Pathway analysis

Setup

Reactome pathway

get_reactome_raw

 get_reactome_raw (gene_list)

Reactome pathway analysis for a given gene set; returns raw output in dataframe.

pi3ks=['PIK3CA','PIK3CB','PIK3CD','PIK3CG','PIK3R1','PIK3R2','PIK3R3','PTEN','AKT1','AKT2','AKT3','MTOR','RICTOR','RPTOR','TSC1','TSC2','PDK1','IRS1','IRS2','INSR','IGF1R','GAB1','HRAS','NRAS','KRAS','EGFR','ERBB2','ERBB3','ERBB4']

raw_out = get_reactome_raw(pi3ks)
raw_out.head()

	stId	dbId	name	llp	inDisease	species.dbId	species.taxId	species.name	entities.resource	entities.total	entities.found	entities.ratio	entities.pValue	entities.fdr	entities.exp	reactions.resource	reactions.total	reactions.found	reactions.ratio
0	R-HSA-1963640	1963640	GRB2 events in ERBB2 signaling	True	False	48887	9606	Homo sapiens	TOTAL	21	9	0.001304	1.110223e-16	1.221245e-15	[]	TOTAL	4	4	0.000255
1	R-HSA-9665348	9665348	Signaling by ERBB2 ECD mutants	True	True	48887	9606	Homo sapiens	TOTAL	23	9	0.001428	1.110223e-16	1.221245e-15	[]	TOTAL	15	15	0.000957
2	R-HSA-9664565	9664565	Signaling by ERBB2 KD Mutants	True	True	48887	9606	Homo sapiens	TOTAL	35	13	0.002174	1.110223e-16	1.221245e-15	[]	TOTAL	17	17	0.001085
3	R-HSA-1227990	1227990	Signaling by ERBB2 in Cancer	False	True	48887	9606	Homo sapiens	TOTAL	36	13	0.002236	1.110223e-16	1.221245e-15	[]	TOTAL	62	62	0.003957
4	R-HSA-9665686	9665686	Signaling by ERBB2 TMD/JMD mutants	True	True	48887	9606	Homo sapiens	TOTAL	30	10	0.001863	1.110223e-16	1.221245e-15	[]	TOTAL	13	13	0.000830

source

get_reactome

 get_reactome (gene_list, p_type='FDR')

Reactome pathway analysis for a given gene set; returns formated output in dataframe with additional -log10(p)

	Type	Default	Details
gene_list
p_type	str	FDR	or p

path = get_reactome(pi3ks,p_type='p')
path.head()

Running pathway anlysis
Done

	name	reactome_id	p	-log10_p
0	GRB2 events in ERBB2 signaling	R-HSA-1963640	1.110223e-16	15.955
1	Signaling by ERBB2 ECD mutants	R-HSA-9665348	1.110223e-16	15.955
2	Signaling by ERBB2 KD Mutants	R-HSA-9664565	1.110223e-16	15.955
3	Signaling by ERBB2 in Cancer	R-HSA-1227990	1.110223e-16	15.955
4	Signaling by ERBB2 TMD/JMD mutants	R-HSA-9665686	1.110223e-16	15.955

path = get_reactome(pi3ks,p_type='FDR')
path.head()

Running pathway anlysis
Done

	name	reactome_id	FDR	-log10_FDR
0	GRB2 events in ERBB2 signaling	R-HSA-1963640	1.221245e-15	14.913
1	Signaling by ERBB2 ECD mutants	R-HSA-9665348	1.221245e-15	14.913
2	Signaling by ERBB2 KD Mutants	R-HSA-9664565	1.221245e-15	14.913
3	Signaling by ERBB2 in Cancer	R-HSA-1227990	1.221245e-15	14.913
4	Signaling by ERBB2 TMD/JMD mutants	R-HSA-9665686	1.221245e-15	14.913

path[path.FDR<0.05]

	name	reactome_id	FDR	-log10_FDR
0	GRB2 events in ERBB2 signaling	R-HSA-1963640	1.221245e-15	14.913
1	Signaling by ERBB2 ECD mutants	R-HSA-9665348	1.221245e-15	14.913
2	Signaling by ERBB2 KD Mutants	R-HSA-9664565	1.221245e-15	14.913
3	Signaling by ERBB2 in Cancer	R-HSA-1227990	1.221245e-15	14.913
4	Signaling by ERBB2 TMD/JMD mutants	R-HSA-9665686	1.221245e-15	14.913
...	...	...	...	...
319	Viral Infection Pathways	R-HSA-9824446	3.888317e-02	1.410
320	RHO GTPase cycle	R-HSA-9012999	3.922694e-02	1.406
321	RUNX3 regulates p14-ARF	R-HSA-8951936	4.374857e-02	1.359
322	Cellular response to chemical stress	R-HSA-9711123	4.654844e-02	1.332
323	Signaling by Rho GTPases	R-HSA-194315	4.672781e-02	1.330

324 rows × 4 columns

Reference

Download 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)

ref = Data.get_reactome_pathway()

ref.head()

