ISMARA results: Gcm1

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GSE53960: rat RNA-Seq transcriptomic Bodymap

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Results for Gcm1

Z-value: 0.82

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Transcription factors associated with Gcm1

Gene Symbol	Gene ID	Gene Info
Gcm1 NCBI RGD Ensembl	ENSRNOG00000007932	glial cells missing homolog 1

Activity-expression correlation:

Gene	Promoter	Pearson corr. coef.	P-value	Plot
Gcm1	rn6_v1_chr8_+_85355766_85355766	-0.17	2.7e-03	Click!

Activity profile of Gcm1 motif

Sorted Z-values of Gcm1 motif

Top targets:

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Promoter	Log-likelihood	Transcript	Gene
chr3_-_16537433 Show fit	28.14	ENSRNOT00000048523	AABR07051533.2 NCBI RGD Ensembl Show fit
chr11_+_85508300 Show fit	26.59	ENSRNOT00000038646	AABR07034730.3 NCBI RGD Ensembl Show fit
chr4_-_103369224 Show fit	26.24	ENSRNOT00000075709	AABR07061057.1 NCBI RGD Ensembl Show fit
chr11_+_85532526 Show fit	26.01	ENSRNOT00000036565	AABR07034730.2 NCBI RGD Ensembl Show fit
chr17_-_31813716 Show fit	24.70	ENSRNOT00000074147	AABR07027451.1 NCBI RGD Ensembl Show fit
chr11_+_85561460 Show fit	23.13	ENSRNOT00000075455	AABR07072262.1 NCBI RGD Ensembl Show fit
chr11_+_85618714 Show fit	22.95	ENSRNOT00000074614	AC109901.1 NCBI RGD Ensembl Show fit
chr3_+_19141133 Show fit	20.40	ENSRNOT00000058323	AABR07051675.1 NCBI RGD Ensembl Show fit
chr14_-_78377825 Show fit	19.26	ENSRNOT00000068104	AABR07015812.1 NCBI RGD Ensembl Show fit
chr3_+_19128400 Show fit	16.35	ENSRNOT00000074272	AABR07051673.1 NCBI RGD Ensembl Show fit

Showing 1 to 10 of 87 entries

Network of associatons between targets according to the STRING database.

First level regulatory network of Gcm1

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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
0.3	18.4	GO:0071277	cellular response to calcium ion(GO:0071277)
1.7	17.0	GO:0006561	proline biosynthetic process(GO:0006561)
2.6	15.6	GO:0046125	pyrimidine deoxyribonucleoside metabolic process(GO:0046125)
2.1	12.7	GO:1990086	lens fiber cell apoptotic process(GO:1990086)
2.9	11.8	GO:0051725	protein de-ADP-ribosylation(GO:0051725)
3.3	9.8	GO:0060399	positive regulation of growth hormone receptor signaling pathway(GO:0060399)
1.9	9.5	GO:0071673	positive regulation of smooth muscle cell chemotaxis(GO:0071673)
1.2	9.4	GO:2000969	positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity(GO:2000969)
0.1	8.8	GO:0006487	protein N-linked glycosylation(GO:0006487)
0.0	8.7	GO:0006281	DNA repair(GO:0006281)

Showing 1 to 10 of 44 entries

Gene overrepresentation in cellular component category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.1	26.1	GO:0043197	dendritic spine(GO:0043197)
0.1	21.5	GO:0005667	transcription factor complex(GO:0005667)
0.1	11.2	GO:0032587	ruffle membrane(GO:0032587)
0.4	9.8	GO:0010369	chromocenter(GO:0010369)
0.0	8.4	GO:0005819	spindle(GO:0005819)
0.2	7.3	GO:0045334	clathrin-coated endocytic vesicle(GO:0045334)
0.0	7.0	GO:0000790	nuclear chromatin(GO:0000790)
0.0	5.1	GO:0000139	Golgi membrane(GO:0000139)
0.0	4.8	GO:0045211	postsynaptic membrane(GO:0045211)
0.2	4.4	GO:0031233	intrinsic component of external side of plasma membrane(GO:0031233)

Showing 1 to 10 of 20 entries

Gene overrepresentation in molecular function category:

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Log-likelihood per target	Total log-likelihood	Term	Description
2.8	17.0	GO:0016774	phosphotransferase activity, carboxyl group as acceptor(GO:0016774)
0.3	16.1	GO:0031491	nucleosome binding(GO:0031491)
3.9	15.6	GO:0019136	pyrimidine nucleoside binding(GO:0001884) deoxynucleoside kinase activity(GO:0019136)
0.5	11.8	GO:0016799	hydrolase activity, hydrolyzing N-glycosyl compounds(GO:0016799)
0.0	11.2	GO:0005085	guanyl-nucleotide exchange factor activity(GO:0005085)
0.0	11.2	GO:0003682	chromatin binding(GO:0003682)
2.4	9.5	GO:0035727	lysophosphatidic acid binding(GO:0035727) lysophosphatidic acid receptor activity(GO:0070915)
2.2	8.8	GO:0030144	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity(GO:0030144)
0.0	8.6	GO:0003713	transcription coactivator activity(GO:0003713)
0.1	7.8	GO:0030971	receptor tyrosine kinase binding(GO:0030971)

Showing 1 to 10 of 36 entries

Gene overrepresentation in curated gene sets: canonical pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.7	12.7	SA REG CASCADE OF CYCLIN EXPR	Expression of cyclins regulates progression through the cell cycle by activating cyclin-dependent kinases.
0.3	11.2	PID RAS PATHWAY	Regulation of Ras family activation
0.3	9.5	ST ERK1 ERK2 MAPK PATHWAY	ERK1/ERK2 MAPK Pathway
0.1	9.5	PID LYSOPHOSPHOLIPID PATHWAY	LPA receptor mediated events
0.4	7.2	PID ANTHRAX PATHWAY	Cellular roles of Anthrax toxin
0.1	7.1	PID RB 1PATHWAY	Regulation of retinoblastoma protein
0.1	7.0	PID RHOA PATHWAY	RhoA signaling pathway
0.1	6.9	PID BCR 5PATHWAY	BCR signaling pathway
0.0	3.4	WNT SIGNALING	Genes related to Wnt-mediated signal transduction
0.2	2.0	SA TRKA RECEPTOR	The TrkA receptor binds nerve growth factor to activate MAP kinase pathways and promote cell growth.

Showing 1 to 10 of 14 entries

Gene overrepresentation in curated gene sets: REACTOME pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
1.0	15.6	REACTOME PURINE SALVAGE	Genes involved in Purine salvage
0.7	12.7	REACTOME CDC6 ASSOCIATION WITH THE ORC ORIGIN COMPLEX	Genes involved in CDC6 association with the ORC:origin complex
0.7	11.2	REACTOME RAP1 SIGNALLING	Genes involved in Rap1 signalling
0.0	9.5	REACTOME G ALPHA Q SIGNALLING EVENTS	Genes involved in G alpha (q) signalling events
0.5	8.4	REACTOME AMINO ACID SYNTHESIS AND INTERCONVERSION TRANSAMINATION	Genes involved in Amino acid synthesis and interconversion (transamination)
0.3	7.3	REACTOME ERK MAPK TARGETS	Genes involved in ERK/MAPK targets
0.1	7.2	REACTOME NUCLEAR SIGNALING BY ERBB4	Genes involved in Nuclear signaling by ERBB4
0.5	7.1	REACTOME INHIBITION OF REPLICATION INITIATION OF DAMAGED DNA BY RB1 E2F1	Genes involved in Inhibition of replication initiation of damaged DNA by RB1/E2F1
0.0	3.4	REACTOME PEPTIDE CHAIN ELONGATION	Genes involved in Peptide chain elongation
0.2	2.2	REACTOME ACTIVATION OF IRF3 IRF7 MEDIATED BY TBK1 IKK EPSILON	Genes involved in Activation of IRF3/IRF7 mediated by TBK1/IKK epsilon

Showing 1 to 10 of 14 entries

Results for Gcm1

Z-value: 0.82

Motif logo

Transcription factors associated with Gcm1

Activity-expression correlation:

Activity profile of Gcm1 motif

Sorted Z-values of Gcm1 motif

Top targets:

Network of associatons between targets according to the STRING database.

First level regulatory network of Gcm1

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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: