Cross-Species Gene Symbol Mapping#

The majority of prior knowledge in OmniPath [TureiKSR16] (and similar databases) is based on human data and thus uses human gene symbols.

However, gene homology can be used to convert these symbols to those of other organisms using decoupler. To achieve this, it uses orthology tables extracted from the HCOP database [YGJB21].

The following organisms are currently supported.

import decoupler as dc

dc.op.show_organisms()

['anole_lizard',
 'c.elegans',
 'cat',
 'cattle',
 'chicken',
 'chimpanzee',
 'dog',
 'fruitfly',
 'horse',
 'macaque',
 'mouse',
 'opossum',
 'pig',
 'platypus',
 'rat',
 's.cerevisiae',
 's.pombe',
 'xenopus',
 'zebrafish']

To demonstrate this functionality in decoupler, here the SIGNOR database (which uses human gene symbols) is loaded.

net = dc.op.resource("SIGNOR")
net

	genesymbol	pathway

0	ABL1	Cell cycle: G2/M phase transition
1	ACE	Focal segmental glomerulosclerosis
2	ACTB	Axon guidance
3	ACTN1	Axon guidance
4	ACTN1	Glutamatergic synapse
...	...	...
2943	YY1	NOTCH Signaling
2944	ZAP70	T cell activation
2945	ZAP70	P38 Signaling
2946	ZBTB16	Acute Myeloid Leukemia
2947	ZFYVE9	TGF-beta Signaling

2948 rows × 2 columns

The obtained resource can easily be converted to mouse gene symbols.

m_net = dc.op.translate(
    net,
    target_organism="mouse",
)
m_net

	genesymbol	pathway
0	Abl1	Cell cycle: G2/M phase transition
1	Ace	Focal segmental glomerulosclerosis
2	Actb	Axon guidance
3	Actg1	Axon guidance
4	Actn1	Axon guidance
...	...	...
1436	Yy1	NOTCH Signaling
1437	Zap70	T cell activation
1438	Zap70	P38 Signaling
1439	Zbtb16	Acute Myeloid Leukemia
1440	Zfyve9	TGF-beta Signaling

1441 rows × 2 columns

Note

Homology conversion may result in the gain or loss of certain genes when mapping between organisms. Adjust the one_to_many parameter to make the behavior more or less strict.

Next, the conversion is performed for the fruit fly.

f_net = dc.op.translate(
    net,
    target_organism="fruitfly",
)
f_net

	genesymbol	pathway
0	Abl	Cell cycle: G2/M phase transition
1	Ance	Focal segmental glomerulosclerosis
2	Acer	Focal segmental glomerulosclerosis
3	Ance-2	Focal segmental glomerulosclerosis
4	Ance-3	Focal segmental glomerulosclerosis
...	...	...
1024	yki	Hippo Signaling
1025	14-3-3zeta	SAPK/JNK Signaling
1026	pho	NOTCH Signaling
1027	phol	NOTCH Signaling
1028	Sara	TGF-beta Signaling

1029 rows × 2 columns

Additionaly, all database functions in decoupler directly accept the parametter organism, which under the hood it runs decoupler.op.translate.

dc.op.resource("SIGNOR", organism="zebrafish")

	genesymbol	pathway
0	abl1	Cell cycle: G2/M phase transition
1	ace	Focal segmental glomerulosclerosis
2	actb2	Axon guidance
3	actb1	Axon guidance
4	actn1	Axon guidance
...	...	...
1981	zap70	T cell activation
1982	zap70	P38 Signaling
1983	zbtb16a	Acute Myeloid Leukemia
1984	zbtb16b	Acute Myeloid Leukemia
1985	zfyve9a	TGF-beta Signaling

1986 rows × 2 columns

dc.op.progeny(organism="anole_lizard")

	source	target	weight	padj
0	Androgen	tmprss2	11.490631	2.384806e-47
1	Androgen	nkx3-1	10.622551	2.205102e-44
2	Androgen	mboat2	10.472733	4.632376e-44
3	Androgen	SLC38A4	7.363805	1.253071e-39
4	Androgen	mtmr9	6.130646	2.534403e-38
...	...	...	...	...
43409	p53	enpp2	2.771405	4.993215e-02
43410	p53	arrdc4	3.494328	4.996747e-02
43411	p53	myo1b	-1.148057	4.997905e-02
43412	p53	ctsc	-1.784693	4.998864e-02
43413	p53	naa50	-1.435013	4.998884e-02

43414 rows × 4 columns

dc.op.collectri(organism="s.cerevisiae")

	source	target	weight	resources	references	sign_decision
0	SPT15	TOA1	1.0	ExTRI	10078202;10523649;10581267;10617594;10675336;1...	default activation
1	TOA1	SPT15	1.0	TRRUST	12818428	default activation
2	MOT1	SPT15	-1.0	TRRUST	14988402;15509807;16858867;20627952	PMID
3	SPT15	MOT1	1.0	ExTRI	10082549	default activation
4	MCM1	MCM1	1.0	ExTRI;NTNU.Curated	10330138;10602487;15531578;17629633;8663310;92...	PMID
...	...	...	...	...	...	...
362	COY1	RDI1	1.0	Pavlidis2021	19635798	PMID
363	COY1	POL1	1.0	Pavlidis2021	12438259;12665598;18347061	PMID
364	HAP2	SSA4	1.0	Pavlidis2021	24041570	PMID
365	HAP3	SSA4	1.0	Pavlidis2021	24041570	PMID
366	HAP5	SSA4	1.0	Pavlidis2021	24041570	PMID

367 rows × 6 columns