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Coexpression cluster:C2734: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2734_occipital_locus_brain_amygdala_cerebellum_temporal_postcentral
|full_id=C2734_occipital_locus_brain_amygdala_cerebellum_temporal_postcentral
|id=C2734
|id=C2734

Revision as of 15:30, 12 September 2012


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


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 termp-valuen
regional part of nervous system4.20e-3294
nervous system4.20e-3294
central nervous system8.22e-3282
neural tube3.00e-2757
neural rod3.00e-2757
future spinal cord3.00e-2757
neural keel3.00e-2757
brain5.76e-2669
future brain5.76e-2669
regional part of brain1.27e-2259
neural plate5.38e-2286
presumptive neural plate5.38e-2286
regional part of forebrain1.08e-2141
forebrain1.08e-2141
future forebrain1.08e-2141
neurectoderm1.36e-2090
anterior neural tube1.84e-2042
gray matter1.06e-1934
brain grey matter1.06e-1934
telencephalon2.21e-1934
regional part of telencephalon9.35e-1933
cerebral hemisphere1.61e-1832
ectoderm-derived structure2.48e-18169
ectoderm1.28e-17173
presumptive ectoderm1.28e-17173
pre-chordal neural plate7.59e-1761
head2.12e-16123
regional part of cerebral cortex2.68e-1522
cerebral cortex1.35e-1425
pallium1.35e-1425
anterior region of body1.71e-14129
craniocervical region1.71e-14129
neocortex3.88e-1420
tube4.71e-13194
organism subdivision5.08e-11365
epithelium2.69e-10309
multi-tissue structure2.97e-10347
cell layer3.43e-10312
anatomical cluster1.27e-09286
anatomical conduit2.51e-09241
organ part1.29e-08219
posterior neural tube6.14e-0815
chordal neural plate6.14e-0815
embryo8.94e-07612
Disease
Ontology termp-valuen
cell type cancer5.24e-14143
carcinoma1.28e-12106
disease of cellular proliferation1.84e-12239
cancer9.31e-12235


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#promotersEnrichmentp-valueq-value
E2F1#186944.907389214879320.001724022357361790.0106661436514725
E2F6#187645.017155731697390.00157802193473060.00998225516906899
GABPB1#255335.300762877136630.01012678824234270.0378740067051757
JUND#372735.245997956403270.01043432751748420.0387067816863868
MAX#414946.452555509007120.0005767613195645490.00485973178329987
MXI1#460149.96157162875930.0001015224754950450.0014260801369505
MYC#460945.22228187160940.001344309395272740.0088876577155719
REST#597849.650028716128020.0001152825614219170.00157323865573548
SMARCC1#6599332.74751948972364.71941722862287e-050.000825060622598165
USF1#739146.361499277207960.0006105011399140830.00508616213716392
USF2#7392412.99219738506963.50833029870167e-050.000682321244070956



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


This analysis result is provided for C0 - C305 clusters.