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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2190_rhabdomyosarcoma_occipital_postcentral_brain_paracentral_temporal_parietal
|full_id=C2190_rhabdomyosarcoma_occipital_postcentral_brain_paracentral_temporal_parietal
|id=C2190
|id=C2190

Revision as of 14:53, 12 September 2012


Full id: C2190_rhabdomyosarcoma_occipital_postcentral_brain_paracentral_temporal_parietal



Phase1 CAGE Peaks

Hg19::chr12:121078397..121078417,+p3@CABP1
Hg19::chr12:121078423..121078446,+p2@CABP1
Hg19::chr12:121078535..121078550,+p1@CABP1
Hg19::chr12:121099132..121099146,+p@chr12:121099132..121099146
+


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
neuron7.55e-086
neuroblast7.55e-086
electrically signaling cell7.55e-086
neuronal stem cell2.75e-078
Uber Anatomy
Ontology termp-valuen
central nervous system1.06e-5182
neural tube1.07e-5057
neural rod1.07e-5057
future spinal cord1.07e-5057
neural keel1.07e-5057
regional part of nervous system3.07e-4694
nervous system3.07e-4694
regional part of brain8.91e-4259
regional part of forebrain1.17e-4141
forebrain1.17e-4141
future forebrain1.17e-4141
anterior neural tube2.47e-4042
brain7.31e-4069
future brain7.31e-4069
telencephalon5.96e-3434
gray matter7.19e-3434
brain grey matter7.19e-3434
neurectoderm1.08e-3390
neural plate1.88e-3386
presumptive neural plate1.88e-3386
regional part of telencephalon1.28e-3233
cerebral hemisphere7.68e-3232
adult organism1.15e-30115
regional part of cerebral cortex6.94e-2822
neocortex1.96e-2520
pre-chordal neural plate5.00e-2561
cerebral cortex1.17e-2325
pallium1.17e-2325
ectoderm8.23e-23173
presumptive ectoderm8.23e-23173
ectoderm-derived structure3.00e-22169
anterior region of body1.03e-20129
craniocervical region1.03e-20129
head4.90e-20123
basal ganglion7.21e-129
nuclear complex of neuraxis7.21e-129
aggregate regional part of brain7.21e-129
collection of basal ganglia7.21e-129
cerebral subcortex7.21e-129
nucleus of brain1.07e-119
neural nucleus1.07e-119
posterior neural tube2.62e-1115
chordal neural plate2.62e-1115
gyrus1.65e-096
telencephalic nucleus2.01e-097
diencephalon4.98e-097
future diencephalon4.98e-097
temporal lobe6.94e-097
segmental subdivision of hindbrain2.87e-0812
hindbrain2.87e-0812
presumptive hindbrain2.87e-0812
occipital lobe4.73e-085
parietal lobe5.89e-085
brainstem7.23e-088
tube8.63e-08194
limbic system9.47e-085
segmental subdivision of nervous system1.91e-0713
anatomical conduit3.67e-07241


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
CTCFL#140690314.80985576923080.0004996291767563340.00440790434121091
GABPB1#255335.300762877136630.01012678824234270.0378428380292698
NANOG#79923321.93358386075950.0001557535816382770.00196458312955556
ZBTB7A#5134135.513931980906920.009038352821081090.0342286072333341



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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