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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4130_neuroblastoma_Burkitt_pons_occipital_optic_temporal_spinal
|full_id=C4130_neuroblastoma_Burkitt_pons_occipital_optic_temporal_spinal
|id=C4130
|id=C4130

Revision as of 17:10, 12 September 2012


Full id: C4130_neuroblastoma_Burkitt_pons_occipital_optic_temporal_spinal



Phase1 CAGE Peaks

Hg19::chr2:137719997..137720001,+p@chr2:137719997..137720001
+
Hg19::chr2:137775568..137775571,+p@chr2:137775568..137775571
+
Hg19::chr2:138173259..138173262,+p@chr2:138173259..138173262
+


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 system2.74e-1994
nervous system2.74e-1994
neural tube2.70e-1757
neural rod2.70e-1757
future spinal cord2.70e-1757
neural keel2.70e-1757
neurectoderm8.52e-1790
neural plate1.31e-1586
presumptive neural plate1.31e-1586
central nervous system6.02e-1482
regional part of brain1.56e-1359
regional part of cerebral cortex2.90e-1322
gray matter3.31e-1334
brain grey matter3.31e-1334
neocortex1.38e-1220
cerebral hemisphere1.64e-1232
ectoderm2.46e-12173
presumptive ectoderm2.46e-12173
telencephalon1.51e-1134
brain2.09e-1169
future brain2.09e-1169
ectoderm-derived structure2.17e-11169
cerebral cortex2.49e-1125
pallium2.49e-1125
regional part of telencephalon1.58e-1033
adult organism2.88e-10115
regional part of forebrain3.25e-1041
forebrain3.25e-1041
future forebrain3.25e-1041
anterior neural tube7.14e-1042
posterior neural tube1.11e-0915
chordal neural plate1.11e-0915
segmental subdivision of nervous system3.88e-0913
brainstem4.07e-098
pre-chordal neural plate3.24e-0861
segmental subdivision of hindbrain1.53e-0712
hindbrain1.53e-0712
presumptive hindbrain1.53e-0712
gyrus1.91e-076
anterior region of body2.67e-07129
craniocervical region2.67e-07129
sympathetic nervous system3.02e-075
autonomic nervous system3.02e-075
medulla oblongata3.88e-073
myelencephalon3.88e-073
future myelencephalon3.88e-073
pons5.73e-073
Disease
Ontology termp-valuen
neuroectodermal tumor6.76e-0710


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

No analysis results for this cluster

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.

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