Coexpression cluster:C2734

Full id: C2734_occipital_locus_brain_amygdala_cerebellum_temporal_postcentral

Phase1 CAGE Peaks

Hg19::chr3:183979256..183979300,-	p2@CAMK2N2
Hg19::chr3:183979335..183979351,-	p4@CAMK2N2
Hg19::chr3:183979353..183979390,-	p3@CAMK2N2
Hg19::chr3:183979460..183979484,-	p5@CAMK2N2

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
epithelial cell	4.68e-07	253

Uber Anatomy

Ontology term	p-value	n
central nervous system	1.20e-31	81
nervous system	2.70e-31	89
neural tube	7.42e-27	56
neural rod	7.42e-27	56
future spinal cord	7.42e-27	56
neural keel	7.42e-27	56
brain	1.35e-25	68
future brain	1.35e-25	68
regional part of nervous system	5.24e-25	53
regional part of brain	5.24e-25	53
neural plate	3.24e-21	82
presumptive neural plate	3.24e-21	82
regional part of forebrain	7.31e-21	41
forebrain	7.31e-21	41
anterior neural tube	7.31e-21	41
future forebrain	7.31e-21	41
brain grey matter	4.90e-20	34
gray matter	4.90e-20	34
neurectoderm	7.00e-20	86
telencephalon	1.19e-19	34
cerebral hemisphere	8.41e-19	32
regional part of telencephalon	1.27e-18	32
pre-chordal neural plate	1.06e-17	61
ecto-epithelium	2.65e-17	104
ectoderm-derived structure	3.85e-16	171
ectoderm	3.85e-16	171
presumptive ectoderm	3.85e-16	171
organ system subdivision	4.53e-16	223
regional part of cerebral cortex	1.33e-15	22
structure with developmental contribution from neural crest	2.96e-15	132
cerebral cortex	8.08e-15	25
pallium	8.08e-15	25
neocortex	2.15e-14	20
anatomical cluster	9.61e-13	373
tube	9.98e-12	192
multi-tissue structure	5.37e-10	342
epithelium	3.86e-09	306
cell layer	5.04e-09	309
anatomical conduit	2.98e-08	240
organ part	1.05e-07	218
posterior neural tube	3.33e-07	15
chordal neural plate	3.33e-07	15

Disease

Ontology term	p-value	n
cell type cancer	1.10e-14	143
carcinoma	1.97e-13	106
disease of cellular proliferation	6.72e-13	239
cancer	3.47e-12	235

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
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106661436514725
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00998225516906899
GABPB1#2553	3	5.30076287713663	0.0101267882423427	0.0378740067051757
JUND#3727	3	5.24599795640327	0.0104343275174842	0.0387067816863868
MAX#4149	4	6.45255550900712	0.000576761319564549	0.00485973178329987
MXI1#4601	4	9.9615716287593	0.000101522475495045	0.0014260801369505
MYC#4609	4	5.2222818716094	0.00134430939527274	0.0088876577155719
REST#5978	4	9.65002871612802	0.000115282561421917	0.00157323865573548
SMARCC1#6599	3	32.7475194897236	4.71941722862287e-05	0.000825060622598165
USF1#7391	4	6.36149927720796	0.000610501139914083	0.00508616213716392
USF2#7392	4	12.9921973850696	3.50833029870167e-05	0.000682321244070956

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.