Coexpression cluster:C1931

Full id: C1931_cholangiocellular_NK_cord_gall_glioma_CD4_mycosis

Phase1 CAGE Peaks

Hg19::chr3:98275070..98275077,-	p@chr3:98275070..98275077 -
Hg19::chr3:98275078..98275089,-	p@chr3:98275078..98275089 -
Hg19::chr3:98275094..98275103,-	p@chr3:98275094..98275103 -
Hg19::chr3:98275107..98275141,-	p@chr3:98275107..98275141 -
Hg19::chr3:98275166..98275178,-	p@chr3:98275166..98275178 -

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><br>

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Cell Type

Ontology term	p-value	n
hematopoietic cell	4.20e-25	182
hematopoietic stem cell	3.67e-24	172
angioblastic mesenchymal cell	3.67e-24	172
hematopoietic oligopotent progenitor cell	4.00e-24	165
hematopoietic multipotent progenitor cell	4.00e-24	165
leukocyte	5.12e-21	140
nongranular leukocyte	1.14e-20	119
hematopoietic lineage restricted progenitor cell	2.42e-20	124
CD14-positive, CD16-negative classical monocyte	3.01e-14	42
myeloid cell	1.85e-13	112
common myeloid progenitor	1.85e-13	112
classical monocyte	7.77e-13	45
lymphoid lineage restricted progenitor cell	5.29e-11	52
lymphocyte	1.15e-10	53
common lymphoid progenitor	1.15e-10	53
macrophage dendritic cell progenitor	4.52e-10	65
monopoietic cell	1.42e-09	63
monocyte	1.42e-09	63
monoblast	1.42e-09	63
promonocyte	1.42e-09	63
myeloid lineage restricted progenitor cell	1.76e-09	70
granulocyte monocyte progenitor cell	2.20e-09	71
T cell	8.04e-09	25
pro-T cell	8.04e-09	25
CD4-positive, alpha-beta T cell	2.94e-08	6
myeloid leukocyte	3.95e-08	76
mature alpha-beta T cell	1.06e-07	18
alpha-beta T cell	1.06e-07	18
immature T cell	1.06e-07	18
mature T cell	1.06e-07	18
immature alpha-beta T cell	1.06e-07	18
circulating cell	7.53e-07	6

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	2.79e-12	102
blood island	2.79e-12	102
hemolymphoid system	5.11e-11	112
bone marrow	2.72e-08	80
bone element	6.99e-08	86
connective tissue	5.25e-07	375
immune system	5.79e-07	115

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
BATF#10538	5	24.3578017923036	1.16482472299935e-07	6.73978555375786e-06
BCL11A#53335	5	28.3694551036071	5.43377642717329e-08	3.44146862509127e-06
BCL3#602	5	34.5471028037383	2.02839878970325e-08	1.44702145626924e-06
BCLAF1#9774	5	21.6526476101218	2.09874458450681e-07	1.12060728865699e-05
CHD2#1106	5	10.3440228341169	8.43981772346334e-06	0.000230383200005433
EBF1#1879	5	8.906466846569	1.78355672307702e-05	0.000406620564508712
EP300#2033	5	6.7739417262232	7.00901578206049e-05	0.00110944922592091
IRF4#3662	5	21.9145126867441	1.97628413609567e-07	1.0722137085179e-05
JUND#3727	5	6.99466394187103	5.97069468343598e-05	0.000985108028504534
MEF2A#4205	5	18.7432309096441	4.31877656850983e-07	2.07188197537252e-05
MEF2C#4208	5	41.3113544926241	8.29287828997783e-09	6.38246069069266e-07
NFKB1#4790	5	5.48806342419384	0.000200816284746232	0.00239309127825327
PAX5#5079	5	6.66956553117783	7.57493746384605e-05	0.00117098711336089
PBX3#5090	5	21.9145126867441	1.97628413609567e-07	1.07277099215018e-05
POU2F2#5452	5	9.10612405774252	1.59639992500654e-05	0.000370091924012782
RXRA#6256	5	20.0746171391333	3.06418769543848e-07	1.54152552371821e-05
SP1#6667	5	5.6983813781409	0.00016639184371255	0.00204468734739322
SRF#6722	5	13.7971782621678	1.9987012616697e-06	7.32429337079024e-05
TAF1#6872	5	3.34304628574529	0.00239460009087031	0.0135505872827484
TBP#6908	5	3.70677068709639	0.00142875510672112	0.00920018216849666
TCF12#6938	5	10.6344649021864	7.34844389925727e-06	0.000211364398896869
TCF7L2#6934	5	10.7701765631373	6.89693748574565e-06	0.000200030339926073
YY1#7528	5	4.91117074985386	0.0003499314082136	0.00353003828285715

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.