Coexpression cluster:C3059

Full id: C3059_thyroid_Renal_Smooth_Hepatic_acute_CD34_Endothelial

Phase1 CAGE Peaks

Hg19::chr10:94449649..94449664,+	p3@HHEX
Hg19::chr10:94449675..94449694,+	p2@HHEX
Hg19::chr10:94449703..94449718,+	p1@HHEX

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
myeloid cell	1.73e-28	112
common myeloid progenitor	1.73e-28	112
hematopoietic stem cell	1.65e-22	172
angioblastic mesenchymal cell	1.65e-22	172
hematopoietic cell	2.86e-21	182
hematopoietic oligopotent progenitor cell	7.68e-21	165
hematopoietic multipotent progenitor cell	7.68e-21	165
myeloid leukocyte	5.33e-17	76
endothelial cell	8.76e-16	35
granulocyte monocyte progenitor cell	3.27e-15	71
myeloid lineage restricted progenitor cell	1.27e-13	70
macrophage dendritic cell progenitor	1.92e-13	65
monopoietic cell	5.86e-13	63
monocyte	5.86e-13	63
monoblast	5.86e-13	63
promonocyte	5.86e-13	63
endothelial cell of vascular tree	8.21e-13	24
meso-epithelial cell	1.03e-11	44
leukocyte	1.03e-11	140
blood vessel endothelial cell	5.06e-10	18
embryonic blood vessel endothelial progenitor cell	5.06e-10	18
classical monocyte	8.68e-10	45
CD14-positive, CD16-negative classical monocyte	3.33e-09	42
hematopoietic lineage restricted progenitor cell	7.54e-09	124
nongranular leukocyte	1.18e-08	119
B cell	1.47e-08	14

Uber Anatomy

Ontology term	p-value	n
lateral plate mesoderm	1.97e-23	216
cardiovascular system	8.16e-18	110
circulatory system	1.04e-17	113
epithelial tube	4.06e-17	118
vessel	7.69e-17	69
immune system	1.66e-16	115
hemolymphoid system	5.11e-16	112
vasculature	1.98e-15	79
vascular system	1.98e-15	79
blood vessel	2.64e-15	60
epithelial tube open at both ends	2.64e-15	60
blood vasculature	2.64e-15	60
vascular cord	2.64e-15	60
splanchnic layer of lateral plate mesoderm	2.47e-13	84
hematopoietic system	3.13e-13	102
blood island	3.13e-13	102
bone marrow	1.20e-11	80
bone element	2.74e-11	86
artery	1.47e-10	42
arterial blood vessel	1.47e-10	42
arterial system	1.47e-10	42
endothelium	5.06e-10	18
blood vessel endothelium	5.06e-10	18
cardiovascular system endothelium	5.06e-10	18
tube	1.17e-09	194
unilaminar epithelium	2.15e-09	138
simple squamous epithelium	9.66e-09	22
anatomical conduit	2.03e-08	241
systemic artery	5.30e-08	33
systemic arterial system	5.30e-08	33
mesoderm	6.75e-08	448
mesoderm-derived structure	6.75e-08	448
presumptive mesoderm	6.75e-08	448
anatomical cluster	1.08e-07	286

Disease

Ontology term	p-value	n
myeloid leukemia	1.43e-14	31
leukemia	3.24e-10	39
hematologic cancer	5.13e-07	51
immune system cancer	5.13e-07	51

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	0.0189094243659719
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0323506076763805
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00435279360127847
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320324024254896
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319006507650966
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0459983306596485
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0153627025695321
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108281894419813
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.027534465538195
SUZ12#23512	3	50.1157809110629	7.93834897779404e-06	0.000221145166415533

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.