ISMARA results: vsx1_shox_shox2_uncx4.1

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PRJNA207719: Tissue specific transcriptome profiling

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Results for vsx1_shox_shox2_uncx4.1_lhx2a

Z-value: 0.56

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Transcription factors associated with vsx1_shox_shox2_uncx4.1_lhx2a

Gene Symbol	Gene ID	Gene Info
vsx1 NCBI UniProt	ENSDARG00000056292	visual system homeobox 1 homolog, chx10-like
vsx1 NCBI UniProt	ENSDARG00000109766	visual system homeobox 1 homolog, chx10-like
shox NCBI UniProt	ENSDARG00000025891	short stature homeobox
shox2 NCBI UniProt	ENSDARG00000075713	short stature homeobox 2
uncx4.1 NCBI UniProt	ENSDARG00000037760	Unc4.1 homeobox (C. elegans)
lhx2a NCBI UniProt	ENSDARG00000037964	LIM homeobox 2a

Activity-expression correlation:

Gene	Promoter	Pearson corr. coef.	P-value	Plot
shox2	dr11_v1_chr15_-_2188332_2188422	0.92	2.5e-02	Click!
uncx4.1	dr11_v1_chr1_+_9290103_9290103	0.82	8.9e-02	Click!
shox	dr11_v1_chr9_+_34641237_34641237	0.80	1.0e-01	Click!
vsx1	dr11_v1_chr17_-_21066075_21066105	0.68	2.0e-01	Click!

Activity profile of vsx1_shox_shox2_uncx4.1_lhx2a motif

Sorted Z-values of vsx1_shox_shox2_uncx4.1_lhx2a motif

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Promoter	Log-likelihood	Transcript	Gene	Gene Info
chr2_+_50608099 Show fit	1.02	ENSDART00000185805 ENSDART00000111135	neurod6b NCBI UniProt Show fit	neuronal differentiation 6b
chr13_+_38430466 Show fit	0.76	ENSDART00000132691	adgrb3 NCBI UniProt Show fit	adhesion G protein-coupled receptor B3
chr5_+_64732270 Show fit	0.74	ENSDART00000134241	olfm1a NCBI UniProt Show fit	olfactomedin 1a
chr16_+_5774977 Show fit	0.74	ENSDART00000134202	ccka NCBI UniProt Show fit	cholecystokinin a
chr4_+_21129752 Show fit	0.74	ENSDART00000169764	syt1a NCBI UniProt Show fit	synaptotagmin Ia
chr9_-_20372977 Show fit	0.71	ENSDART00000113418	igsf3 NCBI UniProt Show fit	immunoglobulin superfamily, member 3
chr23_+_40460333 Show fit	0.71	ENSDART00000184658	soga3b NCBI UniProt Show fit	SOGA family member 3b
chr5_+_64732036 Show fit	0.69	ENSDART00000073950	olfm1a NCBI UniProt Show fit	olfactomedin 1a
chr20_-_45060241 Show fit	0.67	ENSDART00000185227	klhl29 NCBI UniProt Show fit	kelch-like family member 29
chr6_+_39232245 Show fit	0.66	ENSDART00000187351	b4galnt1b NCBI UniProt Show fit	beta-1,4-N-acetyl-galactosaminyl transferase 1b

Showing 1 to 10 of 200 entries

Network of associatons between targets according to the STRING database.

First level regulatory network of vsx1_shox_shox2_uncx4.1_lhx2a

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Gene Ontology Analysis

Gene overrepresentation in biological process category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.2	1.4	GO:1902868	positive regulation of neural retina development(GO:0061075) positive regulation of retina development in camera-type eye(GO:1902868)
0.0	1.0	GO:0048791	calcium ion-regulated exocytosis of neurotransmitter(GO:0048791)
0.2	0.8	GO:0016322	neuron remodeling(GO:0016322)
0.1	0.8	GO:1904071	presynaptic active zone assembly(GO:1904071)
0.1	0.7	GO:0001574	ganglioside biosynthetic process(GO:0001574)
0.0	0.7	GO:0070593	dendrite self-avoidance(GO:0070593)
0.0	0.7	GO:0007586	digestion(GO:0007586)
0.2	0.6	GO:0045938	positive regulation of circadian sleep/wake cycle, sleep(GO:0045938)
0.0	0.6	GO:0051481	adenylate cyclase-inhibiting dopamine receptor signaling pathway(GO:0007195) negative regulation of cytosolic calcium ion concentration(GO:0051481) negative regulation of synaptic transmission, glutamatergic(GO:0051967)
0.0	0.6	GO:1901800	positive regulation of proteasomal ubiquitin-dependent protein catabolic process(GO:0032436) positive regulation of proteasomal protein catabolic process(GO:1901800)

