Data

Load various kinase-relatd datasets

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

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Data

 Data ()

A class for fetching various datasets.

You can change it to local path if you want:

Data.DATASET_DIR=Path('katlas_dataset')

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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:

Data.download(force=True)
# Data.download(force=True)

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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.*

Data.read_file('kinase_info.csv')
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

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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

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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

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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

source

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

source

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

source

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

source

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

source

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

source

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

source

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

source

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

source

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

source

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

source

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

source

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

source

CPTAC

 CPTAC ()

A class for fetching CPTAC phosphoproteomics data.

source

CPTAC.list_cancer

 CPTAC.list_cancer ()

List available CPTAC cancer type

CPTAC.list_cancer()
['HNSCC', 'GBM', 'COAD', 'CCRCC', 'LSCC', 'BRCA', 'UCEC', 'LUAD', 'PDAC', 'OV']

source

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
CPTAC.get_id('CCRCC',is_KB=True, is_Tumor=False)
# tumor
CPTAC.get_id('CCRCC',is_KB=True, is_Tumor=True)

End