.113799 | -0.579696 | 0.214783 | 0.002284 | -0.502364 | -0.125070 | 0.012040 | 0.357301 | 0.0 | 0.0 | 0.0 |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
MAST2 | -0.528628 | 0.760762 | -0.090724 | -20.552054 | -0.838992 | 0.813257 | 0.361717 | -21.989358 | -0.837785 | 1.063081 | -0.412652 | -0.283875 | -19.671043 | 2.884025 | -1.590838 | -1.291829 | -0.974740 | -21.805810 | -0.296229 | 0.784477 | 0.0 | 0.0 | 0.0 | -1.453246 | 1.222693 | 0.365256 | -20.461283 | -0.330500 | -0.142089 | -1.190998 | 0.180083 | 0.138019 | -21.129349 | 0.684414 | 0.904502 | -19.738124 | 2.154697 | -1.618709 | -0.442197 | -1.005072 | -21.893985 | -0.265423 | 0.545967 | 0.0 | 0.0 | 0.0 | -1.450868 | -1.570628 | 0.415703 | -20.450380 | ... | 0.829586 | 0.0 | 0.0 | 0.0 | -22.585576 | -0.465375 | 0.786858 | 0.799349 | 0.458506 | -0.105326 | -0.119057 | -0.750758 | -0.183951 | -20.840923 | 2.124971 | -21.223241 | -19.916025 | -21.076626 | 0.438112 | -0.341170 | -22.110138 | 0.295330 | 0.351480 | -0.158216 | 0.0 | 0.0 | 0.0 | -22.694922 | -1.502811 | -0.499805 | 0.700926 | -0.857265 | 0.930110 | 1.603930 | -0.789927 | -0.760077 | 1.278125 | -0.456257 | -21.453288 | 3.094973 | -21.010260 | -0.553723 | 1.889130 | -22.070431 | 0.399205 | -1.200649 | -1.687266 | 0.0 | 0.0 | 0.0 |
BRAF | 0.505319 | 0.057744 | -0.641739 | -20.552054 | 0.779918 | -0.152796 | 0.395665 | -21.989358 | 0.196162 | 1.097028 | -21.561812 | -0.249928 | -19.671043 | 0.110618 | -1.556891 | 0.327081 | -0.940792 | -0.622702 | 0.737718 | 0.233462 | 0.0 | 0.0 | 0.0 | 0.165663 | -0.550715 | -1.600796 | -20.461283 | 0.440412 | 0.476821 | -22.340159 | 0.798993 | -0.828033 | -21.129349 | -0.281638 | 1.523411 | -19.738124 | 0.188645 | 0.415238 | 0.176712 | -22.154233 | 0.874085 | -1.231475 | 1.065341 | 0.0 | 0.0 | 0.0 | -0.416921 | 0.048281 | 0.034613 | -20.450380 | ... | -1.719752 | 0.0 | 0.0 | 0.0 | -1.332079 | 0.155211 | -1.499446 | -20.418525 | 1.342127 | 0.930298 | -0.083433 | -0.715134 | -0.733289 | 1.412574 | -21.677864 | 0.030256 | -19.916025 | -21.076626 | 0.058698 | 0.694454 | -0.856641 | 0.330954 | -0.197858 | -0.707554 | 0.0 | 0.0 | 0.0 | -1.441424 | 0.117775 | 0.535819 | -20.516947 | 0.500287 | 0.965734 | 0.832199 | 0.245697 | -0.724453 | -20.939748 | -21.674130 | -21.453288 | 1.545635 | -21.010260 | 0.066864 | 0.339792 | -0.816934 | -0.565170 | 0.419937 | -0.066680 | 0.0 | 0.0 | 0.0 |
328 rows × 943 columns
Amino acid
Data.get_aa_info
Data.get_aa_info ()
Get amino acid information.
Data.get_aa_info()
Name | SMILES | MW | pKa1 | pKb2 | pKx3 | pl4 | H | VSC | P1 | P2 | SASA | NCISC | phospho | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
aa | ||||||||||||||
A | Alanine | C[C@@H](C(=O)O)N | 89.10 | 2.34 | 9.69 | NaN | 6.00 | 0.62 | 27.5 | 8.1 | 0.046 | 1.181 | 0.007187 | 0 |
C | Cysteine | C([C@@H](C(=O)O)N)S | 121.16 | 1.96 | 10.28 | 8.18 | 5.07 | 0.29 | 44.6 | 5.5 | 0.128 | 1.461 | -0.036610 | 0 |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
Kac | Acetyllysine | CC(=O)NCCCC[C@H](N)C(=O)O | 188.23 | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | 0 |
Kme3 | Trimethyllysine | C[N+](C)(C)CCCC[C@H](N)C(=O)O | 189.28 | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | 0 |
25 rows × 14 columns
Data.get_aa_rdkit
Data.get_aa_rdkit ()
Get RDKit representations of amino acids.
