Coexpression cluster:C3072

Full id: C3072_epidermoid_Fibroblast_neuroectodermal_Small_Skeletal_Smooth_embryonic

Phase1 CAGE Peaks

Hg19::chr11:102980214..102980231,+	p4@DYNC2H1
Hg19::chr11:102980234..102980243,+	p5@DYNC2H1
Hg19::chr11:102980255..102980304,+	p1@DYNC2H1

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
non-terminally differentiated cell	2.97e-20	180
fibroblast	2.57e-09	75
skin fibroblast	4.01e-07	23
ectodermal cell	9.43e-07	71

Uber Anatomy

Ontology term	p-value	n
organism subdivision	3.80e-12	365
surface structure	1.71e-09	95
ectoderm	1.96e-09	173
presumptive ectoderm	1.96e-09	173
ectoderm-derived structure	2.68e-08	169
multi-tissue structure	3.65e-08	347
somite	5.01e-08	83
paraxial mesoderm	5.01e-08	83
presomitic mesoderm	5.01e-08	83
presumptive segmental plate	5.01e-08	83
trunk paraxial mesoderm	5.01e-08	83
presumptive paraxial mesoderm	5.01e-08	83
multi-cellular organism	1.57e-07	659

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	0.0189111665277893
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0114915907851567
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00658388492302709
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0278217287809672
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0323565305265593
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320373665729346
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319042795503048
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0460045882973943
GATA1#2623	3	13.5603081438004	0.000400961596378263	0.00386845525765815
GATA2#2624	3	12.744931733554	0.000482952770428379	0.00435871970193307
GATA3#2625	3	27.236516357206	4.94721007899563e-05	0.00084840997280825
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108288037027847
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127596726628736
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156145205146702
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0185720477275134
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00718130332145146
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293194410414549
NR2C2#7182	3	32.6146109052409	2.88098172333076e-05	0.000603826711224045
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00469391974951006
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172265365690449
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00661646272724848
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00482898067325997
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275379123730213
SMARCC1#6599	3	43.6633593196315	1.20046018043203e-05	0.000300803408791125
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00307969737925088
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0245427231085457
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0108807493013893
SREBF1#6720	3	47.0058494404883	9.62099323994382e-06	0.000254059902145763
SRF#6722	3	13.7971782621678	0.000380661502580019	0.00373926887396112
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189491901431162
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0327884987519753
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00241894630240793

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.