CREMA results: VSX1

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Transcription factors associated with VSX1

Gene Symbol	Gene ID	Gene Info
VSX1 Ensembl NCBI GeneCards UniProt	ENSG00000100987.10	visual system homeobox 1

Correlations of motif activity and signal intensity at CREs associated with the motif's TFs:

This plot shows correlation between observed signal intensity of a CRE associated with the transcription factor across all samples and activity of the motif.

For each TF, only the top 5 correlated CREs are shown.

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CRE	Gene	Distance	Association probability	Pearson corr. coef.	P-value	Plot
chr20_25057715_25057866	VSX1	4977	0.223332	-0.79	1.1e-02	Click!
chr20_25058000_25058151	VSX1	4692	0.227015	-0.64	6.5e-02	Click!
chr20_25064708_25064859	VSX1	1787	0.376087	-0.68	4.5e-02	Click!
chr20_25071203_25071354	VSX1	8282	0.211093	-0.82	6.9e-03	Click!
chr20_25071716_25071887	VSX1	8805	0.209608	-0.74	2.1e-02	Click!

Showing 1 to 5 of 5 entries

Activity of the VSX1 motif across conditions

Conditions sorted by the z-value of the VSX1 motif activity

Move your cursor over a bar to see sample name and corresponding Z-value.

Top target CREs of the motif:

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Cis Regulatory Element (CRE)	Target Score	Top associated gene	Gene Info	Distance of CRE to TSS	CRE/Gene association probability
chr11_33934050_33934291	0.77	LMO2	LIM domain only 2 (rhombotin-like 1)	20334	0.2
chr12_89453867_89454269	0.67	ENSG00000238302	.	221994	0.02
chr14_101308246_101309004	0.63	ENSG00000214548	.	7020	0.04
chr4_140958813_140959347	0.55	RP11-392B6.1		90089	0.09
chr20_30743365_30743658	0.54	ENSG00000265736	.	36957	0.11
chr2_66735450_66735818	0.50	MEIS1	Meis homeobox 1	425	0.88
chr8_27501056_27501559	0.49	SCARA3	scavenger receptor class A, member 3	9609	0.16
chr3_70882578_70882827	0.49	ENSG00000206939	.	25201	0.23
chr2_207972754_207973110	0.48	ENSG00000253008	.	1865	0.35
chr8_108208326_108208625	0.46	ENSG00000211995	.	58251	0.16

Showing 1 to 10 of 200 entries

Histogram of CRE-TSS distances for CREs targeted by :

Rank distribution of CRE target scores:

Distribution of target CREs across different genomic regions:

Network of associatons between targets according to the STRING database.

First level regulatory network of VSX1

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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
0.1	0.6	GO:0007185	transmembrane receptor protein tyrosine phosphatase signaling pathway(GO:0007185)
0.1	0.6	GO:0060216	definitive hemopoiesis(GO:0060216)
0.0	0.6	GO:0010811	positive regulation of cell-substrate adhesion(GO:0010811)
0.1	0.4	GO:0030210	heparin biosynthetic process(GO:0030210)
0.0	0.4	GO:0042953	lipoprotein transport(GO:0042953) lipoprotein localization(GO:0044872)
0.0	0.4	GO:0015914	phospholipid transport(GO:0015914)
0.1	0.3	GO:0071694	sequestering of extracellular ligand from receptor(GO:0035581) sequestering of TGFbeta in extracellular matrix(GO:0035583) protein localization to extracellular region(GO:0071692) maintenance of protein location in extracellular region(GO:0071694) extracellular regulation of signal transduction(GO:1900115) extracellular negative regulation of signal transduction(GO:1900116)
0.0	0.3	GO:0016322	neuron remodeling(GO:0016322)
0.0	0.3	GO:0061001	dendritic spine morphogenesis(GO:0060997) regulation of dendritic spine morphogenesis(GO:0061001) dendritic spine organization(GO:0097061)
0.0	0.3	GO:0006198	cAMP catabolic process(GO:0006198)

Showing 1 to 10 of 211 entries

Gene overrepresentation in cellular component category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.0	0.6	GO:0030016	myofibril(GO:0030016)
0.0	0.5	GO:0005834	heterotrimeric G-protein complex(GO:0005834)
0.0	0.4	GO:0005614	interstitial matrix(GO:0005614)
0.0	0.4	GO:0001518	voltage-gated sodium channel complex(GO:0001518)
0.0	0.4	GO:0005902	microvillus(GO:0005902)
0.1	0.3	GO:0016327	apicolateral plasma membrane(GO:0016327)
0.0	0.3	GO:0098642	network-forming collagen trimer(GO:0098642) collagen network(GO:0098645)
0.0	0.3	GO:0000145	exocyst(GO:0000145)
0.0	0.3	GO:0030315	T-tubule(GO:0030315)
0.0	0.3	GO:0005811	lipid particle(GO:0005811)

