Coexpression cluster:C3262

Full id: C3262_splenic_myeloma_Gingival_Mallassezderived_Corneal_B_Macrophage

Phase1 CAGE Peaks

Hg19::chr12:15114658..15114684,-	p4@ARHGDIB
Hg19::chr12:15114685..15114697,-	p8@ARHGDIB
Hg19::chr12:15114705..15114712,-	p9@ARHGDIB

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
hematopoietic stem cell	2.16e-29	168
angioblastic mesenchymal cell	2.16e-29	168
hematopoietic cell	1.57e-28	177
hematopoietic oligopotent progenitor cell	1.65e-26	161
hematopoietic multipotent progenitor cell	1.65e-26	161
leukocyte	6.07e-24	136
hematopoietic lineage restricted progenitor cell	2.62e-21	120
nongranular leukocyte	2.72e-20	115
nucleate cell	3.76e-16	55
lymphocyte	4.76e-15	53
common lymphoid progenitor	4.76e-15	53
lymphoid lineage restricted progenitor cell	1.62e-14	52
myeloid cell	3.15e-12	108
common myeloid progenitor	3.15e-12	108
lymphocyte of B lineage	1.03e-10	24
pro-B cell	1.03e-10	24
dendritic cell	2.14e-08	10
endothelial cell of artery	9.98e-08	9
myeloid lineage restricted progenitor cell	2.31e-07	66
conventional dendritic cell	3.47e-07	8
granulocyte monocyte progenitor cell	4.19e-07	67
macrophage dendritic cell progenitor	5.86e-07	61
blood vessel endothelial cell	5.95e-07	18
embryonic blood vessel endothelial progenitor cell	5.95e-07	18

Uber Anatomy

Ontology term	p-value	n
lateral plate mesoderm	1.49e-13	203
hematopoietic system	3.88e-12	98
blood island	3.88e-12	98
hemolymphoid system	3.29e-11	108
blood	8.57e-08	15
haemolymphatic fluid	8.57e-08	15
organism substance	8.57e-08	15
endothelial tube	9.98e-08	9
arterial system endothelium	9.98e-08	9
endothelium of artery	9.98e-08	9
blood vessel endothelium	5.95e-07	18
endothelium	5.95e-07	18
cardiovascular system endothelium	5.95e-07	18
immune system	8.98e-07	93

Disease

Ontology term	p-value	n
hematologic cancer	1.59e-12	51
immune system cancer	1.59e-12	51
leukemia	8.23e-09	39

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
BCLAF1#9774	3	21.6526476101218	9.8473954032885e-05	0.00138942465350452
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320846028252052
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319418253959528
GATA1#2623	3	13.5603081438004	0.000400961596378263	0.00387095841783596
GATA2#2624	3	12.744931733554	0.000482952770428379	0.00436135792397488
GATA3#2625	3	27.236516357206	4.94721007899563e-05	0.000849665636310187
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0185960368816369
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293464300410528
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0268813082349163
PBX3#5090	3	21.9145126867441	9.49854535978121e-05	0.00136247572974892
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.010887013766414

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.