Data.get_aa_rdkit()
MaxAbsEStateIndex | MinAbsEStateIndex | MinEStateIndex | qed | MolWt | MinPartialCharge | MaxAbsPartialCharge | FpDensityMorgan1 | FpDensityMorgan2 | FpDensityMorgan3 | BCUT2D_MWHI | BCUT2D_MWLOW | BCUT2D_CHGHI | BCUT2D_CHGLO | BCUT2D_LOGPHI | BCUT2D_LOGPLOW | BCUT2D_MRLOW | AvgIpc | BalabanJ | BertzCT | Chi0n | Chi0v | Chi1 | Chi1v | Chi2n | Chi2v | Chi3n | Chi3v | Chi4n | Chi4v | HallKierAlpha | Ipc | Kappa1 | Kappa2 | Kappa3 | PEOE_VSA1 | PEOE_VSA10 | PEOE_VSA11 | PEOE_VSA12 | PEOE_VSA14 | PEOE_VSA2 | PEOE_VSA3 | PEOE_VSA4 | PEOE_VSA6 | PEOE_VSA7 | PEOE_VSA8 | PEOE_VSA9 | SMR_VSA1 | SMR_VSA10 | SMR_VSA3 | ... | SlogP_VSA2 | SlogP_VSA3 | SlogP_VSA4 | SlogP_VSA5 | SlogP_VSA8 | TPSA | EState_VSA1 | EState_VSA10 | EState_VSA2 | EState_VSA3 | EState_VSA4 | EState_VSA5 | EState_VSA6 | EState_VSA7 | EState_VSA8 | EState_VSA9 | VSA_EState10 | VSA_EState2 | VSA_EState3 | VSA_EState4 | VSA_EState5 | VSA_EState6 | VSA_EState7 | VSA_EState8 | VSA_EState9 | FractionCSP3 | NHOHCount | NOCount | NumAliphaticHeterocycles | NumAromaticCarbocycles | NumAromaticHeterocycles | NumAromaticRings | NumHAcceptors | NumHDonors | NumHeteroatoms | NumRotatableBonds | RingCount | MolLogP | fr_Al_COO | fr_Al_OH | fr_Ar_N | fr_C_O | fr_NH0 | fr_NH1 | fr_NH2 | fr_SH | fr_imidazole | fr_priamide | fr_sulfide | fr_unbrch_alkane | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
aa | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
A | 9.574074 | 0.731481 | -0.962963 | 0.451352 | 89.094 | -0.480094 | 0.480094 | 2.000000 | 2.166667 | 2.166667 | 16.367425 | 10.385341 | 1.990289 | -1.897069 | 1.676610 | -2.250004 | -0.137563 | 1.360964 | 3.257586 | 59.813538 | 3.510162 | 3.510162 | 2.642734 | 1.627090 | 1.126913 | 1.126913 | 0.389528 | 0.389528 | 0.000000 | 0.000000 | -0.57 | 13.609640 | 5.43 | 1.767634 | 1.721545 | 10.840195 | 6.041841 | 0.0 | 0.00000 | 5.969305 | 4.794537 | 0.0 | 0.000000 | 0.0 | 6.923737 | 0.000000 | 0.000000 | 9.901065 | 5.969305 | 0.000000 | ... | 17.117674 | 4.794537 | 0.0 | 6.923737 | 0.0 | 63.32 | 12.011146 | 4.794537 | 0.000000 | 0.000000 | 0.000000 | 6.923737 | 0.0 | 0.0 | 0.000000 | 10.840195 | 0.000000 | 9.574074 | 7.865741 | 4.835648 | -0.962963 | -0.731481 | 0.000000 | 1.418981 | 0.000000 | 0.666667 | 3.0 | 3.0 | 0.0 | 0.0 | 0.0 | 0.0 | 2.0 | 2.0 | 3.0 | 1.0 | 0.0 | -0.5818 | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
