ISMARA results: Vsx2

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GSE53960: rat RNA-Seq transcriptomic Bodymap

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Results for Vsx2_Dlx3

Z-value: 0.98

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Transcription factors associated with Vsx2_Dlx3

Gene Symbol	Gene ID	Gene Info
Vsx2 NCBI RGD Ensembl	ENSRNOG00000011918	visual system homeobox 2
Dlx3 NCBI RGD Ensembl	ENSRNOG00000004278	distal-less homeobox 3

Activity-expression correlation:

Gene	Promoter	Pearson corr. coef.	P-value	Plot
Dlx3	rn6_v1_chr10_+_82937971_82937971	0.33	1.1e-09	Click!
Vsx2	rn6_v1_chr6_+_108285822_108285822	0.30	4.2e-08	Click!

Activity profile of Vsx2_Dlx3 motif

Sorted Z-values of Vsx2_Dlx3 motif

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Promoter	Log-likelihood	Transcript	Gene	Gene Info
chr1_-_43638161 Show fit	58.76	ENSRNOT00000024460	Ipcef1 NCBI RGD Ensembl Show fit	interaction protein for cytohesin exchange factors 1
chr1_+_59156251 Show fit	56.59	ENSRNOT00000017442	Lix1 NCBI RGD Ensembl Show fit	limb and CNS expressed 1
chr13_-_76049363 Show fit	46.96	ENSRNOT00000075865 ENSRNOT00000007455	Brinp2 NCBI RGD Ensembl Show fit	BMP/retinoic acid inducible neural specific 2
chr2_-_219262901 Show fit	44.17	ENSRNOT00000037068	Gpr88 NCBI RGD Ensembl Show fit	G-protein coupled receptor 88
chr14_+_39964588 Show fit	36.97	ENSRNOT00000003240	Gabrg1 NCBI RGD Ensembl Show fit	gamma-aminobutyric acid type A receptor gamma 1 subunit
chr10_-_87248572 Show fit	35.18	ENSRNOT00000066637 ENSRNOT00000085677	Krt26 NCBI RGD Ensembl Show fit	keratin 26
chr6_+_48452369 Show fit	33.16	ENSRNOT00000044310	Myt1l NCBI RGD Ensembl Show fit	myelin transcription factor 1-like
chr4_-_55011415 Show fit	32.08	ENSRNOT00000056996	Grm8 NCBI RGD Ensembl Show fit	glutamate metabotropic receptor 8
chr9_-_85243001 Show fit	30.82	ENSRNOT00000020219	Scg2 NCBI RGD Ensembl Show fit	secretogranin II
chr4_-_4473307 Show fit	30.45	ENSRNOT00000045773	Dpp6 NCBI RGD Ensembl Show fit	dipeptidyl peptidase like 6

Showing 1 to 10 of 132 entries

Network of associatons between targets according to the STRING database.

First level regulatory network of Vsx2_Dlx3

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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
15.8	47.4	GO:0051867	general adaptation syndrome, behavioral process(GO:0051867)
0.6	47.0	GO:0071300	cellular response to retinoic acid(GO:0071300)
1.4	46.8	GO:0097352	autophagosome maturation(GO:0097352)
8.8	44.2	GO:0061743	motor learning(GO:0061743)
0.5	33.0	GO:0031103	axon regeneration(GO:0031103)
2.9	32.1	GO:0007196	adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway(GO:0007196)
0.8	32.0	GO:0007214	gamma-aminobutyric acid signaling pathway(GO:0007214)
2.1	30.8	GO:0048245	eosinophil chemotaxis(GO:0048245)
0.7	30.5	GO:1901381	positive regulation of establishment of protein localization to plasma membrane(GO:0090004) positive regulation of potassium ion transmembrane transport(GO:1901381)
3.7	29.7	GO:0002091	negative regulation of receptor internalization(GO:0002091)

Showing 1 to 10 of 75 entries

Gene overrepresentation in cellular component category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.2	120.6	GO:0043025	neuronal cell body(GO:0043025)
0.0	59.0	GO:0005829	cytosol(GO:0005829)
0.6	56.7	GO:0042734	presynaptic membrane(GO:0042734)
7.9	47.4	GO:0032280	symmetric synapse(GO:0032280)
0.6	37.0	GO:0034707	chloride channel complex(GO:0034707)
1.9	30.8	GO:0031045	dense core granule(GO:0031045)
0.3	30.5	GO:0008076	voltage-gated potassium channel complex(GO:0008076)
0.6	30.1	GO:0008328	ionotropic glutamate receptor complex(GO:0008328) neurotransmitter receptor complex(GO:0098878)
0.2	29.7	GO:0045211	postsynaptic membrane(GO:0045211)
0.2	28.5	GO:0030027	lamellipodium(GO:0030027)

