Coexpression cluster:C3263

Full id: C3263_testicular_uterus_large_heart_merkel_teratocarcinoma_spinal

Phase1 CAGE Peaks

Hg19::chr12:19282623..19282642,+	p3@PLEKHA5
Hg19::chr12:19282643..19282710,+	p1@PLEKHA5
Hg19::chr12:19282713..19282734,+	p5@PLEKHA5

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><br>uberon_data<br>disease_data<br>

---

Uber Anatomy

Ontology term	p-value	n
organ system subdivision	6.84e-26	223
central nervous system	7.51e-24	81
neural tube	6.78e-23	56
neural rod	6.78e-23	56
future spinal cord	6.78e-23	56
neural keel	6.78e-23	56
ectoderm-derived structure	1.68e-22	171
ectoderm	1.68e-22	171
presumptive ectoderm	1.68e-22	171
adult organism	2.17e-21	114
regional part of nervous system	3.72e-21	53
regional part of brain	3.72e-21	53
brain	4.63e-21	68
future brain	4.63e-21	68
nervous system	6.72e-21	89
neural plate	1.90e-20	82
presumptive neural plate	1.90e-20	82
neurectoderm	7.42e-20	86
anatomical cluster	9.26e-20	373
multi-tissue structure	1.08e-19	342
organ	4.85e-19	503
ecto-epithelium	8.63e-19	104
structure with developmental contribution from neural crest	1.48e-18	132
regional part of forebrain	8.21e-18	41
forebrain	8.21e-18	41
anterior neural tube	8.21e-18	41
future forebrain	8.21e-18	41
telencephalon	4.62e-16	34
brain grey matter	5.07e-16	34
gray matter	5.07e-16	34
cerebral hemisphere	1.89e-15	32
regional part of telencephalon	2.16e-15	32
pre-chordal neural plate	1.14e-14	61
anatomical conduit	7.78e-14	240
organ part	7.57e-13	218
cell layer	2.12e-12	309
epithelium	3.08e-12	306
multi-cellular organism	5.01e-12	656
cerebral cortex	6.11e-12	25
pallium	6.11e-12	25
regional part of cerebral cortex	1.73e-11	22
neocortex	6.30e-11	20
tube	1.17e-10	192
anatomical group	1.91e-10	625
anatomical system	2.03e-10	624
embryo	1.98e-09	592
digestive system	2.65e-09	145
digestive tract	2.65e-09	145
primitive gut	2.65e-09	145
endoderm-derived structure	2.41e-08	160
endoderm	2.41e-08	160
presumptive endoderm	2.41e-08	160
developing anatomical structure	3.54e-07	581
subdivision of digestive tract	8.54e-07	118

Disease

Ontology term	p-value	n
carcinoma	7.37e-07	106

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	0.0189399586152364
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324004271140078
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0460515749058075
NANOG#79923	3	29.2447784810127	3.99627955670032e-05	0.000734931221380921
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00612205560406818
TFAP2A#7020	2	11.0124229153633	0.0105499065521556	0.03899839629068
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00613684476824079
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328251230338489
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0139747538310034

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.