Conversion to other organisms

Most of the prior knowledge stored inside OmniPath is derived from human data, therefore they use human gene names. Despite this, using homology we can convert gene names to other organisms.

Here is the list of available organisms:

[1]:

import decoupler as dc

dc.show_organisms()

[1]:

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

To showcase how to do it inside decoupler, we will load the SIGNOR database and convert it into gene symbols for mouse and fly.

[2]:

net = dc.get_resource('SIGNOR')
net

[2]:

	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

Then, we can easily transform the obtained resource into mouse genes:

[3]:

# Translate targets
m_net = dc.translate_net(
    net,
    target_organism='mouse',
)
m_net

/home/badi/miniforge3/envs/dcp/lib/python3.11/site-packages/liana/resource/_orthology.py:199: DtypeWarning: Columns (0) have mixed types. Specify dtype option on import or set low_memory=False.

[3]:

	genesymbol	pathway
0	Abl1	Cell cycle: G2/M phase transition
1	Ace	Focal segmental glomerulosclerosis
2	Actn1	Axon guidance
3	Actn1	Glutamatergic synapse
4	Acvr1b	Multiple sclerosis
...	...	...
1386	Yy1	NOTCH Signaling
1387	Zap70	T cell activation
1388	Zap70	P38 Signaling
1389	Zbtb16	Acute Myeloid Leukemia
1390	Zfyve9	TGF-beta Signaling

1391 rows × 2 columns

Note that when performing homology convertion we might gain or lose some genes from one organism to another.

Let us try the fruit fly now:

[4]:

# Translate targets
f_net = dc.translate_net(
    net,
    target_organism='fruitfly',
)
f_net

/home/badi/miniforge3/envs/dcp/lib/python3.11/site-packages/liana/resource/_orthology.py:199: DtypeWarning: Columns (0,7) have mixed types. Specify dtype option on import or set low_memory=False.

[4]:

	genesymbol	pathway
0	Abl	Cell cycle: G2/M phase transition
1	Actn	Axon guidance
2	Actn	Glutamatergic synapse
3	babo	Multiple sclerosis
4	put	Multiple sclerosis
...	...	...
725	Diap2	Death Receptor Signaling
726	Diap2	Inhibition of Apoptosis
727	yki	Hippo Signaling
728	14-3-3zeta	SAPK/JNK Signaling
729	Sara	TGF-beta Signaling

730 rows × 2 columns

Additionaly, all OmniPath functions directly accept the parametter organism:

[5]:

dc.get_resource('SIGNOR', organism='zebrafish')

/home/badi/miniforge3/envs/dcp/lib/python3.11/site-packages/liana/resource/_orthology.py:199: DtypeWarning: Columns (0) have mixed types. Specify dtype option on import or set low_memory=False.

[5]:

	genesymbol	pathway
0	abl1	Cell cycle: G2/M phase transition
1	ace	Focal segmental glomerulosclerosis
2	actn1	Axon guidance
3	actn1	Glutamatergic synapse
4	adsl	Nucleotide Biosynthesis
...	...	...
772	xiap	Inhibition of Apoptosis
773	yap1	Hippo Signaling
774	zap70	T cell activation
775	zap70	P38 Signaling
776	zfyve9a	TGF-beta Signaling

777 rows × 2 columns

[6]:

dc.get_progeny(organism='anole_lizard')

[6]:

	source	target	weight	p_value
0	Androgen	tmprss2	11.490631	0.0
1	Androgen	nkx3-1	10.622551	0.0
2	Androgen	mboat2	10.472733	0.0
3	Androgen	SLC38A4	7.363805	0.0
4	Androgen	mtmr9	6.130646	0.0
...	...	...	...	...
153279	p53	tagap	-0.000638	0.998829
153280	p53	MALRD1	-0.000406	0.999307
153281	p53	LOC100559499	-0.000291	0.999398
153282	p53	gsk3a	-0.00006	0.999796
153283	p53	gng4	0.000089	0.99988

153284 rows × 4 columns

[7]:

dc.get_collectri(organism='s.cerevisiae')

[7]:

	source	target	weight	pmid
0	SPT15	TOA1	1	10078202;10523649;10581267;10617594;10675336;1...
1	TOA1	SPT15	1	12818428
2	MOT1	SPT15	-1	14988402;15509807;16858867;20627952
3	SPT15	MOT1	1	10082549
4	SPT15	DFR1	1	10336493
...	...	...	...	...
208	HAP2	SSA4	1	<NA>
209	HAP3	SSA4	1	<NA>
210	HAP3	SSA4	1	<NA>
211	HAP5	SSA4	1	<NA>
212	HAP5	SSA4	1	<NA>

213 rows × 4 columns