Coexpression cluster:C3349

Full id: C3349_Smooth_Fibroblast_parotid_Preadipocyte_cholangiocellular_Neutrophils_salivary

Phase1 CAGE Peaks

Hg19::chr13:100153665..100153688,+	p4@TM9SF2
Hg19::chr13:100153689..100153710,+	p3@TM9SF2
Hg19::chr13:100153718..100153734,+	p2@TM9SF2

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><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
anatomical group	3.04e-18	626
multi-cellular organism	7.44e-18	659
anatomical system	7.79e-18	625
organ	1.96e-17	511
adult organism	3.35e-13	115
embryonic structure	2.02e-10	605
developing anatomical structure	2.02e-10	605
germ layer	3.81e-10	604
embryonic tissue	3.81e-10	604
presumptive structure	3.81e-10	604
epiblast (generic)	3.81e-10	604
embryo	5.14e-10	612

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
BHLHE40#8553	3	44.8718135469774	1.10603738662898e-05	0.000283956338795831
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189504502139708
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324158785282588
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321070265429631
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319575967404835
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0460735348516054
ELK4#2005	3	16.235681658468	0.000233604395574599	0.00255309852128668
FOSL2#2355	3	16.9302006045617	0.000206016205317162	0.00242544543649184
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0153762787999049
GATA1#2623	3	13.5603081438004	0.000400961596378263	0.00387203219270915
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00433082411825263
HNF4A#3172	3	23.1322903629537	8.07584663437677e-05	0.0012259205619879
IRF4#3662	3	21.9145126867441	9.49854535978121e-05	0.00136303734381724
JUN#3725	3	12.5128291923363	0.000510331399272625	0.00443525846788996
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156377254493287
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186067186317962
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.007191080453271
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293628824685947
NANOG#79923	3	29.2447784810127	3.99627955670032e-05	0.000735578851995462
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0268961850764256
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00470045884938236
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172518659861439
REST#5978	3	9.65002871612802	0.00111263624711459	0.00766103751400321
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.0048352373491667
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275862588312275
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0245790636967214
SRF#6722	3	13.7971782621678	0.000380661502580019	0.0037427891798112
STAT1#6772	3	20.7065874971992	0.000112599244104667	0.00154570878746678
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.00641755503771673
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00612295254284249
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189775585213421
YY1#7528	3	4.91117074985386	0.00844145534180826	0.032843465873528
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00242246064102341
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.0038824712922542

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.