C | 9.756435 | 0.189815 | -1.004630 | 0.424382 | 121.161 | -0.480064 | 0.480064 | 2.000000 | 2.428571 | 2.428571 | 32.116867 | 10.376545 | 2.056705 | -1.960761 | 1.795249 | -2.309520 | -0.137419 | 1.645711 | 3.343417 | 75.335159 | 3.664483 | 4.558910 | 3.180739 | 2.406671 | 1.127305 | 1.492453 | 0.513894 | 0.907286 | 0.078093 | 0.234278 | -0.22 | 27.977093 | 6.78 | 2.872925 | 2.472042 | 10.840195 | 6.041841 | 0.0 | 0.00000 | 5.969305 | 4.794537 | 0.0 | 12.628789 | 0.0 | 0.000000 | 5.752854 | 0.000000 | 9.901065 | 18.598094 | 0.000000 | ... | 22.870527 | 4.794537 | 0.0 | 0.000000 | 0.0 | 63.32 | 12.011146 | 4.794537 | 5.752854 | 0.000000 | 0.000000 | 0.000000 | 0.0 | 0.0 | 12.628789 | 10.840195 | 3.649043 | 9.756435 | 8.008102 | 4.939815 | -0.814815 | -0.816358 | 0.000000 | 0.000000 | 0.000000 | 0.666667 | 3.0 | 3.0 | 0.0 | 0.0 | 0.0 | 0.0 | 3.0 | 3.0 | 4.0 | 2.0 | 0.0 | -0.6719 | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
Kac | 10.419084 | 0.067099 | -0.972660 | 0.499039 | 188.227 | -0.480086 | 0.480086 | 1.461538 | 2.076923 | 2.538462 | 16.367568 | 10.120530 | 2.091144 | -2.051830 | 1.973906 | -2.297932 | -0.138286 | 2.022803 | 3.255326 | 182.227953 | 7.746838 | 7.746838 | 6.036581 | 4.265665 | 2.923476 | 2.923476 | 1.633048 | 1.633048 | 0.877145 | 0.877145 | -1.10 | 519.860388 | 11.90 | 6.419740 | 7.266972 | 16.156983 | 6.041841 | 0.0 | 5.90718 | 5.969305 | 9.589074 | 0.0 | 0.000000 | 0.0 | 19.262465 | 13.468494 | 0.000000 | 14.695602 | 11.876485 | 5.316789 | ... | 29.569610 | 9.589074 | 0.0 | 26.186202 | 0.0 | 92.42 | 12.011146 | 9.589074 | 5.907180 | 19.386400 | 6.420822 | 6.923737 | 0.0 | 0.0 | 5.316789 | 10.840195 | 0.000000 | 20.695587 | 11.053315 | 5.271623 | -1.039759 | -0.780252 | 1.933755 | 2.032398 | 0.000000 | 0.750000 | 4.0 | 5.0 | 0.0 | 0.0 | 0.0 | 0.0 | 3.0 | 3.0 | 5.0 | 6.0 | 0.0 | -0.2953 | 1.0 | 0.0 | 0.0 | 2.0 | 0.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 2.0 |
Kme3 | 10.361469 | 0.578704 | -0.897918 | 0.465620 | 189.279 | -0.480086 | 0.480086 | 1.384615 | 1.923077 | 2.307692 | 16.367548 | 10.113915 | 2.114811 | -2.232682 | 2.021932 | -2.354302 | -0.870130 | 1.951693 | 3.414940 | 163.487862 | 8.785803 | 8.785803 | 5.827186 | 4.615856 | 4.454444 | 4.454444 | 1.911260 | 1.911260 | 1.073871 | 1.073871 | -0.61 | 396.193584 | 12.39 | 5.191317 | 7.741185 | 15.323226 | 6.041841 | 0.0 | 0.00000 | 5.969305 | 4.794537 | 0.0 | 0.000000 | 0.0 | 19.262465 | 0.000000 | 27.687772 | 14.384095 | 5.969305 | 0.000000 | ... | 49.288477 | 4.794537 | 0.0 | 19.262465 | 0.0 | 63.32 | 12.011146 | 4.794537 | 0.000000 | 6.420822 | 23.869431 | 0.000000 | 0.0 | 0.0 | 21.143016 | 10.840195 | 0.000000 | 10.361469 | 8.512288 | 5.361669 | -0.897918 | -0.687529 | 2.502778 | 1.061844 | 6.366441 | 0.888889 | 3.0 | 4.0 | 0.0 | 0.0 | 0.0 | 0.0 | 2.0 | 2.0 | 4.0 | 6.0 | 0.0 | 0.2748 | 1.0 | 0.0 | 0.0 | 1.0 | 1.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 |
25 rows × 106 columns
Data.get_aa_morgan
Data.get_aa_morgan ()
Get Morgan fingerprint representations of amino acids.
