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Coexpression cluster:C1016

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Full id: C1016_Mesenchymal_Synoviocyte_tenocyte_lung_mesenchymal_diaphragm_breast



Phase1 CAGE Peaks

Hg19::chr12:48214345..48214362,-p3@HDAC7
Hg19::chr3:45067659..45067668,+p5@CLEC3B
Hg19::chr3:45067692..45067699,+p6@CLEC3B
Hg19::chr3:45067704..45067715,+p4@CLEC3B
Hg19::chr3:45067739..45067785,+p2@CLEC3B
Hg19::chr3:45067788..45067806,+p1@CLEC3B
Hg19::chr3:45067865..45067876,+p3@CLEC3B
Hg19::chr3:45077112..45077116,+p@chr3:45077112..45077116
+


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


GO IDGO nameFDR corrected p-value
GO:0001501skeletal development0.0422112327799364
GO:0005529sugar binding0.0422112327799364
GO:0030246carbohydrate binding0.0422112327799364



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
fibroblast6.75e-1175
non-terminally differentiated cell4.56e-09180
fat cell4.76e-0815
Uber Anatomy
Ontology termp-valuen
adult organism1.24e-30115
regional part of brain1.86e-1359
neural tube1.73e-1257
neural rod1.73e-1257
future spinal cord1.73e-1257
neural keel1.73e-1257
organism subdivision8.13e-12365
brain1.01e-1069
future brain1.01e-1069
multi-cellular organism1.59e-10659
central nervous system2.23e-1082
neural plate2.42e-0986
presumptive neural plate2.42e-0986
anterior neural tube3.28e-0942
neurectoderm5.03e-0990
tissue8.04e-09787
anterior region of body1.06e-08129
craniocervical region1.06e-08129
regional part of forebrain1.10e-0841
forebrain1.10e-0841
future forebrain1.10e-0841
head1.95e-08123
anatomical system1.99e-08625
ectoderm-derived structure2.17e-08169
anatomical group2.43e-08626
multi-tissue structure2.72e-08347
ectoderm2.92e-08173
presumptive ectoderm2.92e-08173
regional part of nervous system3.57e-0894
nervous system3.57e-0894
anatomical cluster4.33e-08286
organ5.17e-08511
gray matter2.79e-0734
brain grey matter2.79e-0734
telencephalon3.01e-0734
regional part of telencephalon4.54e-0733
cerebral hemisphere5.72e-0732


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
EGR1#195874.364656707958878.58120841941444e-050.00128599917651776



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.