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Coexpression cluster:C2262

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Full id: C2262_neuroectodermal_extraskeletal_neuroblastoma_B_carcinoid_plasma_choriocarcinoma



Phase1 CAGE Peaks

Hg19::chr13:33780076..33780094,-p5@STARD13
Hg19::chr13:33780107..33780116,-p9@STARD13
Hg19::chr13:33780118..33780132,-p7@STARD13
Hg19::chr13:33780133..33780168,-p2@STARD13


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
adult organism1.65e-36114
neurectoderm3.68e-1986
neural tube5.35e-1956
neural rod5.35e-1956
future spinal cord5.35e-1956
neural keel5.35e-1956
brain grey matter1.56e-1734
gray matter1.56e-1734
nervous system2.03e-1789
telencephalon3.32e-1734
regional part of nervous system3.76e-1753
regional part of brain3.76e-1753
organ system subdivision6.79e-17223
regional part of forebrain7.36e-1741
forebrain7.36e-1741
anterior neural tube7.36e-1741
future forebrain7.36e-1741
cerebral hemisphere9.74e-1732
brain1.69e-1668
future brain1.69e-1668
neural plate2.32e-1682
presumptive neural plate2.32e-1682
regional part of telencephalon3.55e-1632
central nervous system1.11e-1581
ectoderm-derived structure1.19e-15171
ectoderm1.19e-15171
presumptive ectoderm1.19e-15171
neocortex5.87e-1520
regional part of cerebral cortex8.69e-1522
structure with developmental contribution from neural crest1.93e-14132
cerebral cortex2.61e-1325
pallium2.61e-1325
pre-chordal neural plate1.29e-1161
ecto-epithelium1.77e-11104
anatomical cluster6.21e-11373
multi-tissue structure8.72e-11342
temporal lobe1.72e-076
gyrus7.60e-076


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
EP300#203346.77394172622320.0004748459821442640.00433651972098328
NFKB1#479045.488063424193840.001102199566301980.00767110625783102
TAF1#687243.343046285745290.008005664898701650.0321541220765105
TBP#690843.706770687096390.005296377814784350.0243709918755017



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.