Data.get_aa_morgan()
morgan_1 | morgan_11 | morgan_24 | morgan_27 | morgan_70 | morgan_74 | morgan_79 | morgan_80 | morgan_82 | morgan_116 | morgan_118 | morgan_119 | morgan_132 | morgan_140 | morgan_172 | morgan_192 | morgan_197 | morgan_210 | morgan_222 | morgan_227 | morgan_229 | morgan_245 | morgan_280 | morgan_283 | morgan_294 | morgan_295 | morgan_305 | morgan_310 | morgan_319 | morgan_321 | morgan_322 | morgan_328 | morgan_362 | morgan_364 | morgan_376 | morgan_378 | morgan_394 | morgan_412 | morgan_414 | morgan_425 | morgan_429 | morgan_473 | morgan_482 | morgan_486 | morgan_545 | morgan_550 | morgan_553 | morgan_575 | morgan_592 | morgan_623 | ... | morgan_1431 | morgan_1451 | morgan_1452 | morgan_1456 | morgan_1459 | morgan_1507 | morgan_1517 | morgan_1544 | morgan_1558 | morgan_1564 | morgan_1573 | morgan_1595 | morgan_1602 | morgan_1607 | morgan_1633 | morgan_1644 | morgan_1685 | morgan_1693 | morgan_1716 | morgan_1719 | morgan_1736 | morgan_1737 | morgan_1750 | morgan_1751 | morgan_1752 | morgan_1754 | morgan_1758 | morgan_1773 | morgan_1778 | morgan_1783 | morgan_1785 | morgan_1791 | morgan_1819 | morgan_1838 | morgan_1840 | morgan_1844 | morgan_1847 | morgan_1849 | morgan_1873 | morgan_1876 | morgan_1879 | morgan_1882 | morgan_1898 | morgan_1911 | morgan_1912 | morgan_1926 | morgan_1937 | morgan_1942 | morgan_1946 | morgan_1970 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
aa | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
A | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
C | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
Kac | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
Kme3 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | ... | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
25 rows × 168 columns
Phosphoproteomics
Data.get_cptac_ensembl_site
Data.get_cptac_ensembl_site ()
Get CPTAC dataset with unique EnsemblProteinID+site.
Data.get_cptac_ensembl_site()
gene | site | site_seq | protein | gene_name | gene_site | protein_site | |
---|---|---|---|---|---|---|---|
0 | ENSG00000003056.8 | S267 | DDQLGEESEERDDHL | ENSP00000000412.3 | M6PR | M6PR_S267 | ENSP00000000412_S267 |
1 | ENSG00000003056.8 | S267 | DDQLGEESEERDDHL | ENSP00000440488.2 | M6PR | M6PR_S267 | ENSP00000440488_S267 |
... | ... | ... | ... | ... | ... | ... | ... |
488584 | ENSG00000143631.11 | S648 | ASRNHHGSAQEQSRD | ENSP00000357789.1 | FLG | FLG_S648 | ENSP00000357789_S648 |
488585 | ENSG00000143520.6 | S2310 | DTTRHGHSGYGQSTQ | ENSP00000373370.4 | FLG2 | FLG2_S2310 | ENSP00000373370_S2310 |
488586 rows × 7 columns
Data.get_cptac_unique_site
Data.get_cptac_unique_site ()
Get CPTAC dataset with unique site sequences.
Data.get_cptac_unique_site()
site_seq | gene_site | num_site | acceptor | |
---|---|---|---|---|
0 | AAAAAAASFPWSAFG | ZBTB7A_S182 | 1 | S |
1 | AAAAAAASGAAGGGG | INTS3_S16 | 1 | S |
... | ... | ... | ... | ... |
125474 | ______MYPAGPPAG | TIGD5_Y2 | 1 | Y |
125475 | _______SPASLPLA | RFLNB_S1 | 1 | S |
125476 rows × 4 columns
Data.get_cptac_gene_site
Data.get_cptac_gene_site ()
Get CPTAC dataset with unique Gene+site.
