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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2932_occipital_astrocytoma_gall_medial_postcentral_parietal_brain
|full_id=C2932_occipital_astrocytoma_gall_medial_postcentral_parietal_brain
|id=C2932
|id=C2932

Revision as of 15:44, 12 September 2012


Full id: C2932_occipital_astrocytoma_gall_medial_postcentral_parietal_brain



Phase1 CAGE Peaks

Hg19::chr8:94929594..94929608,+p21@PDP1
Hg19::chr8:94929969..94929980,+p8@PDP1
Hg19::chr8:94930034..94930089,+p2@PDP1
Hg19::chr8:94930100..94930120,+p5@PDP1


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>


Uber Anatomy
Ontology termp-valuen
central nervous system4.52e-3182
regional part of nervous system1.71e-3094
nervous system1.71e-3094
brain4.50e-2769
future brain4.50e-2769
neural tube9.03e-2457
neural rod9.03e-2457
future spinal cord9.03e-2457
neural keel9.03e-2457
regional part of brain1.78e-2359
neural plate4.68e-2386
presumptive neural plate4.68e-2386
anatomical conduit7.60e-23241
head2.08e-22123
tube6.64e-22194
ectoderm-derived structure1.04e-21169
neurectoderm1.20e-2190
regional part of forebrain5.80e-2141
forebrain5.80e-2141
future forebrain5.80e-2141
ectoderm6.16e-21173
presumptive ectoderm6.16e-21173
anterior region of body1.09e-20129
craniocervical region1.09e-20129
epithelium1.58e-20309
cell layer1.62e-20312
anterior neural tube1.01e-1942
telencephalon1.04e-1934
cerebral hemisphere1.41e-1932
gray matter2.06e-1934
brain grey matter2.06e-1934
anatomical cluster2.43e-19286
regional part of telencephalon4.92e-1933
pre-chordal neural plate1.47e-1761
cerebral cortex5.41e-1625
pallium5.41e-1625
organism subdivision6.66e-15365
anatomical system1.38e-14625
anatomical group1.92e-14626
regional part of cerebral cortex3.27e-1422
neocortex3.36e-1320
multi-cellular organism5.00e-13659
vasculature9.80e-1379
vascular system9.80e-1379
artery9.94e-1342
arterial blood vessel9.94e-1342
arterial system9.94e-1342
embryo2.06e-12612
blood vessel2.79e-1160
epithelial tube open at both ends2.79e-1160
blood vasculature2.79e-1160
vascular cord2.79e-1160
germ layer2.89e-11604
embryonic tissue2.89e-11604
presumptive structure2.89e-11604
epiblast (generic)2.89e-11604
embryonic structure3.30e-11605
developing anatomical structure3.30e-11605
vessel3.30e-1169
systemic artery9.83e-1133
systemic arterial system9.83e-1133
multi-tissue structure1.75e-10347
splanchnic layer of lateral plate mesoderm5.85e-0984
circulatory system4.64e-08113
cardiovascular system8.07e-08110
aorta1.93e-0721
aortic system1.93e-0721


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
TAF1#687243.343046285745290.008005664898701650.0323506920625073
TCF7L2#693438.077632422353010.002978381685834620.0158736071079241



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.