Coexpression cluster:C1789

Full id: C1789_Small_MCF7_occipital_temporal_parietal_duodenum_brain

Phase1 CAGE Peaks

Hg19::chr17:61043561..61043617,+	p@chr17:61043561..61043617 +
Hg19::chr17:61043618..61043648,+	p@chr17:61043618..61043648 +
Hg19::chr17:61043653..61043672,+	p@chr17:61043653..61043672 +
Hg19::chr17:61043790..61043869,+	p@chr17:61043790..61043869 +
Hg19::chr17:61043870..61043902,+	p@chr17:61043870..61043902 +

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

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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

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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>

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Cell Type

Ontology term	p-value	n
respiratory epithelial cell	9.65e-08	13

Uber Anatomy

Ontology term	p-value	n
neural tube	1.72e-23	56
neural rod	1.72e-23	56
future spinal cord	1.72e-23	56
neural keel	1.72e-23	56
regional part of nervous system	2.32e-22	53
regional part of brain	2.32e-22	53
central nervous system	4.21e-22	81
nervous system	5.57e-22	89
brain	2.17e-21	68
future brain	2.17e-21	68
regional part of forebrain	1.71e-19	41
forebrain	1.71e-19	41
anterior neural tube	1.71e-19	41
future forebrain	1.71e-19	41
telencephalon	1.67e-18	34
brain grey matter	3.34e-18	34
gray matter	3.34e-18	34
ecto-epithelium	6.86e-18	104
cerebral hemisphere	7.68e-18	32
ectoderm-derived structure	1.41e-17	171
ectoderm	1.41e-17	171
presumptive ectoderm	1.41e-17	171
regional part of telencephalon	1.53e-17	32
anatomical system	1.71e-16	624
anatomical group	4.12e-16	625
multi-cellular organism	8.19e-16	656
neural plate	5.78e-15	82
presumptive neural plate	5.78e-15	82
cerebral cortex	8.10e-14	25
pallium	8.10e-14	25
regional part of cerebral cortex	2.16e-13	22
neurectoderm	7.93e-13	86
neocortex	1.08e-12	20
organ	1.30e-12	503
pre-chordal neural plate	7.21e-12	61
structure with developmental contribution from neural crest	2.46e-11	132
organ system subdivision	1.28e-10	223
embryonic structure	4.65e-10	564
developing anatomical structure	5.54e-10	581
organ part	2.11e-09	218
germ layer	2.56e-09	560
germ layer / neural crest	2.56e-09	560
embryonic tissue	2.56e-09	560
presumptive structure	2.56e-09	560
germ layer / neural crest derived structure	2.56e-09	560
epiblast (generic)	2.56e-09	560
embryo	5.25e-09	592
epithelium	1.43e-08	306
cell layer	3.89e-08	309
tube	3.19e-07	192
anatomical conduit	7.66e-07	240
multi-tissue structure	9.03e-07	342

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

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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

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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
CCNT2#905	5	6.33620157696263	9.78880505817628e-05	0.00139036177270621
CTCF#10664	5	5.36025637307503	0.000225927829993709	0.00249768991602762
CTCFL#140690	5	19.7464743589744	3.32745051287657e-07	1.6572036438451e-05
E2F1#1869	5	4.90738921487932	0.000351281809925646	0.00352730708074459
E2F6#1876	5	5.01715573169739	0.000314497859929779	0.00322777535310595
EGR1#1958	5	4.98817909481014	0.000323739800059071	0.00330767569735564
HMGN3#9324	5	8.17854772335059	2.73180911341838e-05	0.000581903756875998
NR3C1#2908	5	14.973023331173	1.32777388277837e-06	5.2427741604344e-05
TRIM28#10155	3	11.1543150271575	0.00143315927152925	0.00920187637767388
ZBTB7A#51341	5	7.3519093078759	4.65425347594289e-05	0.000815716695375062

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

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This analysis result is provided for C0 - C305 clusters.