Data.get_cptac_gene_site()
gene | site | site_seq | protein | gene_name | gene_site | protein_site | |
---|---|---|---|---|---|---|---|
0 | ENSG00000003056.8 | S267 | DDQLGEESEERDDHL | ENSP00000000412.3 | M6PR | M6PR_S267 | ENSP00000000412_S267 |
1 | ENSG00000048028.11 | S1053 | PPTIRPNSPYDLCSR | ENSP00000003302.4 | USP28 | USP28_S1053 | ENSP00000003302_S1053 |
... | ... | ... | ... | ... | ... | ... | ... |
126223 | ENSG00000143631.11 | S648 | ASRNHHGSAQEQSRD | ENSP00000357789.1 | FLG | FLG_S648 | ENSP00000357789_S648 |
126224 | ENSG00000143520.6 | S2310 | DTTRHGHSGYGQSTQ | ENSP00000373370.4 | FLG2 | FLG2_S2310 | ENSP00000373370_S2310 |
126225 rows × 7 columns
Data.get_psp_human_site
Data.get_psp_human_site ()
Get PhosphoSitePlus human dataset (Gene+site).
Data.get_psp_human_site()
gene | protein | uniprot | site | gene_site | SITE_GRP_ID | species | site_seq | LT_LIT | MS_LIT | MS_CST | CST_CAT# | Ambiguous_Site | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | YWHAB | 14-3-3 beta | P31946 | T2 | YWHAB_T2 | 15718712 | human | ______MtMDksELV | NaN | 3.0 | 1.0 | None | 0 |
1 | YWHAB | 14-3-3 beta | P31946 | S6 | YWHAB_S6 | 15718709 | human | __MtMDksELVQkAk | NaN | 8.0 | NaN | None | 0 |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
240009 | ZZZ3 | ZZZ3 | Q8IYH5 | S677 | ZZZ3_S677 | 23077721 | human | yPPEEVEsRRWQKIA | NaN | NaN | 1.0 | None | 0 |
240010 | ZZZ3 | ZZZ3 | Q8IYH5 | S777 | ZZZ3_S777 | 41455930 | human | NTAVEDAsDDESIPI | NaN | 2.0 | NaN | None | 0 |
240011 rows × 13 columns
Data.get_ochoa_site
Data.get_ochoa_site ()
Get phosphoproteomics dataset from Ochoa et al.
Data.get_ochoa_site()
uniprot | position | residue | is_disopred | disopred_score | log10_hotspot_pval_min | isHotspot | uniprot_position | functional_score | current_uniprot | name | gene | Sequence | is_valid | site_seq | gene_site | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | A0A075B6Q4 | 24 | S | 1.0 | 0.91 | 6.839384 | 1.0 | A0A075B6Q4_24 | 0.149257 | A0A075B6Q4 | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True | VDDEKGDSNDDYDSA | A0A075B6Q4_S24 |
1 | A0A075B6Q4 | 35 | S | 1.0 | 0.87 | 9.192622 | 0.0 | A0A075B6Q4_35 | 0.136966 | A0A075B6Q4 | A0A075B6Q4_HUMAN | None | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | True | YDSAGLLSDEDCMSV | A0A075B6Q4_S35 |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
112279 | V9GYY5 | 134 | T | 1.0 | 0.83 | 2.055830 | 0.0 | V9GYY5_134 | 0.187417 | V9GYY5 | V9GYY5_HUMAN | None | KRDGDDRRPRLVLSFDEEKRREYLTGFHKRKVERKKAAIEEIKQRL... | True | SEEEASSTEKPTKAL | V9GYY5_T134 |
112280 | V9GYY5 | 138 | T | 1.0 | 0.82 | 0.726611 | 0.0 | V9GYY5_138 | 0.121025 | V9GYY5 | V9GYY5_HUMAN | None | KRDGDDRRPRLVLSFDEEKRREYLTGFHKRKVERKKAAIEEIKQRL... | True | ASSTEKPTKALPRKS | V9GYY5_T138 |
112281 rows × 16 columns
Data.get_combine_site_psp_ochoa
Data.get_combine_site_psp_ochoa ()
Get the combined dataset from Ochoa and PhosphoSitePlus.