Showing 1 to 10 of 59 entries

Gene overrepresentation in molecular function category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.0	0.8	GO:0005201	extracellular matrix structural constituent(GO:0005201)
0.0	0.5	GO:0005248	voltage-gated sodium channel activity(GO:0005248) voltage-gated ion channel activity involved in regulation of postsynaptic membrane potential(GO:1905030)
0.0	0.5	GO:0004012	phospholipid-translocating ATPase activity(GO:0004012)
0.0	0.5	GO:0019198	transmembrane receptor protein tyrosine phosphatase activity(GO:0005001) transmembrane receptor protein phosphatase activity(GO:0019198)
0.0	0.4	GO:0004115	3',5'-cyclic-AMP phosphodiesterase activity(GO:0004115)
0.0	0.4	GO:0004653	polypeptide N-acetylgalactosaminyltransferase activity(GO:0004653)
0.0	0.4	GO:0031683	G-protein beta/gamma-subunit complex binding(GO:0031683)
0.0	0.4	GO:0005520	insulin-like growth factor binding(GO:0005520)
0.1	0.3	GO:0004322	ferroxidase activity(GO:0004322) oxidoreductase activity, oxidizing metal ions, oxygen as acceptor(GO:0016724)
0.0	0.3	GO:0004364	glutathione transferase activity(GO:0004364)

Showing 1 to 10 of 145 entries

Gene overrepresentation in curated gene sets: canonical pathways category:

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Total log-likelihood	Term	Description
1.1	NABA COLLAGENS	Genes encoding collagen proteins
0.4	PID S1P S1P2 PATHWAY	S1P2 pathway
0.3	PID INTEGRIN5 PATHWAY	Beta5 beta6 beta7 and beta8 integrin cell surface interactions
0.3	ST G ALPHA S PATHWAY	G alpha s Pathway
0.3	ST GA12 PATHWAY	G alpha 12 Pathway
0.2	PID INTEGRIN A9B1 PATHWAY	Alpha9 beta1 integrin signaling events
0.2	ST MYOCYTE AD PATHWAY	Myocyte Adrenergic Pathway is a specific case of the generalized Adrenergic Pathway.
0.1	PID ECADHERIN KERATINOCYTE PATHWAY	E-cadherin signaling in keratinocytes
0.1	PID AMB2 NEUTROPHILS PATHWAY	amb2 Integrin signaling
0.1	PID PDGFRA PATHWAY	PDGFR-alpha signaling pathway

Showing 1 to 10 of 16 entries

Gene overrepresentation in curated gene sets: REACTOME pathways category:

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Total log-likelihood	Term	Description
0.9	REACTOME COLLAGEN FORMATION	Genes involved in Collagen formation
0.8	REACTOME MYOGENESIS	Genes involved in Myogenesis
0.4	REACTOME ROLE OF DCC IN REGULATING APOPTOSIS	Genes involved in Role of DCC in regulating apoptosis
0.4	REACTOME CGMP EFFECTS	Genes involved in cGMP effects
0.4	REACTOME SMOOTH MUSCLE CONTRACTION	Genes involved in Smooth Muscle Contraction
0.4	REACTOME INTERACTION BETWEEN L1 AND ANKYRINS	Genes involved in Interaction between L1 and Ankyrins
0.3	REACTOME GAP JUNCTION DEGRADATION	Genes involved in Gap junction degradation
0.3	REACTOME REGULATION OF AMPK ACTIVITY VIA LKB1	Genes involved in Regulation of AMPK activity via LKB1
0.3	REACTOME INHIBITION OF VOLTAGE GATED CA2 CHANNELS VIA GBETA GAMMA SUBUNITS	Genes involved in Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits
0.3	REACTOME METAL ION SLC TRANSPORTERS	Genes involved in Metal ion SLC transporters

Showing 1 to 10 of 42 entries

Results for VSX1

Z-value: 1.29

Motif logo

Transcription factors associated with VSX1

Correlations of motif activity and signal intensity at CREs associated with the motif's TFs:

This plot shows correlation between observed signal intensity of a CRE associated with the transcription factor across all samples and activity of the motif.

For each TF, only the top 5 correlated CREs are shown.

Activity of the VSX1 motif across conditions

Conditions sorted by the z-value of the VSX1 motif activity

Top target CREs of the motif:

Histogram of CRE-TSS distances for CREs targeted by :

Rank distribution of CRE target scores:

Distribution of target CREs across different genomic regions:

Network of associatons between targets according to the STRING database.

First level regulatory network of VSX1

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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: