Coexpression cluster:C2832

Full id: C2832_iPS_mesothelioma_testicular_teratocarcinoma_H9_HES3GFP_giant

Phase1 CAGE Peaks

Hg19::chr5:89770664..89770688,+	p2@POLR3G
Hg19::chr5:89770696..89770727,+	p1@POLR3G
Hg19::chr5:89770738..89770749,+	p4@POLR3G
Hg19::chr5:89797743..89797759,+	p@chr5:89797743..89797759 +

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>disease_data<br>

---

Cell Type

Ontology term	p-value	n
epithelial cell	8.11e-19	254
embryonic cell	1.86e-10	248

Uber Anatomy

Ontology term	p-value	n
cell layer	3.61e-08	312
epithelium	5.20e-08	309

Disease

Ontology term	p-value	n
disease of cellular proliferation	3.51e-26	239
cancer	2.65e-25	235
hematologic cancer	4.43e-13	51
immune system cancer	4.43e-13	51
cell type cancer	9.37e-12	143
organ system cancer	1.21e-11	137
leukemia	4.69e-10	39
carcinoma	4.82e-09	106
myeloid leukemia	6.07e-07	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

---

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	4.75215118272197	0.0138620699668949	0.0487389148017955
CHD2#1106	3	7.75801712558764	0.00335152246453634	0.0173076371970783
ETS1#2113	3	7.29657069165175	0.0040085737751139	0.0192112443327423
GTF2F1#2962	3	9.55474565756824	0.00182036231930478	0.010903069350569
HDAC2#3066	3	10.0617151774697	0.0015637275447474	0.00992670441562568
HMGN3#9324	3	6.13391079251294	0.00664069668332472	0.0283103812927484
IRF1#3659	3	5.72787281517293	0.00809711479033333	0.032019028873864
MAX#4149	3	4.83941663175534	0.0131573713783684	0.0466443553762869
MEF2A#4205	3	14.057423182233	0.000583003885418661	0.00488984442573398
MXI1#4601	3	7.47117872156947	0.00374131473855096	0.0186421359723055
NANOG#79923	3	21.9335838607595	0.000155753581638277	0.00196577018884834
NRF1#4899	3	9.15770958578318	0.00206195379173342	0.011966458771663
PAX5#5079	3	5.00217414838337	0.0119653317478641	0.0435204876511519
POU2F2#5452	3	6.82959304330689	0.00486047377520374	0.0227756200919106
REST#5978	3	7.23752153709602	0.00410469730419261	0.0195910100426182
TAF7#6879	3	8.57480205369294	0.0025005543351524	0.0140391030109118
TCF12#6938	3	7.97584867663982	0.00309092039601307	0.0162888603915233
TFAP2C#7022	3	8.10692145739517	0.00294701173986644	0.0157192522522937
THAP1#55145	2	15.6845723014257	0.00584046967835792	0.0262511969675513
TRIM28#10155	3	13.9428937839469	0.000597285818425842	0.004997190866825
USF1#7391	3	4.77112445790597	0.0137046588718802	0.0483335314868569
ZBTB33#10009	3	23.7485437724859	0.000122945190881838	0.00165638193892006
ZNF143#7702	3	10.1256574141709	0.00153486161068818	0.00977077970002824
ZNF263#10127	3	6.16638122775801	0.00653981434797598	0.0279899873243285

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.