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Coexpression cluster:C4414

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Full id: C4414_chronic_smallcell_neuroblastoma_testis_iPS_testicular_acute



Phase1 CAGE Peaks

Hg19::chr4:42154262..42154274,-p9@BEND4
Hg19::chr4:42154275..42154297,-p3@BEND4
Hg19::chr4:42154395..42154413,-p2@BEND4


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
B cell2.18e-1214
lymphocyte of B lineage2.14e-1024
pro-B cell2.14e-1024
neuron4.23e-076
neuroblast4.23e-076
electrically signaling cell4.23e-076
neuronal stem cell8.43e-078
Uber Anatomy
Ontology termp-valuen
regional part of nervous system5.34e-1994
nervous system5.34e-1994
central nervous system3.28e-1882
cerebral cortex5.92e-1525
pallium5.92e-1525
gray matter1.55e-1434
brain grey matter1.55e-1434
telencephalon2.72e-1434
brain5.87e-1469
future brain5.87e-1469
regional part of telencephalon1.23e-1333
cerebral hemisphere1.44e-1332
regional part of forebrain1.97e-1341
forebrain1.97e-1341
future forebrain1.97e-1341
regional part of cerebral cortex4.85e-1322
anterior neural tube6.75e-1342
adult organism6.86e-13115
neural tube1.86e-1257
neural rod1.86e-1257
future spinal cord1.86e-1257
neural keel1.86e-1257
neocortex1.80e-1120
pre-chordal neural plate5.01e-1161
regional part of brain6.84e-1159
neural plate6.98e-1086
presumptive neural plate6.98e-1086
neurectoderm1.94e-0990
ectoderm-derived structure7.71e-07169


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#5090321.91451268674419.49854535978121e-050.00137227635749093



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.