Data.get_combine_site_psp_ochoa()
uniprot | gene | site | site_seq | source | AM_pathogenicity | CDDM_upper | CDDM_max_score | |
---|---|---|---|---|---|---|---|---|
0 | A0A024R4G9 | C19orf48 | S20 | ITGSRLLSMVPGPAR | psp | NaN | PRKX,AKT1,PKG1,P90RSK,HIPK4,AKT3,HIPK1,PKACB,H... | 2.407041 |
1 | A0A075B6Q4 | None | S24 | VDDEKGDSNDDYDSA | ochoa | NaN | CK2A2,CK2A1,GRK7,GRK5,CK1G1,CK1A,IKKA,CK1G2,CA... | 2.295654 |
... | ... | ... | ... | ... | ... | ... | ... | ... |
121417 | V9GYY5 | None | T134 | SEEEASSTEKPTKAL | ochoa | NaN | ASK1,PERK,EEF2K,MAP2K4,MEKK2,MST1,BMPR1B,OSR1,... | 1.832532 |
121418 | V9GYY5 | None | T138 | ASSTEKPTKALPRKS | ochoa | NaN | ASK1,MEK2,MPSK1,TNIK,PBK,MST2,MINK,NEK4,LKB1,MEK5 | 1.807565 |
121419 rows × 8 columns
Data.get_combine_site_phosphorylated
Data.get_combine_site_phosphorylated ()
Get the combined phosphorylated dataset from Ochoa and PhosphoSitePlus.
Data.get_combine_site_phosphorylated()
uniprot | gene | site | site_seq | source | AM_pathogenicity | CDDM | PSPA | CDDM_max_score | PSPA_max_score | |
---|---|---|---|---|---|---|---|---|---|---|
0 | A0A024R4G9 | C19orf48 | S20 | ITGSRLLsMVPGPAR | psp | NaN | PRKX,PKG1,AKT1,AKT3,HIPK4,P90RSK,PKACB,PKACA,P... | MAPKAPK5,AKT1,RSK3,P70S6K,MAPKAPK3,AKT2,DYRK1A... | 2.339278 | 3.726109 |
1 | A0A075B6Q4 | None | S24 | VDDEKGDsNDDYDSA | ochoa | NaN | CK2A2,CK2A1,GRK7,GRK5,CK1G1,IKKA,CAMK1D,MARK2,... | CAMK2B,CK2A2,CAMK2A,CK2A1,GRK7,TLK2,FAM20C,CAM... | 2.253027 | 4.940056 |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
120102 | V9GYY5 | None | T134 | sEEEAsstEKPtKAL | ochoa | NaN | PERK,ASK1,EEF2K,MST1,BMPR1B,PBK,MEKK2,OSR1,MST... | CK1G2,GSK3A,ALPHAK3,GRK1,GRK7,GSK3B,BMPR1B,BMP... | 1.723089 | 7.009429 |
120103 | V9GYY5 | None | T138 | AsstEKPtKALPRKS | ochoa | NaN | ASK1,PBK,TNIK,MPSK1,MINK,MST2,NEK4,MEK2,MST1,BUB1 | CK1G3,CK1G2,CK1A2,CK1D,CK1A,GRK3,PASK,GRK2,CK1... | 1.651888 | 4.350109 |
120104 rows × 10 columns
get_human_site
get_human_site ()
Get the combined phosphorylated dataset from Ochoa and PhosphoSitePlus (20-length version).
