Coexpression cluster:C3983

Full id: C3983_Mast_Reticulocytes_blood_Whole_acute_liver_chronic

Phase1 CAGE Peaks

Hg19::chr1:47697881..47697910,-	p4@TAL1
Hg19::chr1:47698007..47698019,-	p13@TAL1
Hg19::chr4:159963463..159963478,-	p@chr4:159963463..159963478 -

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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No GOStat results

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
endothelial cell of vascular tree	1.90e-21	24
endothelial cell	3.16e-21	35
blood vessel endothelial cell	6.28e-16	18
embryonic blood vessel endothelial progenitor cell	6.28e-16	18
meso-epithelial cell	8.34e-16	44
lining cell	9.83e-11	57
barrier cell	9.83e-11	57
endothelial cell of artery	2.76e-09	9
vein endothelial cell	1.33e-07	6
histamine secreting cell	1.68e-07	5
biogenic amine secreting cell	1.68e-07	5
granulocytopoietic cell	1.68e-07	5
mast cell	1.68e-07	5
mast cell progenitor	1.68e-07	5
basophil mast progenitor cell	1.68e-07	5
lymphangioblast	4.30e-07	6
endothelial cell of lymphatic vessel	4.30e-07	6
vascular lymphangioblast	4.30e-07	6

Uber Anatomy

Ontology term	p-value	n
adult organism	3.73e-37	115
endothelium	6.28e-16	18
blood vessel endothelium	6.28e-16	18
cardiovascular system endothelium	6.28e-16	18
blood	5.52e-15	15
haemolymphatic fluid	5.52e-15	15
organism substance	5.52e-15	15
circulatory system	1.77e-12	113
simple squamous epithelium	5.87e-12	22
cardiovascular system	4.11e-11	110
squamous epithelium	5.82e-11	25
endothelial tube	2.76e-09	9
arterial system endothelium	2.76e-09	9
endothelium of artery	2.76e-09	9
anatomical conduit	1.05e-07	241

Disease

Ontology term	p-value	n
myeloid leukemia	2.05e-09	31
leukemia	5.10e-08	39
chronic leukemia	5.24e-08	8

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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190242181280527
CTBP2#1488	2	41.8113335595521	0.000754340825991485	0.00593510633763181
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322623568574778
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0320977937201568
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167623500748561
FOSL1#8061	2	26.4757198109153	0.00186983370259098	0.0110254946965277
GATA1#2623	3	13.5603081438004	0.000400961596378263	0.00388208289275511
GATA2#2624	3	12.744931733554	0.000482952770428379	0.00437156390975641
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00391505504109802
JUNB#3726	2	20.4070884398808	0.00313146219943874	0.0164502178284384
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156940225477371
REST#5978	3	9.65002871612802	0.00111263624711459	0.00768434182068514
SIRT6#51548	2	102.425602660017	0.000126437939273122	0.00168302981643457
SMARCA4#6597	2	104.510602205259	0.000121451859247127	0.00164474983505067
SMARCB1#6598	2	12.1684771874383	0.00867500222192174	0.0329949581942272
STAT2#6773	3	65.2637711864407	3.59360517547754e-06	0.000118432480568539
SUZ12#23512	2	33.4105206073753	0.0011782676453603	0.00799851118711628
TAL1#6886	3	29.8686166774402	3.75103522793067e-05	0.000720401559709178

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.