Coexpression cluster:C580

Full id: C580_chronic_thymus_Hodgkin_acute_iPS_vein_Burkitt

Phase1 CAGE Peaks

Hg19::chr10:15183694..15183716,-	p4@NMT2
Hg19::chr16:89165074..89165092,+	p5@ACSF3
Hg19::chr1:198488823..198488834,-	p@chr1:198488823..198488834 -
Hg19::chr1:198488915..198488926,-	p@chr1:198488915..198488926 -
Hg19::chr1:32398355..32398370,-	p@chr1:32398355..32398370 -
Hg19::chr1:32403130..32403147,-	p@chr1:32403130..32403147 -
Hg19::chr1:32739715..32739730,+	p3@LCK
Hg19::chr1:32739735..32739746,+	p4@LCK
Hg19::chr2:136578012..136578026,+	p3@LOC100507600
Hg19::chr4:109084747..109084756,-	p@chr4:109084747..109084756 -
Hg19::chr4:109084760..109084771,-	p@chr4:109084760..109084771 -
Hg19::chr4:145580820..145580831,+	p@chr4:145580820..145580831 +
Hg19::chr4:40192723..40192736,+	p10@RHOH
Hg19::chr7:2106220..2106240,-	p@chr7:2106220..2106240 -
Hg19::chrX:123538949..123538959,-	p@chrX:123538949..123538959 -

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:0030217	T cell differentiation	0.00187293756729479
GO:0030098	lymphocyte differentiation	0.00230026342169233
GO:0002521	leukocyte differentiation	0.0027079740611187
GO:0042110	T cell activation	0.0027079740611187
GO:0042610	CD8 receptor binding	0.00374128978289831
GO:0046649	lymphocyte activation	0.00374128978289831
GO:0030097	hemopoiesis	0.00374128978289831
GO:0048534	hemopoietic or lymphoid organ development	0.00374128978289831
GO:0045321	leukocyte activation	0.00374128978289831
GO:0002520	immune system development	0.00374128978289831
GO:0001775	cell activation	0.00398500640042086
GO:0050862	positive regulation of T cell receptor signaling pathway	0.00398500640042086
GO:0042609	CD4 receptor binding	0.00398500640042086
GO:0051117	ATPase binding	0.00517959338214823
GO:0006882	cellular zinc ion homeostasis	0.00517959338214823
GO:0009249	protein lipoylation	0.00517959338214823
GO:0055069	zinc ion homeostasis	0.00517959338214823
GO:0019899	enzyme binding	0.00517959338214823
GO:0043548	phosphoinositide 3-kinase binding	0.00517959338214823
GO:0018065	protein-cofactor linkage	0.00517959338214823
GO:0006499	N-terminal protein myristoylation	0.00517959338214823
GO:0004379	glycylpeptide N-tetradecanoyltransferase activity	0.00517959338214823
GO:0018319	protein amino acid myristoylation	0.00517959338214823
GO:0018377	protein myristoylation	0.00517959338214823
GO:0043124	negative regulation of I-kappaB kinase/NF-kappaB cascade	0.00517959338214823
GO:0001948	glycoprotein binding	0.00517959338214823
GO:0050857	positive regulation of antigen receptor-mediated signaling pathway	0.00517959338214823
GO:0000242	pericentriolar material	0.00517959338214823
GO:0019107	myristoyltransferase activity	0.00517959338214823
GO:0050856	regulation of T cell receptor signaling pathway	0.00517959338214823
GO:0006498	N-terminal protein lipidation	0.00584766978870286
GO:0051283	negative regulation of sequestering of calcium ion	0.00609310113743239
GO:0051282	regulation of sequestering of calcium ion	0.00609310113743239
GO:0051209	release of sequestered calcium ion into cytosol	0.00609310113743239
GO:0005095	GTPase inhibitor activity	0.00699821430729356
GO:0051208	sequestering of calcium ion	0.00699821430729356
GO:0050854	regulation of antigen receptor-mediated signaling pathway	0.00699821430729356
GO:0051238	sequestering of metal ion	0.00885709258062343
GO:0018409	peptide or protein amino-terminal blocking	0.0092934224497359
GO:0050852	T cell receptor signaling pathway	0.0110012908396699
GO:0042169	SH2 domain binding	0.0110932487759747
GO:0031365	N-terminal protein amino acid modification	0.0110932487759747
GO:0044450	microtubule organizing center part	0.0138420057461097
GO:0050851	antigen receptor-mediated signaling pathway	0.0158772036844918
GO:0002429	immune response-activating cell surface receptor signaling pathway	0.0167375395149149
GO:0043543	protein amino acid acylation	0.0167375395149149
GO:0002768	immune response-regulating cell surface receptor signaling pathway	0.0167375395149149
GO:0002757	immune response-activating signal transduction	0.0167375395149149
GO:0017048	Rho GTPase binding	0.0167375395149149
GO:0007264	small GTPase mediated signal transduction	0.0167375395149149
GO:0002764	immune response-regulating signal transduction	0.0167375395149149
GO:0004715	non-membrane spanning protein tyrosine kinase activity	0.0196329023784135
GO:0050870	positive regulation of T cell activation	0.0196329023784135
GO:0051235	maintenance of localization	0.0196329023784135
GO:0019210	kinase inhibitor activity	0.0197452133423667
GO:0006919	caspase activation	0.0208632269515984
GO:0045121	lipid raft	0.0208632269515984
GO:0043280	positive regulation of caspase activity	0.0222824936971152
GO:0051251	positive regulation of lymphocyte activation	0.0223419340034754
GO:0006497	protein amino acid lipidation	0.0228291034560098
GO:0042158	lipoprotein biosynthetic process	0.0229369435690701
GO:0048513	organ development	0.0229369435690701
GO:0050863	regulation of T cell activation	0.0241969489110459
GO:0043281	regulation of caspase activity	0.024221511413098
GO:0042493	response to drug	0.0250379984664169
GO:0004722	protein serine/threonine phosphatase activity	0.0254392012708153
GO:0051480	cytosolic calcium ion homeostasis	0.0265722426642582
GO:0007204	elevation of cytosolic calcium ion concentration	0.0265722426642582
GO:0002253	activation of immune response	0.0265722426642582
GO:0008022	protein C-terminus binding	0.0272315094563042
GO:0051345	positive regulation of hydrolase activity	0.0272315094563042
GO:0051249	regulation of lymphocyte activation	0.0272315094563042
GO:0017016	Ras GTPase binding	0.0272315094563042
GO:0050865	regulation of cell activation	0.0277089471060443
GO:0002376	immune system process	0.0277089471060443
GO:0019901	protein kinase binding	0.0277421206030372
GO:0042157	lipoprotein metabolic process	0.0277421206030372
GO:0031267	small GTPase binding	0.0277421206030372
GO:0050778	positive regulation of immune response	0.0277421206030372
GO:0002684	positive regulation of immune system process	0.0277421206030372
GO:0008632	apoptotic program	0.0280059165722411
GO:0016410	N-acyltransferase activity	0.0280059165722411
GO:0051020	GTPase binding	0.0299891491571014
GO:0050776	regulation of immune response	0.0299891491571014
GO:0019900	kinase binding	0.0299891491571014
GO:0002682	regulation of immune system process	0.0299891491571014
GO:0009968	negative regulation of signal transduction	0.0307661597671867
GO:0051240	positive regulation of multicellular organismal process	0.0307661597671867
GO:0048731	system development	0.0309378657180192
GO:0043122	regulation of I-kappaB kinase/NF-kappaB cascade	0.0309378657180192
GO:0006874	cellular calcium ion homeostasis	0.0324956904139546
GO:0055074	calcium ion homeostasis	0.0324956904139546
GO:0018193	peptidyl-amino acid modification	0.0330107331571969
GO:0019207	kinase regulator activity	0.0330107331571969
GO:0006875	cellular metal ion homeostasis	0.0330107331571969
GO:0055065	metal ion homeostasis	0.0330107331571969
GO:0019904	protein domain specific binding	0.0337269077482176
GO:0005813	centrosome	0.0339054720560488
GO:0048869	cellular developmental process	0.034846178409539
GO:0030154	cell differentiation	0.034846178409539
GO:0007249	I-kappaB kinase/NF-kappaB cascade	0.0354329812943836
GO:0005815	microtubule organizing center	0.0370918001383408
GO:0007242	intracellular signaling cascade	0.0396255033883722
GO:0048856	anatomical structure development	0.0407925640331565
GO:0030005	cellular di-, tri-valent inorganic cation homeostasis	0.0440565636089676
GO:0055066	di-, tri-valent inorganic cation homeostasis	0.044362402403937
GO:0030003	cellular cation homeostasis	0.047914710907547
GO:0055080	cation homeostasis	0.047914710907547
GO:0043687	post-translational protein modification	0.047914710907547
GO:0006917	induction of apoptosis	0.0492119839151446
GO:0012502	induction of programmed cell death	0.0492119839151446
GO:0007275	multicellular organismal development	0.0492119839151446