Data.get_human_site()
substrate_uniprot | substrate_genes | site | source | AM_pathogenicity | substrate_sequence | substrate_species | sub_site | substrate_phosphoseq | position | site_seq | |
---|---|---|---|---|---|---|---|---|---|---|---|
0 | A0A024R4G9 | C19orf48 MGC13170 hCG_2008493 | S20 | psp | NaN | MTVLEAVLEIQAITGSRLLSMVPGPARPPGSCWDPTQCTRTWLLSH... | Homo sapiens (Human) | A0A024R4G9_S20 | MTVLEAVLEIQAITGSRLLsMVPGPARPPGSCWDPTQCTRTWLLSH... | 20 | _MTVLEAVLEIQAITGSRLLsMVPGPARPPGSCWDPTQCTR |
1 | A0A075B6Q4 | None | S24 | ochoa | NaN | MDIQKSENEDDSEWEDVDDEKGDSNDDYDSAGLLSDEDCMSVPGKT... | Homo sapiens (Human) | A0A075B6Q4_S24 | MDIQKSENEDDSEWEDVDDEKGDsNDDYDSAGLLsDEDCMSVPGKT... | 24 | QKSENEDDSEWEDVDDEKGDsNDDYDSAGLLsDEDCMSVPG |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
121330 | V9GYY5 | None | T134 | ochoa | NaN | KRDGDDRRPRLVLSFDEEKRREYLTGFHKRKVERKKAAIEEIKQRL... | Homo sapiens (Human) | V9GYY5_T134 | KRDGDDRRPRLVLSFDEEKRREYLTGFHKRKVERKKAAIEEIKQRL... | 134 | LGLtPPEGGAGDRsEEEAsstEKPtKALPRKSRDPLLSQRI |
121331 | V9GYY5 | None | T138 | ochoa | NaN | KRDGDDRRPRLVLSFDEEKRREYLTGFHKRKVERKKAAIEEIKQRL... | Homo sapiens (Human) | V9GYY5_T138 | KRDGDDRRPRLVLSFDEEKRREYLTGFHKRKVERKKAAIEEIKQRL... | 138 | PPEGGAGDRsEEEAsstEKPtKALPRKSRDPLLSQRISSLT |
119955 rows × 11 columns
Reactome
get_reactome_pathway_lo
get_reactome_pathway_lo ()
Get lowest reactome pathways with Uniprot ID as identifier.
Data.get_reactome_pathway_lo()
uniprot | reactome_id | pathway | type | species | |
---|---|---|---|---|---|
0 | A0A023GPK8 | R-DME-373753 | Nephrin family interactions | IEA | Drosophila melanogaster |
1 | A0A023GRW3 | R-DME-72163 | mRNA Splicing - Major Pathway | IEA | Drosophila melanogaster |
... | ... | ... | ... | ... | ... |
306903 | Z4YHD9 | R-BTA-9734091 | Drug-mediated inhibition of MET activation | IEA | Bos taurus |
306904 | Z4YJC3 | R-GGA-983168 | Antigen processing: Ubiquitination & Proteasom... | IEA | Gallus gallus |
306905 rows × 5 columns
get_reactome_pathway
get_reactome_pathway ()
Get all level reactome pathways with Uniprot ID as identifier.
The data is from from Reactome/Download_data: https://reactome.org/download-data
Download UniProt to All pathways
under Identifier mapping files
For type, there are IEA (Inferred from Electronic Annotation) and TAS (Traceable Author Statement, higher confidence)
Data.get_reactome_pathway()
uniprot | reactome_id | pathway | type | species | |
---|---|---|---|---|---|
0 | A0A023GPK8 | R-DME-1500931 | Cell-Cell communication | IEA | Drosophila melanogaster |
1 | A0A023GPK8 | R-DME-373753 | Nephrin family interactions | IEA | Drosophila melanogaster |
... | ... | ... | ... | ... | ... |
888430 | Z4YJC3 | R-GGA-983168 | Antigen processing: Ubiquitination & Proteasom... | IEA | Gallus gallus |
888431 | Z4YJC3 | R-GGA-983169 | Class I MHC mediated antigen processing & pres... | IEA | Gallus gallus |
888432 rows × 5 columns
CPTAC
CPTAC
CPTAC ()
A class for fetching CPTAC phosphoproteomics data.
CPTAC.list_cancer
CPTAC.list_cancer ()
List available CPTAC cancer type
CPTAC.list_cancer()
['HNSCC', 'GBM', 'COAD', 'CCRCC', 'LSCC', 'BRCA', 'UCEC', 'LUAD', 'PDAC', 'OV']
CPTAC.get_id
CPTAC.get_id (cancer_type:str, is_Tumor:bool=True, is_KB:bool=False)
Get CPTAC phosphorylation sites information given a cancer type
Type | Default | Details | |
---|---|---|---|
cancer_type | str | ||
is_Tumor | bool | True | tumor tissue or normal |
is_KB | bool | False | whether it is for LinkedOmicsKB or LinkedOmics |
Use CPTAC.get_id()
to load CPTAC phosphorylation site information. Fold change of various conditions can be acquired through LinkedOmics or LinkedOmicsKB. Use is_KB
to indicate whether the phosphorylation site information is for LinkedOmics or LinkedOmicsKB.
# normal tissue
'CCRCC',is_KB=True, is_Tumor=False) CPTAC.get_id(
# tumor
'CCRCC',is_KB=True, is_Tumor=True) CPTAC.get_id(