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Coexpression cluster:C2797

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Full id: C2797_medulloblastoma_neuroectodermal_peripheral_pineal_carcinoid_neuroepithelioma_small



Phase1 CAGE Peaks

Hg19::chr4:87515454..87515486,+p1@PTPN13
Hg19::chr4:87515493..87515510,+p2@PTPN13
Hg19::chr4:87521610..87521614,+p@chr4:87521610..87521614
+
Hg19::chr4:87526137..87526140,+p@chr4:87526137..87526140
+


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
skin fibroblast4.60e-0923
fibroblast1.64e-0775
Uber Anatomy
Ontology termp-valuen
ectoderm3.40e-24173
presumptive ectoderm3.40e-24173
ectoderm-derived structure4.42e-22169
head4.65e-20123
organism subdivision9.56e-20365
anterior region of body1.86e-19129
craniocervical region1.86e-19129
surface structure8.04e-1795
regional part of nervous system1.45e-1694
nervous system1.45e-1694
central nervous system1.62e-1482
neurectoderm7.87e-1390
neural tube2.17e-1257
neural rod2.17e-1257
future spinal cord2.17e-1257
neural keel2.17e-1257
brain4.04e-1269
future brain4.04e-1269
regional part of forebrain1.09e-1141
forebrain1.09e-1141
future forebrain1.09e-1141
regional part of brain1.83e-1159
anterior neural tube2.23e-1142
pre-chordal neural plate3.45e-1161
neural plate5.89e-1186
presumptive neural plate5.89e-1186
adult organism1.51e-09115
multi-cellular organism1.70e-09659
multi-tissue structure3.92e-09347
skin of body6.25e-0940
gray matter1.16e-0834
brain grey matter1.16e-0834
subdivision of head1.60e-0848
telencephalon1.67e-0834
orifice2.19e-0835
regional part of telencephalon2.26e-0833
mouth2.51e-0828
stomodeum2.51e-0828
organ2.96e-08511
integument3.36e-0845
integumental system3.36e-0845
cerebral hemisphere1.19e-0732
organ part1.40e-07219


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
PBX3#5090210.95725634337210.01174530180688030.0428634976381569
RFX5#599339.035933120396320.002144561191324070.0123873583463688
SMARCC1#6599221.83167965981570.003051207456162050.0160933819258678



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.