Coexpression cluster:C3755

Full id: C3755_CD14CD16_acute_CD19_granulocyte_CD133_CD14_Whole

Phase1 CAGE Peaks

Hg19::chr19:13213662..13213686,-	p1@LYL1
Hg19::chr19:13213691..13213696,-	p9@LYL1
Hg19::chr19:13213954..13214021,-	p4@LYL1

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	7.46e-47	172
angioblastic mesenchymal cell	7.46e-47	172
hematopoietic cell	1.67e-45	182
hematopoietic oligopotent progenitor cell	2.41e-45	165
hematopoietic multipotent progenitor cell	2.41e-45	165
myeloid cell	2.39e-41	112
common myeloid progenitor	2.39e-41	112
leukocyte	1.04e-31	140
myeloid leukocyte	6.27e-30	76
nongranular leukocyte	4.73e-28	119
hematopoietic lineage restricted progenitor cell	5.79e-28	124
myeloid lineage restricted progenitor cell	6.15e-27	70
granulocyte monocyte progenitor cell	7.58e-25	71
monopoietic cell	7.79e-24	63
monocyte	7.79e-24	63
monoblast	7.79e-24	63
promonocyte	7.79e-24	63
CD14-positive, CD16-negative classical monocyte	4.68e-22	42
macrophage dendritic cell progenitor	6.25e-22	65
classical monocyte	1.26e-18	45
endothelial cell	1.95e-11	35
lymphocyte of B lineage	7.34e-11	24
pro-B cell	7.34e-11	24
B cell	6.28e-09	14
endothelial cell of vascular tree	3.08e-08	24
meso-epithelial cell	2.02e-07	44
blood vessel endothelial cell	5.02e-07	18
embryonic blood vessel endothelial progenitor cell	5.02e-07	18

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	1.96e-30	112
hematopoietic system	1.05e-28	102
blood island	1.05e-28	102
bone marrow	2.95e-21	80
immune system	4.57e-21	115
adult organism	7.87e-21	115
lateral plate mesoderm	1.04e-20	216
bone element	2.38e-17	86
skeletal element	9.79e-13	101
skeletal system	9.79e-13	101
blood	5.36e-09	15
haemolymphatic fluid	5.36e-09	15
organism substance	5.36e-09	15
endothelium	5.02e-07	18
blood vessel endothelium	5.02e-07	18
cardiovascular system endothelium	5.02e-07	18

Disease

Ontology term	p-value	n
myeloid leukemia	2.72e-14	31
leukemia	2.92e-12	39
hematologic cancer	1.85e-10	51
immune system cancer	1.85e-10	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
BCLAF1#9774	3	21.6526476101218	9.8473954032885e-05	0.00139168082344255
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189960484468673
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00914864459756452
GATA1#2623	3	13.5603081438004	0.000400961596378263	0.00387812818708552
JUNB#3726	2	20.4070884398808	0.00313146219943874	0.0164485631266501
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186433073830626
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294395110212288
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.027661416297236
SMARCA4#6597	2	104.510602205259	0.000121451859247127	0.00164453659119807
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246380783430444
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0109039639089404
STAT2#6773	2	43.5091807909604	0.000696899089886823	0.00560864946048315
TAL1#6886	2	19.9124111182935	0.00328717660874055	0.0170123606461969
THAP1#55145	3	31.3691446028513	3.23800758564397e-05	0.000646728388290439
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190193789100566
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00421507833631558
ZBTB33#10009	2	21.1098166866541	0.00292859706060324	0.0156370014525737
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140127570540695

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.