ISMARA results: Sox2

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GSE53960: rat RNA-Seq transcriptomic Bodymap

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Results for Sox2

Z-value: 1.57

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Transcription factors associated with Sox2

Gene Symbol	Gene ID	Gene Info
Sox2 NCBI RGD Ensembl	ENSRNOG00000012199	SRY box 2

Activity-expression correlation:

Gene	Promoter	Pearson corr. coef.	P-value	Plot
Sox2	rn6_v1_chr2_+_121165137_121165137	0.30	3.0e-08	Click!

Activity profile of Sox2 motif

Sorted Z-values of Sox2 motif

Top targets:

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Promoter	Log-likelihood	Transcript	Gene	Gene Info
chr10_+_45289741 Show fit	44.84	ENSRNOT00000066190	Hist3h2ba NCBI RGD Ensembl Show fit	histone cluster 3, H2ba
chr5_+_64326733 Show fit	36.24	ENSRNOT00000065775	Tmeff1 NCBI RGD Ensembl Show fit	transmembrane protein with EGF-like and two follistatin-like domains 1
chr5_-_48165317 Show fit	35.28	ENSRNOT00000088179	Ankrd6 NCBI RGD Ensembl Show fit	ankyrin repeat domain 6
chr9_-_61810417 Show fit	32.01	ENSRNOT00000020910	Rftn2 NCBI RGD Ensembl Show fit	raftlin family member 2
chr18_+_79406381 Show fit	28.40	ENSRNOT00000022303 ENSRNOT00000058295 ENSRNOT00000058296 ENSRNOT00000022280	Mbp NCBI RGD Ensembl Show fit	myelin basic protein
chr17_+_9679628 Show fit	28.18	ENSRNOT00000019569 ENSRNOT00000019393	Dbn1 NCBI RGD Ensembl Show fit	drebrin 1
chr18_+_30562178 Show fit	26.96	ENSRNOT00000040998	LOC108348771 NCBI RGD Ensembl Show fit	protocadherin beta-16-like
chr16_+_22250470 Show fit	24.68	ENSRNOT00000015799	Lzts1 NCBI RGD Ensembl Show fit	leucine zipper tumor suppressor 1
chr5_+_152681101 Show fit	24.31	ENSRNOT00000076052 ENSRNOT00000022574	Stmn1 NCBI RGD Ensembl Show fit	stathmin 1
chr11_+_86512797 Show fit	24.30	ENSRNOT00000051680	Gp1bb NCBI RGD Ensembl Show fit	glycoprotein Ib platelet beta subunit

Showing 1 to 10 of 200 entries

Network of associatons between targets according to the STRING database.

First level regulatory network of Sox2

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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
0.6	80.7	GO:0007156	homophilic cell adhesion via plasma membrane adhesion molecules(GO:0007156)
0.2	66.7	GO:0007017	microtubule-based process(GO:0007017)
0.9	46.7	GO:0036465	synaptic vesicle recycling(GO:0036465)
0.5	46.2	GO:0006334	nucleosome assembly(GO:0006334)
1.2	42.6	GO:0007026	negative regulation of microtubule depolymerization(GO:0007026)
1.0	40.8	GO:0046426	negative regulation of JAK-STAT cascade(GO:0046426) negative regulation of STAT cascade(GO:1904893)
2.2	39.1	GO:0001573	ganglioside metabolic process(GO:0001573)
1.7	36.4	GO:0021819	layer formation in cerebral cortex(GO:0021819)
5.0	35.3	GO:2000096	positive regulation of Wnt signaling pathway, planar cell polarity pathway(GO:2000096)
3.2	34.8	GO:0035414	negative regulation of catenin import into nucleus(GO:0035414)

Showing 1 to 10 of 524 entries

Gene overrepresentation in cellular component category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.2	172.2	GO:0005887	integral component of plasma membrane(GO:0005887)
0.6	138.0	GO:0005874	microtubule(GO:0005874)
0.3	101.2	GO:0005813	centrosome(GO:0005813)
0.4	92.5	GO:0060076	excitatory synapse(GO:0060076)
0.8	75.2	GO:0000786	nucleosome(GO:0000786)
0.3	59.3	GO:0005578	proteinaceous extracellular matrix(GO:0005578)
0.7	47.8	GO:0032580	Golgi cisterna membrane(GO:0032580)
0.6	43.4	GO:0042734	presynaptic membrane(GO:0042734)
0.4	41.5	GO:0030027	lamellipodium(GO:0030027)
1.1	41.0	GO:0044295	axonal growth cone(GO:0044295)

