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Coexpression cluster:C3375: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3375_testis_parietal_brain_occipital_temporal_cerebellum_duodenum
|full_id=C3375_testis_parietal_brain_occipital_temporal_cerebellum_duodenum
|id=C3375
|id=C3375

Revision as of 16:17, 12 September 2012


Full id: C3375_testis_parietal_brain_occipital_temporal_cerebellum_duodenum



Phase1 CAGE Peaks

Hg19::chr13:45915545..45915601,+p1@ENST00000412946
p1@ENST00000520590
p1@ENST00000520622
Hg19::chr15:77197781..77197801,-p3@SCAPER
Hg19::chr22:42486923..42487002,+p1@LOC100132273


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>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
lymphoid lineage restricted progenitor cell6.63e-0752
Uber Anatomy
Ontology termp-valuen
adult organism1.28e-43115
neural tube6.64e-3257
neural rod6.64e-3257
future spinal cord6.64e-3257
neural keel6.64e-3257
regional part of nervous system1.50e-3094
nervous system1.50e-3094
central nervous system7.39e-3082
regional part of brain1.46e-2859
brain6.16e-2669
future brain6.16e-2669
neurectoderm1.70e-2490
anterior neural tube4.07e-2442
regional part of forebrain4.18e-2441
forebrain4.18e-2441
future forebrain4.18e-2441
neural plate3.45e-2386
presumptive neural plate3.45e-2386
telencephalon4.42e-2034
gray matter6.17e-2034
brain grey matter6.17e-2034
regional part of telencephalon1.82e-1933
cerebral hemisphere5.61e-1932
pre-chordal neural plate1.39e-1661
ectoderm8.73e-16173
presumptive ectoderm8.73e-16173
regional part of cerebral cortex1.27e-1522
cerebral cortex6.67e-1525
pallium6.67e-1525
ectoderm-derived structure1.01e-14169
neocortex2.15e-1420
anterior region of body1.82e-12129
craniocervical region1.82e-12129
head5.81e-11123
posterior neural tube7.33e-0915
chordal neural plate7.33e-0915
segmental subdivision of nervous system1.06e-0713
segmental subdivision of hindbrain3.77e-0712
hindbrain3.77e-0712
presumptive hindbrain3.77e-0712


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
ATF3#467322.46317452600878.81932387510763e-050.00129401709214999
CCNT2#90536.336201576962630.003930750035764890.0189530749300669
CTCF#1066435.360256373075030.0064925092527670.0278754850503488
E2F1#186934.907389214879320.008460985347239390.0324194463323306
E2F6#187635.017155731697390.00791769806886330.0321132609170491
ELF1#199734.258097958807540.01295179875054610.0460829526695153
HNF4A#3172215.42152690863580.005444210486686610.0246718692623042
HNF4G#3174219.16894835096450.003543986611284220.0179692405911211
IRF1#365937.63716375356390.002244692747297240.0127777547192989
MAX#414936.452555509007120.003721913834265510.0186093909870191
MYC#460935.22228187160940.007020843755740150.029369939157484
SP1#666735.69838137814090.005403962701712170.0245833461366024
TRIM28#10155212.39368336350830.008368344129438470.0328972594773375



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.