Showing 1 to 10 of 88 entries

Gene overrepresentation in cellular component category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.0	2.8	GO:0030424	axon(GO:0030424)
0.1	0.8	GO:0043083	synaptic cleft(GO:0043083)
0.1	0.8	GO:0098982	GABA-ergic synapse(GO:0098982)
0.1	0.7	GO:0042584	chromaffin granule membrane(GO:0042584)
0.0	0.6	GO:0098978	glutamatergic synapse(GO:0098978)
0.0	0.6	GO:0031225	anchored component of membrane(GO:0031225)
0.0	0.6	GO:0043204	perikaryon(GO:0043204)
0.0	0.6	GO:0098839	postsynaptic density membrane(GO:0098839) postsynaptic specialization membrane(GO:0099634)
0.0	0.4	GO:0032593	insulin-responsive compartment(GO:0032593)
0.0	0.4	GO:0046658	anchored component of plasma membrane(GO:0046658)

Showing 1 to 10 of 37 entries

Gene overrepresentation in molecular function category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.0	1.0	GO:0001786	phosphatidylserine binding(GO:0001786)
0.0	0.9	GO:0005184	neuropeptide hormone activity(GO:0005184)
0.2	0.8	GO:0031841	neuropeptide Y receptor binding(GO:0031841) type 2 neuropeptide Y receptor binding(GO:0031843)
0.0	0.8	GO:0098882	structural constituent of presynaptic active zone(GO:0098882)
0.0	0.8	GO:0017075	syntaxin-1 binding(GO:0017075)
0.0	0.7	GO:0098632	protein binding involved in cell-cell adhesion(GO:0098632)
0.0	0.7	GO:0031624	ubiquitin conjugating enzyme binding(GO:0031624)
0.0	0.7	GO:0008376	acetylgalactosaminyltransferase activity(GO:0008376)
0.0	0.6	GO:0001591	dopamine neurotransmitter receptor activity, coupled via Gi/Go(GO:0001591)
0.0	0.6	GO:0042577	lipid phosphatase activity(GO:0042577)

Showing 1 to 10 of 67 entries

Gene overrepresentation in curated gene sets: canonical pathways category:

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Total log-likelihood	Term	Description
0.4	PID BMP PATHWAY	BMP receptor signaling
0.3	PID ARF 3PATHWAY	Arf1 pathway
0.2	PID IL12 STAT4 PATHWAY	IL12 signaling mediated by STAT4

Showing 1 to 3 of 3 entries

Gene overrepresentation in curated gene sets: REACTOME pathways category:

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Total log-likelihood	Term	Description
0.6	REACTOME LIGAND GATED ION CHANNEL TRANSPORT	Genes involved in Ligand-gated ion channel transport
0.3	REACTOME RETROGRADE NEUROTROPHIN SIGNALLING	Genes involved in Retrograde neurotrophin signalling
0.3	REACTOME DARPP 32 EVENTS	Genes involved in DARPP-32 events
0.3	REACTOME LATENT INFECTION OF HOMO SAPIENS WITH MYCOBACTERIUM TUBERCULOSIS	Genes involved in Latent infection of Homo sapiens with Mycobacterium tuberculosis
0.3	REACTOME OTHER SEMAPHORIN INTERACTIONS	Genes involved in Other semaphorin interactions
0.1	REACTOME ACETYLCHOLINE NEUROTRANSMITTER RELEASE CYCLE	Genes involved in Acetylcholine Neurotransmitter Release Cycle
0.1	REACTOME PURINE CATABOLISM	Genes involved in Purine catabolism

Showing 1 to 7 of 7 entries

Results for vsx1_shox_shox2_uncx4.1_lhx2a

Z-value: 0.56

Motif logo

Transcription factors associated with vsx1_shox_shox2_uncx4.1_lhx2a

Activity-expression correlation:

Activity profile of vsx1_shox_shox2_uncx4.1_lhx2a motif

Sorted Z-values of vsx1_shox_shox2_uncx4.1_lhx2a motif

Top targets:

Network of associatons between targets according to the STRING database.

First level regulatory network of vsx1_shox_shox2_uncx4.1_lhx2a

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Gene Ontology Analysis

Gene overrepresentation in biological process category:

Gene overrepresentation in cellular component category:

Gene overrepresentation in molecular function category:

Gene overrepresentation in curated gene sets: canonical pathways category:

Gene overrepresentation in curated gene sets: REACTOME pathways category: