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Coexpression cluster:C1823

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Full id: C1823_acute_CD4_Neutrophils_thymus_Whole_CD8_duodenum



Phase1 CAGE Peaks

Hg19::chr19:42400575..42400597,+p10@ARHGEF1
Hg19::chr19:42400603..42400645,+p3@ARHGEF1
Hg19::chr19:42400648..42400676,+p9@ARHGEF1
Hg19::chr19:42400678..42400701,+p4@ARHGEF1
Hg19::chr19:42400731..42400770,+p7@ARHGEF1


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
adult organism1.68e-21115
neural tube4.29e-1457
neural rod4.29e-1457
future spinal cord4.29e-1457
neural keel4.29e-1457
anterior neural tube9.91e-1242
regional part of forebrain1.54e-1141
forebrain1.54e-1141
future forebrain1.54e-1141
central nervous system9.09e-1182
regional part of brain2.62e-1059
brain9.47e-1069
future brain9.47e-1069
regional part of nervous system1.71e-0994
nervous system1.71e-0994
gray matter4.96e-0934
brain grey matter4.96e-0934
hematopoietic system8.72e-09102
blood island8.72e-09102
regional part of telencephalon1.17e-0833
telencephalon1.20e-0834
blood2.34e-0815
haemolymphatic fluid2.34e-0815
organism substance2.34e-0815
neurectoderm5.94e-0890
cerebral hemisphere1.03e-0732
regional part of cerebral cortex3.35e-0722
neural plate3.38e-0786
presumptive neural plate3.38e-0786
hemolymphoid system7.03e-07112
Disease
Ontology termp-valuen
hematologic cancer2.32e-0851
immune system cancer2.32e-0851
leukemia1.53e-0739


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
CTCF#1066455.360256373075030.0002259278299937090.00249848333722077
MYC#460944.177825497287520.005691969036823440.02568320894482



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.