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
T cell	1.52e-27	25
pro-T cell	1.52e-27	25
lymphoid lineage restricted progenitor cell	3.64e-16	52
lymphocyte	7.70e-16	53
common lymphoid progenitor	7.70e-16	53
mature alpha-beta T cell	3.05e-15	18
alpha-beta T cell	3.05e-15	18
immature T cell	3.05e-15	18
mature T cell	3.05e-15	18
immature alpha-beta T cell	3.05e-15	18
nucleate cell	3.17e-15	55
CD8-positive, alpha-beta T cell	1.38e-09	11
CD4-positive, alpha-beta T cell	2.52e-08	6
leukocyte	2.90e-08	136
nongranular leukocyte	3.33e-08	115
regulatory T cell	7.20e-07	2
CD4-positive, CD25-positive, alpha-beta regulatory T cell	7.20e-07	2
naive regulatory T cell	7.20e-07	2

Uber Anatomy

Ontology term	p-value	n
hemopoietic organ	5.55e-15	7
immune organ	5.55e-15	7
thymus	2.08e-12	4
hemolymphoid system gland	2.08e-12	4
thymic region	2.08e-12	4
pharyngeal gland	2.08e-12	4
thymus primordium	2.08e-12	4
tonsil	4.31e-12	1
mucosa-associated lymphoid tissue	4.31e-12	1
lymphoid tissue	4.31e-12	1
tonsillar ring	4.31e-12	1
neck	8.93e-11	10
chordate pharynx	1.13e-10	10
pharyngeal region of foregut	1.13e-10	10
pharynx	9.40e-10	11
pharyngeal epithelium	1.44e-08	6
throat	7.61e-07	2

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.