	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
2	A0A023GRW3	R-DME-72163	mRNA Splicing - Major Pathway	IEA	Drosophila melanogaster
3	A0A023GRW3	R-DME-72172	mRNA Splicing	IEA	Drosophila melanogaster
4	A0A023GRW3	R-DME-72203	Processing of Capped Intron-Containing Pre-mRNA	IEA	Drosophila melanogaster

source

query_reactome

 query_reactome (uniprot_id)

Query uniprot ID in Reactome all level pathway database.

uniprot='P31751' # AKT2
akt_path = query_reactome(uniprot) # AKT2

akt_path

	reactome_id	uniprot	pathway	type	species	lowest
0	R-HSA-109581	P31751	Apoptosis	IEA	Homo sapiens	0
1	R-HSA-109606	P31751	Intrinsic Pathway for Apoptosis	IEA	Homo sapiens	0
2	R-HSA-109703	P31751	PKB-mediated events	IEA	Homo sapiens	0
3	R-HSA-109704	P31751	PI3K Cascade	IEA, TAS	Homo sapiens	0
4	R-HSA-111447	P31751	Activation of BAD and translocation to mitocho...	IEA	Homo sapiens	1
...	...	...	...	...	...	...
93	R-HSA-9755511	P31751	KEAP1-NFE2L2 pathway	TAS	Homo sapiens	1
94	R-HSA-9755779	P31751	SARS-CoV-2 targets host intracellular signalli...	TAS	Homo sapiens	1
95	R-HSA-9824446	P31751	Viral Infection Pathways	TAS	Homo sapiens	0
96	R-HSA-9824585	P31751	Regulation of MITF-M-dependent genes involved ...	IEA	Homo sapiens	1
97	R-HSA-9856651	P31751	MITF-M-dependent gene expression	IEA	Homo sapiens	0

98 rows × 6 columns

# lowest
akt_path[akt_path.lowest==1].shape

(32, 6)

source

add_reactome_ref

 add_reactome_ref (df, uniprot)

out = add_reactome_ref(path,uniprot)
out.shape

(403, 6)

Bar plot of pathways

source

plot_path

 plot_path (react_df, p_type='FDR', ref_id_list=None, ref_col=None,
            top_n=10, max_label_length=80)

Plot the output of get_reactome. If ref_df is provided, bars corresponding to pathways in ref_df are shown in dark red.

	Type	Default	Details
react_df			the output df of get_reactome
p_type	str	FDR
ref_id_list	NoneType	None	list of reactome_id
ref_col	NoneType	None	column in reac_df, 1 or 0 to indicate whether it’s in ref
top_n	int	10
max_label_length	int	80

plot_path(out)
plt.title('PI3K Pathways');

# All level
plot_path(out,p_type='FDR',ref_id_list=akt_path.reactome_id,top_n=15)
plt.title('PI3K Pathways (with highlight as overlap with all level Reactome database)');

out.head()

	name	reactome_id	FDR	-log10_FDR
0	GRB2 events in ERBB2 signaling	R-HSA-1963640	1.221245e-15	14.913
1	Signaling by ERBB2 ECD mutants	R-HSA-9665348	1.221245e-15	14.913
2	Signaling by ERBB2 KD Mutants	R-HSA-9664565	1.221245e-15	14.913
3	Signaling by ERBB2 in Cancer	R-HSA-1227990	1.221245e-15	14.913
4	Signaling by ERBB2 TMD/JMD mutants	R-HSA-9665686	1.221245e-15	14.913

# All level, use ref_col
plot_path(out,p_type='FDR',ref_col='ref_path',top_n=15)
plt.title('PI3K Pathways (with highlight as overlap with all level Reactome database)');

# All level
plot_path(out,p_type='FDR',ref_col='ref_path_lowest',top_n=15)
plt.title('PI3K Pathways (with highlight as overlap with lowest level Reactome database)');

Overlap

source

get_overlap

 get_overlap (react_df, ref_id_list=None, ref_col=None, p_type='FDR',
              thr=0.05, plot=True, figsize=(5, 3), **kwargs)

	Type	Default	Details
react_df
ref_id_list	NoneType	None
ref_col	NoneType	None	column in react_df, 1 or 0 to indicate whether it’s in ref
p_type	str	FDR
thr	float	0.05	original threshold of p value, will be log10 transformed
plot	bool	True
figsize	tuple	(5, 3)
kwargs	VAR_KEYWORD

get_overlap(out, ref_id_list=akt_path.reactome_id,plot=True)

0.8979591836734694

get_overlap(out, ref_col='ref_path')

0.8979591836734694

get_overlap(out, ref_col='ref_path_lowest')

0.96875

Pipeline

out = get_reactome(pi3ks,p_type='FDR')
out = add_reactome_ref(out,'P31749') # kinase uniprot
accuracy = get_overlap(out, ref_col='ref_path',plot=True) # if lowest, change all to lo

Setup

Reactome pathway

get_reactome_raw

get_reactome

Reference

query_reactome

add_reactome_ref

Bar plot of pathways

plot_path

Overlap

get_overlap

Pipeline

End