ISMARA results: Smad1

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GSE53960: rat RNA-Seq transcriptomic Bodymap

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Results for Smad1

Z-value: 2.58

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Transcription factors associated with Smad1

Gene Symbol	Gene ID	Gene Info
Smad1 NCBI RGD Ensembl	ENSRNOG00000018483	SMAD family member 1

Activity-expression correlation:

Gene	Promoter	Pearson corr. coef.	P-value	Plot
Smad1	rn6_v1_chr19_+_32188267_32188267	-0.30	3.1e-08	Click!

Activity profile of Smad1 motif

Sorted Z-values of Smad1 motif

Top targets:

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Promoter	Log-likelihood	Transcript	Gene	Gene Info
chr1_+_219329574 Show fit	125.69	ENSRNOT00000071109	Cabp2 NCBI RGD Ensembl Show fit	calcium binding protein 2
chr7_-_71226150 Show fit	99.16	ENSRNOT00000005875	RGD1561812 NCBI RGD Ensembl Show fit	similar to Retinol dehydrogenase type II (RODH II) (29 k-protein)
chr1_+_83711251 Show fit	90.25	ENSRNOT00000028237 ENSRNOT00000092008	Cyp2a1 NCBI RGD Ensembl Show fit	cytochrome P450, family 2, subfamily a, polypeptide 1
chr6_+_127946686 Show fit	82.42	ENSRNOT00000082680	LOC500712 NCBI RGD Ensembl Show fit	Ab1-233
chr16_-_56900052 Show fit	77.79	ENSRNOT00000017339	Msr1 NCBI RGD Ensembl Show fit	macrophage scavenger receptor 1
chr3_-_7141522 Show fit	74.32	ENSRNOT00000014572	Cel NCBI RGD Ensembl Show fit	carboxyl ester lipase
chr19_-_64303 Show fit	67.27	ENSRNOT00000015451	Ces2a NCBI RGD Ensembl Show fit	carboxylesterase 2A
chr2_+_186685104 Show fit	65.06	ENSRNOT00000057022	Cd5l NCBI RGD Ensembl Show fit	Cd5 molecule-like
chr3_-_2853272 Show fit	64.40	ENSRNOT00000023022	Fcna NCBI RGD Ensembl Show fit	ficolin A
chr5_-_78985990 Show fit	64.18	ENSRNOT00000009248	Ambp NCBI RGD Ensembl Show fit	alpha-1-microglobulin/bikunin precursor

Showing 1 to 10 of 200 entries

Network of associatons between targets according to the STRING database.

First level regulatory network of Smad1

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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
6.7	336.0	GO:0006953	acute-phase response(GO:0006953)
12.9	154.8	GO:0001867	complement activation, lectin pathway(GO:0001867)
21.7	152.2	GO:0009804	coumarin metabolic process(GO:0009804)
21.4	149.5	GO:0042904	9-cis-retinoic acid biosynthetic process(GO:0042904) 9-cis-retinoic acid metabolic process(GO:0042905)
0.8	142.6	GO:0010951	negative regulation of endopeptidase activity(GO:0010951)
11.4	136.2	GO:0006707	cholesterol catabolic process(GO:0006707) sterol catabolic process(GO:0016127)
8.8	123.4	GO:0006958	complement activation, classical pathway(GO:0006958)
4.0	121.4	GO:0030212	hyaluronan metabolic process(GO:0030212)
11.1	111.3	GO:0010886	positive regulation of cholesterol storage(GO:0010886)
10.1	100.8	GO:0006957	complement activation, alternative pathway(GO:0006957)

Showing 1 to 10 of 900 entries

Gene overrepresentation in cellular component category:

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Log-likelihood per target	Total log-likelihood	Term	Description
10.1	1147.9	GO:0072562	blood microparticle(GO:0072562)
0.8	986.8	GO:0005615	extracellular space(GO:0005615)
0.9	713.1	GO:0042175	nuclear outer membrane-endoplasmic reticulum membrane network(GO:0042175)
3.2	252.7	GO:0005788	endoplasmic reticulum lumen(GO:0005788)
6.4	197.9	GO:0042588	zymogen granule(GO:0042588)
11.9	167.0	GO:0034385	very-low-density lipoprotein particle(GO:0034361) triglyceride-rich lipoprotein particle(GO:0034385)
0.7	147.5	GO:0009897	external side of plasma membrane(GO:0009897)
2.0	146.5	GO:0045095	keratin filament(GO:0045095)
1.0	128.5	GO:0005777	peroxisome(GO:0005777) microbody(GO:0042579)
27.6	110.2	GO:0044218	other organism cell membrane(GO:0044218) other organism membrane(GO:0044279)

