Coexpression cluster:C496

Full id: C496_thymus_CD4_CD8_hairy_vein_chronic_Peripheral

Phase1 CAGE Peaks

Hg19::chr11:3968515..3968532,+	p3@STIM1
Hg19::chr14:22265490..22265505,+	p4@TRAV8-1
Hg19::chr14:22320634..22320645,+	p1@TRAV8-3
Hg19::chr15:22466523..22466550,-	p1@uc001yui.1
Hg19::chr16:56742627..56742637,+	p@chr16:56742627..56742637 +
Hg19::chr17:78717112..78717159,+	p2@RPTOR
Hg19::chr2:95740646..95740655,+	p@chr2:95740646..95740655 +
Hg19::chr4:40192677..40192712,+	p4@RHOH
Hg19::chr6:128222238..128222249,-	p5@THEMIS
Hg19::chr7:142028105..142028159,+	p1@TRBV6-1
Hg19::chr7:142162390..142162425,-	p1@TRBV6-6
Hg19::chr7:142180964..142180969,-	p4@TRBV6-5
Hg19::chr7:142180978..142181006,-	p1@TRBV6-5
Hg19::chr7:142198109..142198132,-	p2@TRBV11-2
Hg19::chr7:142334728..142334737,+	p1@AB306258
Hg19::chr7:142344506..142344509,+	p1@AJ296363 p1@AJ296373 p1@HM236738
Hg19::chr7:142498815..142498839,+	p1@AJ568018
Hg19::chr7:142507125..142507136,+	p@chr7:142507125..142507136 +
Hg19::chr9:33446618..33446630,+	p@chr9:33446618..33446630 +

Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

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No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

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GO ID	GO name	FDR corrected p-value
GO:0032236	positive regulation of calcium ion transport via store-operated calcium channel	0.00473317045069122
GO:0032237	activation of store-operated calcium channel activity	0.00473317045069122
GO:0043270	positive regulation of ion transport	0.00473317045069122
GO:0032234	regulation of calcium ion transport via store-operated calcium channel	0.00473317045069122
GO:0051928	positive regulation of calcium ion transport	0.00473317045069122
GO:0043124	negative regulation of I-kappaB kinase/NF-kappaB cascade	0.011831532856717
GO:0005513	detection of calcium ion	0.0135209557288322
GO:0005095	GTPase inhibitor activity	0.0147876746201048
GO:0051924	regulation of calcium ion transport	0.015772590875712
GO:0043269	regulation of ion transport	0.0193538515139206
GO:0009593	detection of chemical stimulus	0.0193538515139206
GO:0017048	Rho GTPase binding	0.0315266113806201
GO:0051050	positive regulation of transport	0.0330931953761501
GO:0030217	T cell differentiation	0.0330931953761501
GO:0019210	kinase inhibitor activity	0.0330931953761501
GO:0030176	integral to endoplasmic reticulum membrane	0.038264986352189
GO:0002376	immune system process	0.038264986352189
GO:0031227	intrinsic to endoplasmic reticulum membrane	0.0397855755213595
GO:0030098	lymphocyte differentiation	0.0397855755213595
GO:0017016	Ras GTPase binding	0.043249602836329
GO:0051606	detection of stimulus	0.043249602836329
GO:0031267	small GTPase binding	0.043249602836329
GO:0002521	leukocyte differentiation	0.043249602836329
GO:0051020	GTPase binding	0.043249602836329
GO:0009615	response to virus	0.043249602836329
GO:0042110	T cell activation	0.043249602836329
GO:0009968	negative regulation of signal transduction	0.043249602836329
GO:0048771	tissue remodeling	0.043249602836329
GO:0043122	regulation of I-kappaB kinase/NF-kappaB cascade	0.043249602836329
GO:0051049	regulation of transport	0.043249602836329
GO:0045087	innate immune response	0.0433713217382676
GO:0019207	kinase regulator activity	0.0449538569971292
GO:0031301	integral to organelle membrane	0.048180952305821
GO:0007249	I-kappaB kinase/NF-kappaB cascade	0.048180952305821

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

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Cell Type

Ontology term	p-value	n
leukocyte	3.61e-25	140
lymphocyte	3.59e-23	53
common lymphoid progenitor	3.59e-23	53
lymphoid lineage restricted progenitor cell	8.92e-23	52
nongranular leukocyte	1.27e-21	119
hematopoietic stem cell	1.81e-18	172
angioblastic mesenchymal cell	1.81e-18	172
hematopoietic lineage restricted progenitor cell	2.81e-18	124
T cell	6.05e-18	25
pro-T cell	6.05e-18	25
hematopoietic cell	1.02e-16	182
hematopoietic oligopotent progenitor cell	1.34e-15	165
hematopoietic multipotent progenitor cell	1.34e-15	165
mature alpha-beta T cell	1.17e-14	18
alpha-beta T cell	1.17e-14	18
immature T cell	1.17e-14	18
mature T cell	1.17e-14	18
immature alpha-beta T cell	1.17e-14	18
CD8-positive, alpha-beta T cell	1.13e-09	11

Uber Anatomy

Ontology term	p-value	n
adult organism	2.93e-20	115
hematopoietic system	6.72e-09	102
blood island	6.72e-09	102
blood	1.54e-08	15
haemolymphatic fluid	1.54e-08	15
organism substance	1.54e-08	15
hemolymphoid system	1.61e-07	112

Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

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Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}

ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

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No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

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This analysis result is provided for C0 - C305 clusters.