Coexpression cluster:C4241

Full id: C4241_mature_Hepatocyte_iPS_H9_HES3GFP_Olfactory_liver

Phase1 CAGE Peaks

Hg19::chr2:64068986..64068997,+	p6@UGP2
Hg19::chr2:64069016..64069039,+	p1@UGP2
Hg19::chr2:64069042..64069056,+	p5@UGP2

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

---

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

---

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>

---

Cell Type

Ontology term	p-value	n
non-terminally differentiated cell	3.62e-12	180
fibroblast	8.58e-10	75
fat cell	1.73e-08	15
skin fibroblast	1.05e-07	23
muscle precursor cell	4.72e-07	57
myoblast	4.72e-07	57
multi-potent skeletal muscle stem cell	4.72e-07	57

Uber Anatomy

Ontology term	p-value	n
somite	8.25e-14	83
paraxial mesoderm	8.25e-14	83
presomitic mesoderm	8.25e-14	83
presumptive segmental plate	8.25e-14	83
trunk paraxial mesoderm	8.25e-14	83
presumptive paraxial mesoderm	8.25e-14	83
dermomyotome	2.32e-10	70
surface structure	3.83e-10	95
multilaminar epithelium	7.46e-10	82
trunk mesenchyme	8.05e-09	143
muscle tissue	1.96e-08	63
musculature	1.96e-08	63
musculature of body	1.96e-08	63
skeletal muscle tissue	2.09e-08	61
striated muscle tissue	2.09e-08	61
myotome	2.09e-08	61
integument	1.18e-07	45
integumental system	1.18e-07	45
mesenchyme	1.91e-07	238
entire embryonic mesenchyme	1.91e-07	238

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

---

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

---

(#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	0.0190533557498027
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0280287356915399
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326397831300681
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.032322888973694
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321542175397504
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0463641100157081
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.0039232239847563
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108930696001306
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270204168781643
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00665909517844012
RDBP#7936	3	153.638403990025	2.75057764221434e-07	1.40130526036695e-05
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277579840176428
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.00644013097258988
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00544468102557812
YY1#7528	3	4.91117074985386	0.00844145534180826	0.033024316543419
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140554765894004

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

---

This analysis result is provided for C0 - C305 clusters.