Showing 1 to 10 of 246 entries

Gene overrepresentation in molecular function category:

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Log-likelihood per target	Total log-likelihood	Term	Description
5.5	631.8	GO:0004867	serine-type endopeptidase inhibitor activity(GO:0004867)
2.6	562.6	GO:0004252	serine-type endopeptidase activity(GO:0004252)
10.1	412.6	GO:0070330	aromatase activity(GO:0070330)
1.9	254.8	GO:0052689	carboxylic ester hydrolase activity(GO:0052689)
6.2	242.2	GO:0004364	glutathione transferase activity(GO:0004364)
1.0	232.9	GO:0030246	carbohydrate binding(GO:0030246)
8.4	210.7	GO:0042288	MHC class I protein binding(GO:0042288)
6.7	208.4	GO:0015020	glucuronosyltransferase activity(GO:0015020)
2.1	196.4	GO:0004866	endopeptidase inhibitor activity(GO:0004866)
7.7	161.2	GO:0004745	retinol dehydrogenase activity(GO:0004745)

Showing 1 to 10 of 496 entries

Gene overrepresentation in curated gene sets: canonical pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
2.9	667.7	NABA ECM REGULATORS	Genes encoding enzymes and their regulators involved in the remodeling of the extracellular matrix
8.2	253.3	PID INTEGRIN2 PATHWAY	Beta2 integrin cell surface interactions
4.4	241.9	PID HNF3B PATHWAY	FOXA2 and FOXA3 transcription factor networks
3.5	147.0	PID AMB2 NEUTROPHILS PATHWAY	amb2 Integrin signaling
2.3	87.1	PID IL2 STAT5 PATHWAY	IL2 signaling events mediated by STAT5
0.5	81.6	NABA ECM AFFILIATED	Genes encoding proteins affiliated structurally or functionally to extracellular matrix proteins
1.1	76.3	PID CMYB PATHWAY	C-MYB transcription factor network
6.3	69.1	ST JAK STAT PATHWAY	Jak-STAT Pathway
2.1	59.5	PID IL1 PATHWAY	IL1-mediated signaling events
3.4	57.7	SA MMP CYTOKINE CONNECTION	Cytokines can induce activation of matrix metalloproteinases, which degrade extracellular matrix.

Showing 1 to 10 of 83 entries

Gene overrepresentation in curated gene sets: REACTOME pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
13.3	265.2	REACTOME INITIAL TRIGGERING OF COMPLEMENT	Genes involved in Initial triggering of complement
7.0	222.4	REACTOME LIPID DIGESTION MOBILIZATION AND TRANSPORT	Genes involved in Lipid digestion, mobilization, and transport
1.4	209.5	REACTOME METABOLISM OF AMINO ACIDS AND DERIVATIVES	Genes involved in Metabolism of amino acids and derivatives
9.2	175.0	REACTOME GLUCURONIDATION	Genes involved in Glucuronidation
9.6	172.8	REACTOME HDL MEDIATED LIPID TRANSPORT	Genes involved in HDL-mediated lipid transport
11.5	160.8	REACTOME COMPLEMENT CASCADE	Genes involved in Complement cascade
1.3	144.8	REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE	Genes involved in SRP-dependent cotranslational protein targeting to membrane
2.8	142.5	REACTOME PHASE II CONJUGATION	Genes involved in Phase II conjugation
13.7	136.6	REACTOME GAMMA CARBOXYLATION TRANSPORT AND AMINO TERMINAL CLEAVAGE OF PROTEINS	Genes involved in Gamma-carboxylation, transport, and amino-terminal cleavage of proteins
5.1	131.8	REACTOME DEGRADATION OF THE EXTRACELLULAR MATRIX	Genes involved in Degradation of the extracellular matrix

Showing 1 to 10 of 167 entries

Results for Smad1

Z-value: 2.58

Motif logo

Transcription factors associated with Smad1

Activity-expression correlation:

Activity profile of Smad1 motif

Sorted Z-values of Smad1 motif

Top targets:

Network of associatons between targets according to the STRING database.

First level regulatory network of Smad1

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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: