Coexpression cluster:C4705

Full id: C4705_thyroid_small_smallcell_heart_neuroectodermal_tenocyte_Osteoblast

Phase1 CAGE Peaks

Hg19::chr7:90893790..90893806,+	p2@FZD1
Hg19::chr7:90893846..90893907,+	p1@FZD1
Hg19::chr7:90893910..90893932,+	p5@FZD1

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	3.43e-17	180
fibroblast	3.32e-13	75
stromal cell	4.14e-07	27
preadipocyte	5.16e-07	12

Uber Anatomy

Ontology term	p-value	n
multi-cellular organism	1.12e-18	659
organ	7.58e-14	511
anatomical system	9.95e-14	625
anatomical group	1.00e-13	626
embryonic structure	1.06e-12	605
developing anatomical structure	1.06e-12	605
embryo	1.11e-12	612
germ layer	2.64e-12	604
embryonic tissue	2.64e-12	604
presumptive structure	2.64e-12	604
epiblast (generic)	2.64e-12	604
organism subdivision	3.93e-09	365
surface structure	7.48e-09	95
organ component layer	3.27e-08	57

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	0.00139507885041244
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0191163493823166
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0327778051367015
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0324344565057468
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0322515836015251
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0464995843832342
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0168514712619923
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154833268045315
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00435998791702874
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0109223637736848
IRF3#3661	3	46.9819522114896	9.63568551583244e-06	0.000254190795551408
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157694472853186
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0296095098128633
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00668750630769465
REST#5978	3	9.65002871612802	0.00111263624711459	0.00771444048412671
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00486874967586917
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.0031087363994547
STAT1#6772	3	20.7065874971992	0.000112599244104667	0.00155367320056114
SUZ12#23512	3	50.1157809110629	7.93834897779404e-06	0.000223590406928757
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00617497230809271
TRIM28#10155	3	18.5905250452625	0.000155596929725528	0.00198127136596005
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0191215854338497
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0331273120070309
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00390462213610436
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0110154393235724
ZZZ3#26009	3	239.413212435233	7.25894005043406e-08	4.38978830299527e-06

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.