ISMARA results: Rest

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GSE53960: rat RNA-Seq transcriptomic Bodymap

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Results for Rest

Z-value: 3.87

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Transcription factors associated with Rest

Gene Symbol	Gene ID	Gene Info
Rest NCBI RGD Ensembl	ENSRNOG00000002074	RE1-silencing transcription factor

Activity-expression correlation:

Gene	Promoter	Pearson corr. coef.	P-value	Plot
Rest	rn6_v1_chr14_-_33164141_33164141	-0.62	2.5e-35	Click!

Activity profile of Rest motif

Sorted Z-values of Rest motif

Top targets:

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Promoter	Log-likelihood	Transcript	Gene	Gene Info
chr3_+_125428260 Show fit	325.28	ENSRNOT00000028892	Chgb NCBI RGD Ensembl Show fit	chromogranin B
chr3_-_176816114 Show fit	318.85	ENSRNOT00000079262 ENSRNOT00000018697	Stmn3 NCBI RGD Ensembl Show fit	stathmin 3
chr10_-_20622600 Show fit	314.21	ENSRNOT00000020554	Fbll1 NCBI RGD Ensembl Show fit	fibrillarin-like 1
chr18_-_24182012 Show fit	307.02	ENSRNOT00000023594	Syt4 NCBI RGD Ensembl Show fit	synaptotagmin 4
chr12_+_41073824 Show fit	287.52	ENSRNOT00000001844	Rph3a NCBI RGD Ensembl Show fit	rabphilin 3A
chr4_+_145238947 Show fit	281.25	ENSRNOT00000067396 ENSRNOT00000091934	Cpne9 NCBI RGD Ensembl Show fit	copine family member 9
chr6_+_126434226 Show fit	263.75	ENSRNOT00000090857	Chga NCBI RGD Ensembl Show fit	chromogranin A
chr1_+_84470829 Show fit	251.64	ENSRNOT00000025472	Ttc9b NCBI RGD Ensembl Show fit	tetratricopeptide repeat domain 9B
chr2_-_189096785 Show fit	240.22	ENSRNOT00000028200	Chrnb2 NCBI RGD Ensembl Show fit	cholinergic receptor nicotinic beta 2 subunit
chr2_-_179704629 Show fit	237.99	ENSRNOT00000083361 ENSRNOT00000077941	Gria2 NCBI RGD Ensembl Show fit	glutamate ionotropic receptor AMPA type subunit 2

Showing 1 to 10 of 90 entries

Network of associatons between targets according to the STRING database.

First level regulatory network of Rest

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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
153.7	615.0	GO:0021586	pons maturation(GO:0021586)
49.7	546.4	GO:0060012	synaptic transmission, glycinergic(GO:0060012)
86.3	518.1	GO:0031339	negative regulation of vesicle fusion(GO:0031339)
12.4	460.3	GO:0048791	calcium ion-regulated exocytosis of neurotransmitter(GO:0048791)
31.9	318.9	GO:0035021	negative regulation of Rac protein signal transduction(GO:0035021)
104.7	314.2	GO:0018364	peptidyl-glutamine methylation(GO:0018364)
9.4	281.2	GO:1903861	positive regulation of dendrite extension(GO:1903861)
87.9	263.7	GO:1900738	positive regulation of phospholipase C-activating G-protein coupled receptor signaling pathway(GO:1900738)
4.8	255.9	GO:0000381	regulation of alternative mRNA splicing, via spliceosome(GO:0000381)
80.1	240.2	GO:0060084	synaptic transmission involved in micturition(GO:0060084)

Showing 1 to 10 of 55 entries

Gene overrepresentation in cellular component category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.2	1059.5	GO:0016021	integral component of membrane(GO:0016021)
16.5	643.4	GO:0060077	inhibitory synapse(GO:0060077)
1.6	473.8	GO:0030141	secretory granule(GO:0030141)
112.5	449.8	GO:0044307	dendritic branch(GO:0044307)
6.3	393.1	GO:0030672	synaptic vesicle membrane(GO:0030672) exocytic vesicle membrane(GO:0099501)
9.3	333.8	GO:0032590	dendrite membrane(GO:0032590)
0.4	324.5	GO:0005887	integral component of plasma membrane(GO:0005887)
1.7	318.9	GO:0030426	growth cone(GO:0030426)
39.3	314.2	GO:0031428	box C/D snoRNP complex(GO:0031428)
21.9	307.0	GO:0031045	dense core granule(GO:0031045)

Showing 1 to 10 of 42 entries

Gene overrepresentation in molecular function category:

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Log-likelihood per target	Total log-likelihood	Term	Description
90.0	449.8	GO:1904315	transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential(GO:1904315)
3.0	383.8	GO:0000149	SNARE binding(GO:0000149)
1.2	323.7	GO:0008022	protein C-terminus binding(GO:0008022)
24.2	314.2	GO:0008649	rRNA methyltransferase activity(GO:0008649)
61.4	307.0	GO:0030348	syntaxin-3 binding(GO:0030348)
35.9	287.5	GO:0008430	selenium binding(GO:0008430)
14.1	240.2	GO:0022848	acetylcholine-gated cation channel activity(GO:0022848)
79.3	238.0	GO:0004971	AMPA glutamate receptor activity(GO:0004971)
9.9	236.5	GO:0005112	Notch binding(GO:0005112)
15.4	231.2	GO:0005313	L-glutamate transmembrane transporter activity(GO:0005313)

Showing 1 to 10 of 49 entries

Gene overrepresentation in curated gene sets: canonical pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
4.8	238.0	PID NCADHERIN PATHWAY	N-cadherin signaling events
3.2	236.5	PID NOTCH PATHWAY	Notch signaling pathway
0.7	167.9	NABA ECM REGULATORS	Genes encoding enzymes and their regulators involved in the remodeling of the extracellular matrix
5.0	165.2	PID LIS1 PATHWAY	Lissencephaly gene (LIS1) in neuronal migration and development
1.9	133.9	PID IL4 2PATHWAY	IL4-mediated signaling events
2.5	131.5	PID INTEGRIN3 PATHWAY	Beta3 integrin cell surface interactions
0.3	95.0	NABA SECRETED FACTORS	Genes encoding secreted soluble factors
1.1	60.5	PID CERAMIDE PATHWAY	Ceramide signaling pathway
1.6	56.9	ST WNT BETA CATENIN PATHWAY	Wnt/beta-catenin Pathway
2.1	19.0	ST STAT3 PATHWAY	STAT3 Pathway

Showing 1 to 10 of 11 entries

Gene overrepresentation in curated gene sets: REACTOME pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
38.2	687.8	REACTOME UNBLOCKING OF NMDA RECEPTOR GLUTAMATE BINDING AND ACTIVATION	Genes involved in Unblocking of NMDA receptor, glutamate binding and activation
4.8	517.0	REACTOME TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES	Genes involved in Transport of inorganic cations/anions and amino acids/oligopeptides
13.8	385.1	REACTOME LIGAND GATED ION CHANNEL TRANSPORT	Genes involved in Ligand-gated ion channel transport
20.0	240.2	REACTOME PRESYNAPTIC NICOTINIC ACETYLCHOLINE RECEPTORS	Genes involved in Presynaptic nicotinic acetylcholine receptors
7.9	236.5	REACTOME ACTIVATED NOTCH1 TRANSMITS SIGNAL TO THE NUCLEUS	Genes involved in Activated NOTCH1 Transmits Signal to the Nucleus
8.3	216.9	REACTOME GABA SYNTHESIS RELEASE REUPTAKE AND DEGRADATION	Genes involved in GABA synthesis, release, reuptake and degradation
5.3	211.1	REACTOME AMINE LIGAND BINDING RECEPTORS	Genes involved in Amine ligand-binding receptors
0.9	211.1	REACTOME ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION	Genes involved in Antigen processing: Ubiquitination & Proteasome degradation
7.3	174.7	REACTOME GLUCAGON TYPE LIGAND RECEPTORS	Genes involved in Glucagon-type ligand receptors
6.0	167.9	REACTOME DEGRADATION OF THE EXTRACELLULAR MATRIX	Genes involved in Degradation of the extracellular matrix

Showing 1 to 10 of 19 entries

Results for Rest

Z-value: 3.87

Motif logo

Transcription factors associated with Rest

Activity-expression correlation:

Activity profile of Rest motif

Sorted Z-values of Rest motif

Top targets:

Network of associatons between targets according to the STRING database.

First level regulatory network of Rest

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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: