Coexpression cluster:C3978

Full id: C3978_smallcell_somatostatinoma_small_merkel_Hep2_carcinoid_gastrointestinal

Phase1 CAGE Peaks

Hg19::chr1:38259459..38259532,+	p2@MANEAL
Hg19::chr1:38259540..38259569,+	p3@MANEAL
Hg19::chr1:38259727..38259807,+	p1@MANEAL

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	1.11e-08	254

Uber Anatomy

Ontology term	p-value	n
central nervous system	8.83e-17	82
regional part of nervous system	3.25e-15	94
nervous system	3.25e-15	94
neural tube	8.85e-14	57
neural rod	8.85e-14	57
future spinal cord	8.85e-14	57
neural keel	8.85e-14	57
brain	1.20e-13	69
future brain	1.20e-13	69
adult organism	6.47e-13	115
regional part of forebrain	1.72e-11	41
forebrain	1.72e-11	41
future forebrain	1.72e-11	41
anterior neural tube	2.46e-11	42
regional part of brain	2.64e-10	59
telencephalon	5.76e-09	34
gray matter	8.70e-09	34
brain grey matter	8.70e-09	34
cerebral hemisphere	9.94e-09	32
regional part of telencephalon	1.36e-08	33
subdivision of digestive tract	2.01e-08	129
endodermal part of digestive tract	2.01e-08	129
neurectoderm	2.23e-08	90
regional part of cerebral cortex	2.69e-08	22
neural plate	2.83e-08	86
presumptive neural plate	2.83e-08	86
neocortex	6.10e-08	20
foregut	7.75e-08	98
ectoderm	1.80e-07	173
presumptive ectoderm	1.80e-07	173
larynx	1.84e-07	9
ectoderm-derived structure	2.61e-07	169
digestive system	3.50e-07	155
digestive tract	3.50e-07	155
primitive gut	3.50e-07	155

Disease

Ontology term	p-value	n
cancer	6.46e-43	235
disease of cellular proliferation	1.78e-41	239
cell type cancer	2.26e-34	143
carcinoma	1.11e-31	106
organ system cancer	1.10e-16	137
disease of anatomical entity	1.42e-07	39
adenocarcinoma	1.70e-07	25
hematologic cancer	6.46e-07	51
immune system cancer	6.46e-07	51

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
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0325700065858367
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322598396057431
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0462784532385057
ESR1#2099	2	20.5124021974363	0.00309974157709518	0.0163131222257618
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.015425191660084
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294833092483211
REST#5978	3	9.65002871612802	0.00111263624711459	0.00768281765371244
SUZ12#23512	3	50.1157809110629	7.93834897779404e-06	0.000222689559197376
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190497470364275
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109531507836175

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.