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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1263_neuroectodermal_glioblastoma_pons_pineal_parietal_rhabdomyosarcoma_occipital
|full_id=C1263_neuroectodermal_glioblastoma_pons_pineal_parietal_rhabdomyosarcoma_occipital
|id=C1263
|id=C1263

Revision as of 13:46, 12 September 2012


Full id: C1263_neuroectodermal_glioblastoma_pons_pineal_parietal_rhabdomyosarcoma_occipital



Phase1 CAGE Peaks

Hg19::chr2:139537884..139537895,-p3@NXPH2
Hg19::chr2:139537925..139537946,-p2@NXPH2
Hg19::chr2:139537950..139537983,-p1@NXPH2
Hg19::chr2:139538247..139538266,-p5@NXPH2
Hg19::chr2:139538362..139538376,-p4@NXPH2
Hg19::chr2:139538440..139538457,-p@chr2:139538440..139538457
-
Hg19::chr2:139538474..139538479,-p@chr2:139538474..139538479
-


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
neural cell2.47e-1225
neuronal stem cell7.52e-098
mesothelial cell1.89e-0819
neurectodermal cell1.20e-0759
neuron3.55e-076
neuroblast3.55e-076
electrically signaling cell3.55e-076
Uber Anatomy
Ontology termp-valuen
regional part of nervous system7.95e-5094
nervous system7.95e-5094
central nervous system1.51e-4882
neurectoderm3.63e-4190
neural tube1.77e-3957
neural rod1.77e-3957
future spinal cord1.77e-3957
neural keel1.77e-3957
neural plate8.14e-3886
presumptive neural plate8.14e-3886
brain1.22e-3669
future brain1.22e-3669
ectoderm4.58e-33173
presumptive ectoderm4.58e-33173
regional part of brain2.66e-3259
ectoderm-derived structure2.58e-30169
regional part of forebrain1.04e-2941
forebrain1.04e-2941
future forebrain1.04e-2941
anterior neural tube1.14e-2842
cerebral hemisphere6.97e-2832
gray matter1.96e-2734
brain grey matter1.96e-2734
telencephalon2.57e-2734
pre-chordal neural plate6.52e-2761
cerebral cortex1.81e-2625
pallium1.81e-2625
regional part of telencephalon3.33e-2633
regional part of cerebral cortex2.94e-2422
anterior region of body7.54e-24129
craniocervical region7.54e-24129
head1.46e-23123
neocortex1.07e-2220
adult organism6.91e-19115
posterior neural tube9.97e-1215
chordal neural plate9.97e-1215
segmental subdivision of nervous system3.70e-1013
epithelium1.15e-09309
cell layer1.23e-09312
segmental subdivision of hindbrain2.05e-0912
hindbrain2.05e-0912
presumptive hindbrain2.05e-0912
temporal lobe2.55e-097
organ part7.30e-09219
embryo1.38e-08612
organism subdivision1.98e-08365
gyrus1.27e-076
tube1.47e-07194
occipital lobe9.14e-075


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#687273.343046285745290.0002142336319622450.00246766805873



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.