Coexpression cluster:C2968

Full id: C2968_CD14_acute_medulloblastoma_liver_Fibroblast_myelodysplastic_granulocyte

Phase1 CAGE Peaks

Hg19::chr10:101945654..101945676,-	p5@ERLIN1
Hg19::chr10:101945681..101945710,-	p3@ERLIN1
Hg19::chr10:101945716..101945735,-	p2@ERLIN1

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
animal cell	1.17e-17	679
eukaryotic cell	1.17e-17	679
somatic cell	1.21e-10	588
embryonic cell	1.27e-08	250
non-terminally differentiated cell	2.00e-07	106
fibroblast	2.92e-07	76
skin fibroblast	4.20e-07	23
stem cell	5.06e-07	441

Uber Anatomy

Ontology term	p-value	n
unilaminar epithelium	7.08e-08	148

Disease

Ontology term	p-value	n
myeloid leukemia	2.11e-08	31

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	0.00138773732090682
BHLHE40#8553	3	44.8718135469774	1.10603738662898e-05	0.000283538140947825
BRCA1#672	3	20.1842306432238	0.000121570486027164	0.00163870676176961
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0188981081335566
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00658067035969716
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0323245728748705
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00434984455412313
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320150400175777
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.031881311176879
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0459655059707858
ELK4#2005	3	16.235681658468	0.000233604395574599	0.00255016300506068
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0166725116644504
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00894325252757503
FOSL2#2355	3	16.9302006045617	0.000206016205317162	0.00242216891445672
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00579104265630468
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00389706208740819
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108245053401014
JUN#3725	3	12.5128291923363	0.000510331399272625	0.00442899293739685
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156081312678737
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0185596332571073
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00717935108458278
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0292971831950514
NANOG#79923	3	29.2447784810127	3.99627955670032e-05	0.000733897381083568
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0268379162926485
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.0046912324641378
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172164256158128
REST#5978	3	9.65002871612802	0.00111263624711459	0.00764994187046746
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275218345226847
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00611310064816374
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00247224376172205
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00612547855700905
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189368056296946
WRNIP1#56897	3	109.819964349376	7.53682839543883e-07	3.31986006238395e-05
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0327689991987479
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0108852527977623

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.