Coexpression cluster:C4006

Full id: C4006_immature_CD4_embryonic_Natural_CD19_hepatoblastoma_CD8

Phase1 CAGE Peaks

Hg19::chr1:91487774..91487802,-	p2@ZNF644
Hg19::chr1:91487806..91487826,-	p5@ZNF644
Hg19::chr1:91487836..91487854,-	p3@ZNF644

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
leukocyte	9.89e-33	140
hematopoietic stem cell	3.87e-30	172
angioblastic mesenchymal cell	3.87e-30	172
hematopoietic cell	2.73e-27	182
hematopoietic oligopotent progenitor cell	9.00e-27	165
hematopoietic multipotent progenitor cell	9.00e-27	165
hematopoietic lineage restricted progenitor cell	1.27e-24	124
nongranular leukocyte	2.29e-24	119
CD14-positive, CD16-negative classical monocyte	2.81e-15	42
lymphocyte	4.72e-15	53
common lymphoid progenitor	4.72e-15	53
lymphoid lineage restricted progenitor cell	1.08e-14	52
classical monocyte	8.52e-14	45
myeloid leukocyte	1.63e-12	76
myeloid cell	1.83e-12	112
common myeloid progenitor	1.83e-12	112
granulocyte monocyte progenitor cell	9.83e-11	71
myeloid lineage restricted progenitor cell	8.71e-10	70
macrophage dendritic cell progenitor	9.96e-10	65
mature alpha-beta T cell	2.41e-09	18
alpha-beta T cell	2.41e-09	18
immature T cell	2.41e-09	18
mature T cell	2.41e-09	18
immature alpha-beta T cell	2.41e-09	18
monopoietic cell	8.00e-09	63
monocyte	8.00e-09	63
monoblast	8.00e-09	63
promonocyte	8.00e-09	63
T cell	4.47e-08	25
pro-T cell	4.47e-08	25
B cell	5.44e-08	14

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	1.85e-10	102
blood island	1.85e-10	102
hemolymphoid system	3.75e-09	112
bone element	3.01e-08	86
bone marrow	2.37e-07	80
immune system	2.96e-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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190268633196723
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115320835542973
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0325784120587057
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00437690366383349
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322711703330477
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00915884881139251
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321075923292448
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0462911231548641
ESR1#2099	3	30.7686032961545	3.43136389821584e-05	0.00067693278081935
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154300195760965
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.0043453570850924
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156956369930151
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186782451077245
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269869457710152
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00471552937676857
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00485095020106098
SETDB1#9869	3	40.3200261780105	1.52461559299059e-05	0.00035927194926973
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246854944934662
SRF#6722	3	13.7971782621678	0.000380661502580019	0.00375480795881702
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00543832437743182
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00616429654532976
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190542211185912
WRNIP1#56897	3	109.819964349376	7.53682839543883e-07	3.32687582752002e-05
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0329798426770579
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00389530237336327

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.