Coexpression cluster:C4596

Full id: C4596_non_CD4_acute_Natural_Peripheral_CD8_blood

Phase1 CAGE Peaks

Hg19::chr6:36515033..36515051,-	p5@STK38
Hg19::chr6:36515067..36515090,-	p3@STK38
Hg19::chr6:36515092..36515172,-	p2@STK38

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 stem cell	4.55e-27	172
angioblastic mesenchymal cell	4.55e-27	172
hematopoietic cell	1.32e-26	182
hematopoietic oligopotent progenitor cell	4.27e-24	165
hematopoietic multipotent progenitor cell	4.27e-24	165
leukocyte	1.15e-23	140
nongranular leukocyte	6.89e-22	119
hematopoietic lineage restricted progenitor cell	2.96e-18	124
classical monocyte	3.64e-17	45
CD14-positive, CD16-negative classical monocyte	2.49e-16	42
mature alpha-beta T cell	1.29e-12	18
alpha-beta T cell	1.29e-12	18
immature T cell	1.29e-12	18
mature T cell	1.29e-12	18
immature alpha-beta T cell	1.29e-12	18
myeloid cell	2.51e-12	112
common myeloid progenitor	2.51e-12	112
myeloid leukocyte	2.81e-12	76
lymphocyte	4.00e-12	53
common lymphoid progenitor	4.00e-12	53
lymphoid lineage restricted progenitor cell	5.50e-12	52
T cell	5.12e-11	25
pro-T cell	5.12e-11	25
granulocyte monocyte progenitor cell	5.21e-09	71
monopoietic cell	6.14e-09	63
monocyte	6.14e-09	63
monoblast	6.14e-09	63
promonocyte	6.14e-09	63
CD8-positive, alpha-beta T cell	2.06e-08	11
myeloid lineage restricted progenitor cell	2.19e-08	70
macrophage dendritic cell progenitor	5.12e-08	65

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	8.48e-13	102
blood island	8.48e-13	102
hemolymphoid system	1.02e-12	112
blood	2.83e-08	15
haemolymphatic fluid	2.83e-08	15
organism substance	2.83e-08	15

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	0.0190994511484716
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115709142975072
CTCF#10664	3	5.36025637307503	0.006492509252767	0.02811123808506
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0327413705094792
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00438737204194806
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0324064924800727
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0464660406618901
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0109117498383839
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128661141449414
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00722897227527209
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270736796128402
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.0047326484603146
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173616366634751
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00885424729870856
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.027810622419699
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00203913749734525
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0109392885635106

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.