Coexpression cluster:C2655

Full id: C2655_stomach_adenocarcinoma_gall_CD14_Macrophage_small_kidney

Phase1 CAGE Peaks

Hg19::chr2:108905305..108905321,+	p3@SULT1C2
Hg19::chr2:108905325..108905378,+	p1@SULT1C2
Hg19::chr2:108905407..108905419,+	p4@SULT1C2
Hg19::chr2:108905427..108905436,+	p7@SULT1C2

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
macrophage	5.33e-09	6
pigment cell	3.47e-07	14

Uber Anatomy

Ontology term	p-value	n
organ	5.86e-09	503
pigment epithelium of eye	6.52e-08	11
gastrointestinal system	3.87e-07	25
intestine	4.19e-07	17
multi-tissue structure	9.96e-07	342

Disease

Ontology term	p-value	n
adenocarcinoma	9.67e-07	25

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
BHLHE40#8553	4	44.8718135469774	2.46312701995675e-07	1.28558981927668e-05
CTCF#10664	4	5.36025637307503	0.00121114538164362	0.0081818119348951
ESR1#2099	4	30.7686032961545	1.11467714392546e-06	4.61235206950994e-05
FOXA1#3169	4	11.0814197493855	6.62943068949433e-05	0.00107194784297894
FOXA2#3170	4	24.6304637526652	2.71504128667089e-06	9.4487236567351e-05
HDAC2#3066	4	13.4156202366263	3.0859005065161e-05	0.000627142173574693
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0186330295565112
NR3C1#2908	4	14.973023331173	1.98868032687801e-05	0.000443510110311365
RXRA#6256	4	20.0746171391333	6.1537798808435e-06	0.000182428219408292
SP1#6667	4	5.6983813781409	0.000948260606533398	0.00684892043469858
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0322695344019877
TRIM28#10155	4	18.5905250452625	8.36730015875654e-06	0.000230330116310062
USF1#7391	4	6.36149927720796	0.000610501139914083	0.00508453975689689
USF2#7392	4	12.9921973850696	3.50833029870167e-05	0.000681686526634611
ZNF263#10127	4	8.22184163701068	0.000218787118095832	0.00249289851918073

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.