Coexpression cluster:C3487

Full id: C3487_mucinous_brain_temporal_cerebral_stomach_postcentral_occipital

Phase1 CAGE Peaks

Hg19::chr15:41786021..41786055,+	p2@ITPKA
Hg19::chr15:41786065..41786081,+	p1@ITPKA
Hg19::chr15:41786087..41786090,+	p8@ITPKA

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

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Uber Anatomy

Ontology term	p-value	n
cerebral hemisphere	5.83e-17	32
telencephalon	5.98e-17	34
regional part of telencephalon	3.15e-16	33
gray matter	9.78e-15	34
brain grey matter	9.78e-15	34
anterior neural tube	1.14e-13	42
regional part of forebrain	1.56e-13	41
forebrain	1.56e-13	41
future forebrain	1.56e-13	41
regional part of cerebral cortex	2.87e-13	22
brain	3.09e-13	69
future brain	3.09e-13	69
cerebral cortex	8.05e-13	25
pallium	8.05e-13	25
neocortex	3.65e-12	20
neural tube	2.77e-11	57
neural rod	2.77e-11	57
future spinal cord	2.77e-11	57
neural keel	2.77e-11	57
pre-chordal neural plate	3.57e-11	61
multi-tissue structure	6.60e-11	347
regional part of nervous system	2.39e-10	94
nervous system	2.39e-10	94
head	2.52e-10	123
regional part of brain	4.55e-10	59
neural plate	8.91e-10	86
presumptive neural plate	8.91e-10	86
anterior region of body	1.03e-09	129
craniocervical region	1.03e-09	129
central nervous system	1.09e-09	82
neurectoderm	1.14e-09	90
gastrointestinal system	1.79e-08	35
organ part	8.19e-08	219
digestive system	1.06e-07	155
digestive tract	1.06e-07	155
primitive gut	1.06e-07	155
ectoderm	1.53e-07	173
presumptive ectoderm	1.53e-07	173
ectoderm-derived structure	1.67e-07	169
organism subdivision	7.10e-07	365

Disease

Ontology term	p-value	n
cancer	7.97e-23	235
disease of cellular proliferation	1.28e-22	239
cell type cancer	2.44e-14	143
carcinoma	8.62e-13	106
organ system cancer	3.83e-12	137
disease of anatomical entity	7.08e-08	39

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	3	6.33620157696263	0.00393075003576489	0.018964457106539
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324504002306318
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00436388823237774
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.032138222643374
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319855380742108
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269168109852266
SMARCC1#6599	3	43.6633593196315	1.20046018043203e-05	0.00030130944672949
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246004908292266
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00247753198367226
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00614231554583672
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0139866542015019

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.