Showing 1 to 10 of 238 entries

Gene overrepresentation in molecular function category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.9	223.4	GO:0008017	microtubule binding(GO:0008017)
0.7	76.7	GO:0005200	structural constituent of cytoskeleton(GO:0005200)
3.7	66.7	GO:0005522	profilin binding(GO:0005522)
5.2	62.3	GO:0019911	structural constituent of myelin sheath(GO:0019911)
1.1	59.2	GO:0005080	protein kinase C binding(GO:0005080)
0.2	52.7	GO:0005096	GTPase activator activity(GO:0005096)
0.1	52.4	GO:0005509	calcium ion binding(GO:0005509)
0.5	46.2	GO:0015631	tubulin binding(GO:0015631)
1.3	46.0	GO:0046875	ephrin receptor binding(GO:0046875)
5.7	45.7	GO:1990430	extracellular matrix protein binding(GO:1990430)

Showing 1 to 10 of 315 entries

Gene overrepresentation in curated gene sets: canonical pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
2.2	86.4	PID LIS1 PATHWAY	Lissencephaly gene (LIS1) in neuronal migration and development
2.0	75.1	ST WNT BETA CATENIN PATHWAY	Wnt/beta-catenin Pathway
2.2	48.6	PID SYNDECAN 3 PATHWAY	Syndecan-3-mediated signaling events
1.1	47.5	PID AURORA B PATHWAY	Aurora B signaling
1.0	47.0	NABA COLLAGENS	Genes encoding collagen proteins
0.2	39.3	NABA ECM GLYCOPROTEINS	Genes encoding structural ECM glycoproteins
2.7	35.6	PID P38 GAMMA DELTA PATHWAY	Signaling mediated by p38-gamma and p38-delta
0.6	34.0	PID TRKR PATHWAY	Neurotrophic factor-mediated Trk receptor signaling
1.6	33.3	PID INTEGRIN5 PATHWAY	Beta5 beta6 beta7 and beta8 integrin cell surface interactions
0.6	31.7	PID EPHB FWD PATHWAY	EPHB forward signaling

Showing 1 to 10 of 81 entries

Gene overrepresentation in curated gene sets: REACTOME pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
3.2	58.2	REACTOME CRMPS IN SEMA3A SIGNALING	Genes involved in CRMPs in Sema3A signaling
1.2	49.9	REACTOME NCAM1 INTERACTIONS	Genes involved in NCAM1 interactions
0.6	47.2	REACTOME L1CAM INTERACTIONS	Genes involved in L1CAM interactions
0.4	45.8	REACTOME SIGNALING BY RHO GTPASES	Genes involved in Signaling by Rho GTPases
1.6	43.6	REACTOME GENERATION OF SECOND MESSENGER MOLECULES	Genes involved in Generation of second messenger molecules
0.6	41.9	REACTOME INTEGRIN CELL SURFACE INTERACTIONS	Genes involved in Integrin cell surface interactions
2.3	41.2	REACTOME POST CHAPERONIN TUBULIN FOLDING PATHWAY	Genes involved in Post-chaperonin tubulin folding pathway
0.7	37.7	REACTOME AMINO ACID AND OLIGOPEPTIDE SLC TRANSPORTERS	Genes involved in Amino acid and oligopeptide SLC transporters
0.9	37.1	REACTOME SIGNALING BY ROBO RECEPTOR	Genes involved in Signaling by Robo receptor
0.6	33.7	REACTOME TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES	Genes involved in Transport of inorganic cations/anions and amino acids/oligopeptides

Showing 1 to 10 of 136 entries

Results for Sox2

Z-value: 1.57

Motif logo

Transcription factors associated with Sox2

Activity-expression correlation:

Activity profile of Sox2 motif

Sorted Z-values of Sox2 motif

Top targets:

Network of associatons between targets according to the STRING database.

First level regulatory network of Sox2

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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: