ISMARA results: SOX3

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ENCODE cell lines, expression (Ernst 2011)

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Results for SOX3_SOX2

Z-value: 2.80

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Transcription factors associated with SOX3_SOX2

Gene Symbol	Gene ID	Gene Info
SOX3 Ensembl NCBI GeneCards UniProt	ENSG00000134595.6	SOX3
SOX2 Ensembl NCBI GeneCards UniProt	ENSG00000181449.2	SOX2

Activity-expression correlation:

Gene	Promoter	Pearson corr. coef.	P-value	Plot
SOX3	hg19_v2_chrX_-_139587225_139587234	-0.05	8.4e-01	Click!
SOX2	hg19_v2_chr3_+_181429704_181429722	0.03	9.0e-01	Click!

Activity profile of SOX3_SOX2 motif

Sorted Z-values of SOX3_SOX2 motif

Network of associatons between targets according to the STRING database.

First level regulatory network of SOX3_SOX2

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Top targets:

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Promoter	Score	Transcript	Gene	Gene Info
chr13_-_110959478	11.04	ENST00000543140.1 ENST00000375820.4	COL4A1	collagen, type IV, alpha 1
chr1_-_95391315	10.68	ENST00000545882.1 ENST00000415017.1	CNN3	calponin 3, acidic
chr7_+_102553430	10.22	ENST00000339431.4 ENST00000249377.4	LRRC17	leucine rich repeat containing 17
chr5_-_16936340	9.91	ENST00000507288.1 ENST00000513610.1	MYO10	myosin X
chr6_-_128841503	9.74	ENST00000368215.3 ENST00000532331.1 ENST00000368213.5 ENST00000368207.3 ENST00000525459.1 ENST00000368210.3 ENST00000368226.4 ENST00000368227.3	PTPRK	protein tyrosine phosphatase, receptor type, K
chr2_-_1748214	9.54	ENST00000433670.1 ENST00000425171.1 ENST00000252804.4	PXDN	peroxidasin homolog (Drosophila)
chr4_+_146403912	9.02	ENST00000507367.1 ENST00000394092.2 ENST00000515385.1	SMAD1	SMAD family member 1
chrX_-_38080077	7.74	ENST00000378533.3 ENST00000544439.1 ENST00000432886.2 ENST00000538295.1	SRPX	sushi-repeat containing protein, X-linked
chr6_+_114178512	6.32	ENST00000368635.4	MARCKS	myristoylated alanine-rich protein kinase C substrate
chr9_+_103235365	5.98	ENST00000374879.4	TMEFF1	transmembrane protein with EGF-like and two follistatin-like domains 1

Showing 1 to 10 of 200 entries

Gene Ontology Analysis

Gene overrepresentation in biological_process category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.1	13.8	GO:0021987	cerebral cortex development(GO:0021987)
0.2	13.2	GO:0071480	cellular response to gamma radiation(GO:0071480)
3.2	12.6	GO:0035026	leading edge cell differentiation(GO:0035026)
0.6	12.6	GO:0032780	negative regulation of ATPase activity(GO:0032780)
0.6	12.3	GO:0051764	actin crosslink formation(GO:0051764)
2.9	11.4	GO:0061304	retinal blood vessel morphogenesis(GO:0061304)
0.7	11.1	GO:0010839	negative regulation of keratinocyte proliferation(GO:0010839)
0.0	10.5	GO:0043687	post-translational protein modification(GO:0043687)
2.6	10.2	GO:0048539	bone marrow development(GO:0048539)
0.3	9.9	GO:0003298	physiological muscle hypertrophy(GO:0003298) physiological cardiac muscle hypertrophy(GO:0003301) cell growth involved in cardiac muscle cell development(GO:0061049)

Showing 1 to 10 of 386 entries

Gene overrepresentation in C2:CP category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.2	36.0	NABA ECM GLYCOPROTEINS	Genes encoding structural ECM glycoproteins
0.3	18.0	PID SYNDECAN 4 PATHWAY	Syndecan-4-mediated signaling events
0.3	15.5	NABA COLLAGENS	Genes encoding collagen proteins
0.2	12.2	SIG REGULATION OF THE ACTIN CYTOSKELETON BY RHO GTPASES	Genes related to regulation of the actin cytoskeleton
0.1	12.1	PID AR PATHWAY	Coregulation of Androgen receptor activity
0.1	11.5	PID TGFBR PATHWAY	TGF-beta receptor signaling
0.0	11.5	NABA SECRETED FACTORS	Genes encoding secreted soluble factors
0.2	10.3	PID NETRIN PATHWAY	Netrin-mediated signaling events
0.5	9.8	PID ALK2 PATHWAY	ALK2 signaling events
0.1	6.7	PID ECADHERIN STABILIZATION PATHWAY	Stabilization and expansion of the E-cadherin adherens junction

Showing 1 to 10 of 60 entries

Gene overrepresentation in C2:CP:REACTOME category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.4	23.8	REACTOME SMOOTH MUSCLE CONTRACTION	Genes involved in Smooth Muscle Contraction
0.2	15.2	REACTOME NCAM1 INTERACTIONS	Genes involved in NCAM1 interactions
0.7	12.6	REACTOME GAP JUNCTION DEGRADATION	Genes involved in Gap junction degradation
0.3	12.5	REACTOME SIGNALING BY BMP	Genes involved in Signaling by BMP
0.2	10.8	REACTOME SIGNALING BY ROBO RECEPTOR	Genes involved in Signaling by Robo receptor
0.6	10.0	REACTOME PLATELET ADHESION TO EXPOSED COLLAGEN	Genes involved in Platelet Adhesion to exposed collagen
0.2	9.5	REACTOME NETRIN1 SIGNALING	Genes involved in Netrin-1 signaling
0.1	8.1	REACTOME PHASE II CONJUGATION	Genes involved in Phase II conjugation
0.1	7.7	REACTOME SIGNALING BY RHO GTPASES	Genes involved in Signaling by Rho GTPases
0.3	7.3	REACTOME CRMPS IN SEMA3A SIGNALING	Genes involved in CRMPs in Sema3A signaling

Showing 1 to 10 of 90 entries

Gene overrepresentation in molecular_function category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.2	16.6	GO:0005201	extracellular matrix structural constituent(GO:0005201)
0.1	15.3	GO:0008201	heparin binding(GO:0008201)
0.2	13.7	GO:0005518	collagen binding(GO:0005518)
0.5	13.4	GO:0098641	cadherin binding involved in cell-cell adhesion(GO:0098641)
0.1	12.8	GO:0035257	nuclear hormone receptor binding(GO:0035257)
0.5	12.1	GO:0005523	tropomyosin binding(GO:0005523)
0.5	11.8	GO:0098748	clathrin adaptor activity(GO:0035615) endocytic adaptor activity(GO:0098748)
0.0	11.5	GO:0005096	GTPase activator activity(GO:0005096)
1.4	11.0	GO:0030023	extracellular matrix constituent conferring elasticity(GO:0030023)
1.2	10.9	GO:0060002	plus-end directed microfilament motor activity(GO:0060002)

Showing 1 to 10 of 249 entries

Gene overrepresentation in cellular_component category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.1	31.1	GO:0005925	focal adhesion(GO:0005925)
0.1	23.7	GO:0031256	leading edge membrane(GO:0031256)
0.1	17.9	GO:0005788	endoplasmic reticulum lumen(GO:0005788)
2.0	15.7	GO:0005587	collagen type IV trimer(GO:0005587)
0.1	14.8	GO:0043197	dendritic spine(GO:0043197)
1.6	14.7	GO:0070022	transforming growth factor beta receptor homodimeric complex(GO:0070022)
0.9	14.0	GO:0030478	actin cap(GO:0030478)
0.0	13.4	GO:0005578	proteinaceous extracellular matrix(GO:0005578)
0.6	12.7	GO:0001527	microfibril(GO:0001527) fibril(GO:0043205)
0.1	12.2	GO:0030027	lamellipodium(GO:0030027)

Showing 1 to 10 of 163 entries

Results for SOX3_SOX2

Z-value: 2.80

Motif logo

Transcription factors associated with SOX3_SOX2

Activity-expression correlation:

Activity profile of SOX3_SOX2 motif

Sorted Z-values of SOX3_SOX2 motif

Network of associatons between targets according to the STRING database.

First level regulatory network of SOX3_SOX2

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Top targets:

Gene Ontology Analysis

Gene overrepresentation in biological_process category:

Gene overrepresentation in C2:CP category:

Gene overrepresentation in C2:CP:REACTOME category:

Gene overrepresentation in molecular_function category:

Gene overrepresentation in cellular_component category: