ISMARA results: Srf

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GSE53960: rat RNA-Seq transcriptomic Bodymap

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Results for Srf

Z-value: 2.37

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Transcription factors associated with Srf

Gene Symbol	Gene ID	Gene Info
Srf NCBI RGD Ensembl	ENSRNOG00000018232	serum response factor

Activity-expression correlation:

Gene	Promoter	Pearson corr. coef.	P-value	Plot
Srf	rn6_v1_chr9_+_16737642_16737642	0.71	7.1e-50	Click!

Activity profile of Srf motif

Sorted Z-values of Srf motif

Top targets:

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Promoter	Log-likelihood	Transcript	Gene	Gene Info
chr3_-_105512939 Show fit	300.50	ENSRNOT00000011773	Actc1 NCBI RGD Ensembl Show fit	actin, alpha, cardiac muscle 1
chr8_+_119030875 Show fit	181.77	ENSRNOT00000028458	Myl3 NCBI RGD Ensembl Show fit	myosin light chain 3
chr6_-_127248372 Show fit	161.82	ENSRNOT00000085517	Asb2 NCBI RGD Ensembl Show fit	ankyrin repeat and SOCS box-containing 2
chr5_+_164808323 Show fit	159.99	ENSRNOT00000011005	Nppa NCBI RGD Ensembl Show fit	natriuretic peptide A
chr10_+_70262361 Show fit	151.56	ENSRNOT00000064625 ENSRNOT00000076973	Unc45b NCBI RGD Ensembl Show fit	unc-45 myosin chaperone B
chrX_+_71342775 Show fit	142.98	ENSRNOT00000004888	Itgb1bp2 NCBI RGD Ensembl Show fit	integrin subunit beta 1 binding protein 2
chr14_-_86146744 Show fit	133.80	ENSRNOT00000019335	Myl7 NCBI RGD Ensembl Show fit	myosin light chain 7
chr10_+_53621375 Show fit	120.01	ENSRNOT00000004147	Myh3 NCBI RGD Ensembl Show fit	myosin heavy chain 3
chr2_+_104416972 Show fit	98.28	ENSRNOT00000017125	Trim55 NCBI RGD Ensembl Show fit	tripartite motif-containing 55
chr12_+_49761120 Show fit	93.56	ENSRNOT00000070961	Myo18b NCBI RGD Ensembl Show fit	myosin XVIIIb

Showing 1 to 10 of 100 entries

Network of associatons between targets according to the STRING database.

First level regulatory network of Srf

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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
78.1	390.7	GO:0090131	mesenchyme migration(GO:0090131)
1.7	184.7	GO:0007229	integrin-mediated signaling pathway(GO:0007229)
5.2	181.8	GO:0002026	regulation of the force of heart contraction(GO:0002026)
2.1	161.8	GO:0045445	myoblast differentiation(GO:0045445)
53.3	160.0	GO:1902304	positive regulation of potassium ion export(GO:1902304)
2.2	151.6	GO:0061077	chaperone-mediated protein folding(GO:0061077)
2.6	120.0	GO:0003009	skeletal muscle contraction(GO:0003009)
2.6	112.5	GO:0045214	sarcomere organization(GO:0045214)
2.0	99.7	GO:0070527	platelet aggregation(GO:0070527)
7.8	93.6	GO:0048739	cardiac muscle fiber development(GO:0048739)

Showing 1 to 10 of 56 entries

Gene overrepresentation in cellular component category:

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Log-likelihood per target	Total log-likelihood	Term	Description
4.4	374.5	GO:0042641	actomyosin(GO:0042641)
7.4	357.3	GO:0031672	A band(GO:0031672)
1.9	227.5	GO:0030018	Z disc(GO:0030018)
14.0	210.2	GO:0032982	myosin filament(GO:0032982)
20.2	161.8	GO:0031466	Cul5-RING ubiquitin ligase complex(GO:0031466)
5.7	160.0	GO:0042629	mast cell granule(GO:0042629)
11.1	99.7	GO:0016460	myosin II complex(GO:0016460)
10.4	93.6	GO:0016461	unconventional myosin complex(GO:0016461)
0.5	90.4	GO:0005741	mitochondrial outer membrane(GO:0005741)
27.7	83.0	GO:0014701	junctional sarcoplasmic reticulum membrane(GO:0014701)

Showing 1 to 10 of 41 entries

Gene overrepresentation in molecular function category:

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Log-likelihood per target	Total log-likelihood	Term	Description
4.6	300.5	GO:0017022	myosin binding(GO:0017022)
6.1	181.8	GO:0003785	actin monomer binding(GO:0003785)
1.4	165.3	GO:0005178	integrin binding(GO:0005178)
0.7	161.8	GO:0061630	ubiquitin protein ligase activity(GO:0061630)
6.4	160.0	GO:0051428	peptide hormone receptor binding(GO:0051428)
3.8	151.6	GO:0051879	Hsp90 protein binding(GO:0051879)
5.0	110.0	GO:0000146	microfilament motor activity(GO:0000146)
0.8	90.4	GO:0003774	motor activity(GO:0003774)
5.3	84.5	GO:0051371	muscle alpha-actinin binding(GO:0051371)
2.4	82.5	GO:0008307	structural constituent of muscle(GO:0008307)

Showing 1 to 10 of 50 entries

Gene overrepresentation in curated gene sets: canonical pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
1.6	134.2	PID AP1 PATHWAY	AP-1 transcription factor network
1.6	79.7	SIG REGULATION OF THE ACTIN CYTOSKELETON BY RHO GTPASES	Genes related to regulation of the actin cytoskeleton
1.1	78.5	PID AJDISS 2PATHWAY	Posttranslational regulation of adherens junction stability and dissassembly
2.3	55.0	PID PDGFRA PATHWAY	PDGFR-alpha signaling pathway
0.2	54.2	NABA ECM REGULATORS	Genes encoding enzymes and their regulators involved in the remodeling of the extracellular matrix
1.3	49.9	PID ECADHERIN STABILIZATION PATHWAY	Stabilization and expansion of the E-cadherin adherens junction
1.1	46.5	PID ILK PATHWAY	Integrin-linked kinase signaling
0.5	36.2	PID AR PATHWAY	Coregulation of Androgen receptor activity
1.2	22.3	PID INTEGRIN5 PATHWAY	Beta5 beta6 beta7 and beta8 integrin cell surface interactions
0.5	18.5	PID P38 ALPHA BETA DOWNSTREAM PATHWAY	Signaling mediated by p38-alpha and p38-beta

Showing 1 to 10 of 15 entries

Gene overrepresentation in curated gene sets: REACTOME pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
10.2	395.9	REACTOME STRIATED MUSCLE CONTRACTION	Genes involved in Striated Muscle Contraction
9.3	186.6	REACTOME MUSCLE CONTRACTION	Genes involved in Muscle contraction
5.7	160.0	REACTOME YAP1 AND WWTR1 TAZ STIMULATED GENE EXPRESSION	Genes involved in YAP1- and WWTR1 (TAZ)-stimulated gene expression
0.6	148.6	REACTOME ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION	Genes involved in Antigen processing: Ubiquitination & Proteasome degradation
3.7	78.5	REACTOME REGULATION OF INSULIN LIKE GROWTH FACTOR IGF ACTIVITY BY INSULIN LIKE GROWTH FACTOR BINDING PROTEINS IGFBPS	Genes involved in Regulation of Insulin-like Growth Factor (IGF) Activity by Insulin-like Growth Factor Binding Proteins (IGFBPs)
2.2	74.6	REACTOME INTERACTIONS OF VPR WITH HOST CELLULAR PROTEINS	Genes involved in Interactions of Vpr with host cellular proteins
1.9	47.2	REACTOME CGMP EFFECTS	Genes involved in cGMP effects
2.5	42.3	REACTOME CELL EXTRACELLULAR MATRIX INTERACTIONS	Genes involved in Cell-extracellular matrix interactions
1.1	41.7	REACTOME GLYCOLYSIS	Genes involved in Glycolysis
1.4	39.4	REACTOME CASPASE MEDIATED CLEAVAGE OF CYTOSKELETAL PROTEINS	Genes involved in Caspase-mediated cleavage of cytoskeletal proteins

Showing 1 to 10 of 22 entries

Results for Srf

Z-value: 2.37

Motif logo

Transcription factors associated with Srf

Activity-expression correlation:

Activity profile of Srf motif

Sorted Z-values of Srf motif

Top targets:

Network of associatons between targets according to the STRING database.

First level regulatory network of Srf

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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: