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Coexpression cluster:C4604

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Full id: C4604_Placental_Amniotic_osteosarcoma_Fibroblast_Mesenchymal_Pericytes_Osteoblast



Phase1 CAGE Peaks

Hg19::chr6:43044003..43044086,+p1@PTK7
Hg19::chr6:43044168..43044181,+p3@PTK7
Hg19::chr6:43044196..43044216,+p2@PTK7


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
embryonic cell3.28e-17250
fibroblast4.22e-1676
somatic cell1.60e-11588
animal cell1.90e-11679
eukaryotic cell1.90e-11679
non-terminally differentiated cell2.64e-10106
ectodermal cell1.09e-0972
epithelial cell1.32e-08253
contractile cell3.63e-0859
skin fibroblast4.80e-0823
ecto-epithelial cell1.67e-0734
single fate stem cell8.56e-0720
Uber Anatomy
Ontology termp-valuen
organism subdivision4.27e-16264
surface structure1.97e-1599
skin of body2.53e-1241
multi-cellular organism1.29e-11656
integument1.36e-1146
integumental system1.36e-1146
trunk6.14e-10199
mesenchyme1.12e-09160
entire embryonic mesenchyme1.12e-09160
multilaminar epithelium5.85e-0983
ectodermal placode8.61e-0931
cell layer1.73e-08309
organ component layer2.17e-0866
anatomical system3.29e-08624
epithelium4.02e-08306
epithelial vesicle4.73e-0878
anatomical group5.44e-08625
head1.33e-0756
multi-tissue structure2.05e-07342
subdivision of head4.10e-0749
trunk mesenchyme5.06e-07122
urinary system structure7.23e-0747
dense mesenchyme tissue9.55e-0773
organ part9.59e-07218


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
E2F1#186934.907389214879320.008460985347239390.0327437969644768
EGR1#195834.988179094810140.008056488137383440.0322281126313846
SP1#666735.69838137814090.005403962701712170.024776524895918
ZBTB7A#5134137.35190930787590.002516255860282270.0140841012804555



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.