Showing 1 to 10 of 42 entries

Gene overrepresentation in molecular function category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.1	60.3	GO:0019904	protein domain specific binding(GO:0019904)
7.9	47.4	GO:0001515	opioid peptide activity(GO:0001515)
0.3	44.2	GO:0003774	motor activity(GO:0003774)
2.4	40.8	GO:0050811	GABA receptor binding(GO:0050811)
0.1	36.8	GO:0004842	ubiquitin-protein transferase activity(GO:0004842)
4.1	33.2	GO:0044323	retinoic acid-responsive element binding(GO:0044323)
8.0	32.1	GO:0001642	group III metabotropic glutamate receptor activity(GO:0001642)
0.3	31.7	GO:0004860	protein kinase inhibitor activity(GO:0004860)
0.1	31.0	GO:0005085	guanyl-nucleotide exchange factor activity(GO:0005085)
1.1	30.8	GO:0042056	chemoattractant activity(GO:0042056)

Showing 1 to 10 of 61 entries

Gene overrepresentation in curated gene sets: canonical pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
3.2	67.3	SA PTEN PATHWAY	PTEN is a tumor suppressor that dephosphorylates the lipid messenger phosphatidylinositol triphosphate.
0.6	47.4	PID AP1 PATHWAY	AP-1 transcription factor network
0.9	38.0	PID NCADHERIN PATHWAY	N-cadherin signaling events
0.1	32.5	NABA SECRETED FACTORS	Genes encoding secreted soluble factors
1.1	20.3	PID ARF6 DOWNSTREAM PATHWAY	Arf6 downstream pathway
0.3	16.4	PID CDC42 PATHWAY	CDC42 signaling events
0.1	15.6	NABA ECM AFFILIATED	Genes encoding proteins affiliated structurally or functionally to extracellular matrix proteins
0.4	14.3	PID P38 ALPHA BETA PATHWAY	Regulation of p38-alpha and p38-beta
0.3	13.7	NABA PROTEOGLYCANS	Genes encoding proteoglycans
0.3	12.4	PID TRKR PATHWAY	Neurotrophic factor-mediated Trk receptor signaling

Showing 1 to 10 of 18 entries

Gene overrepresentation in curated gene sets: REACTOME pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.3	57.1	REACTOME PEPTIDE LIGAND BINDING RECEPTORS	Genes involved in Peptide ligand-binding receptors
1.7	46.7	REACTOME REGULATION OF GENE EXPRESSION IN BETA CELLS	Genes involved in Regulation of gene expression in beta cells
0.3	34.3	REACTOME P75 NTR RECEPTOR MEDIATED SIGNALLING	Genes involved in p75 NTR receptor-mediated signalling
1.5	32.1	REACTOME CLASS C 3 METABOTROPIC GLUTAMATE PHEROMONE RECEPTORS	Genes involved in Class C/3 (Metabotropic glutamate/pheromone receptors)
1.0	27.4	REACTOME ADHERENS JUNCTIONS INTERACTIONS	Genes involved in Adherens junctions interactions
0.8	21.4	REACTOME BASIGIN INTERACTIONS	Genes involved in Basigin interactions
1.2	18.8	REACTOME IONOTROPIC ACTIVITY OF KAINATE RECEPTORS	Genes involved in Ionotropic activity of Kainate Receptors
1.0	17.5	REACTOME UNBLOCKING OF NMDA RECEPTOR GLUTAMATE BINDING AND ACTIVATION	Genes involved in Unblocking of NMDA receptor, glutamate binding and activation
0.9	15.6	REACTOME OTHER SEMAPHORIN INTERACTIONS	Genes involved in Other semaphorin interactions
0.2	9.2	REACTOME O LINKED GLYCOSYLATION OF MUCINS	Genes involved in O-linked glycosylation of mucins

Showing 1 to 10 of 19 entries

Results for Vsx2_Dlx3

Z-value: 0.98

Motif logo

Transcription factors associated with Vsx2_Dlx3

Activity-expression correlation:

Activity profile of Vsx2_Dlx3 motif

Sorted Z-values of Vsx2_Dlx3 motif

Top targets:

Network of associatons between targets according to the STRING database.

First level regulatory network of Vsx2_Dlx3

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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: