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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2820_pineal_epithelioid_cerebellum_occipital_temporal_parietal_myxofibrosarcoma
|full_id=C2820_pineal_epithelioid_cerebellum_occipital_temporal_parietal_myxofibrosarcoma
|id=C2820
|id=C2820

Revision as of 15:36, 12 September 2012


Full id: C2820_pineal_epithelioid_cerebellum_occipital_temporal_parietal_myxofibrosarcoma



Phase1 CAGE Peaks

Hg19::chr5:24644931..24644947,-p4@CDH10
Hg19::chr5:24645032..24645068,-p1@CDH10
Hg19::chr5:24645078..24645096,-p2@CDH10
Hg19::chr8:12809475..12809502,+p7@KIAA1456


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><br>

Uber Anatomy
Ontology termp-valuen
regional part of nervous system5.31e-3794
nervous system5.31e-3794
central nervous system1.01e-3482
neurectoderm5.77e-3390
neural tube5.92e-3357
neural rod5.92e-3357
future spinal cord5.92e-3357
neural keel5.92e-3357
neural plate6.42e-3186
presumptive neural plate6.42e-3186
brain2.49e-2969
future brain2.49e-2969
ectoderm6.98e-29173
presumptive ectoderm6.98e-29173
regional part of forebrain3.31e-2841
forebrain3.31e-2841
future forebrain3.31e-2841
regional part of brain8.93e-2859
ectoderm-derived structure4.77e-27169
anterior neural tube5.75e-2742
pre-chordal neural plate4.91e-2561
gray matter5.39e-2434
brain grey matter5.39e-2434
telencephalon6.92e-2434
regional part of telencephalon3.72e-2333
cerebral hemisphere7.14e-2332
head4.99e-21123
anterior region of body5.14e-20129
craniocervical region5.14e-20129
cerebral cortex1.57e-1825
pallium1.57e-1825
organism subdivision2.96e-18365
adult organism4.43e-18115
regional part of cerebral cortex1.61e-1722
neocortex3.20e-1620
tube1.69e-13194
multi-cellular organism6.67e-13659
organ part1.25e-12219
epithelium5.48e-12309
cell layer2.20e-11312
anatomical conduit2.66e-11241
anatomical system5.61e-11625
anatomical group8.25e-11626
anatomical cluster3.82e-09286
embryo4.11e-09612
multi-tissue structure5.05e-09347
organ8.05e-09511
embryonic structure5.78e-08605
developing anatomical structure5.78e-08605
germ layer1.04e-07604
embryonic tissue1.04e-07604
presumptive structure1.04e-07604
epiblast (generic)1.04e-07604
posterior neural tube2.70e-0715
chordal neural plate2.70e-0715
temporal lobe5.47e-077
basal ganglion6.45e-079
nuclear complex of neuraxis6.45e-079
aggregate regional part of brain6.45e-079
collection of basal ganglia6.45e-079
cerebral subcortex6.45e-079
nucleus of brain6.54e-079
neural nucleus6.54e-079


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
JUND#372735.245997956403270.01043432751748420.0387150323859078
NANOG#79923321.93358386075950.0001557535816382770.00196553266224263
RAD21#588537.766275421592250.0033411193858720.0172761247421074
RXRA#6256315.055962854350.0004758307997303580.00434020025266715
TAF1#687243.343046285745290.008005664898701650.032311935243295
TCF12#693837.975848676639820.003090920396013070.0162880385104803



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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