Personal tools

Coexpression cluster:C563

From FANTOM5_SSTAR

Revision as of 16:25, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C563_Mesenchymal_Fibroblast_Adipocyte_tenocyte_Placental_Hair_Synoviocyte



Phase1 CAGE Peaks

Hg19::chr11:66082644..66082662,-p@chr11:66082644..66082662
-
Hg19::chr11:66082821..66082867,+p@chr11:66082821..66082867
+
Hg19::chr11:66082875..66082914,-p@chr11:66082875..66082914
-
Hg19::chr11:66082877..66082889,+p@chr11:66082877..66082889
+
Hg19::chr11:66082890..66082979,+p@chr11:66082890..66082979
+
Hg19::chr11:66082918..66082935,-p@chr11:66082918..66082935
-
Hg19::chr11:66083010..66083055,-p@chr11:66083010..66083055
-
Hg19::chr11:66083107..66083156,-p4@CD248
Hg19::chr11:66083180..66083195,-p8@CD248
Hg19::chr11:66083196..66083252,-p2@CD248
Hg19::chr11:66083335..66083379,+p@chr11:66083335..66083379
+
Hg19::chr11:66083418..66083442,-p3@CD248
Hg19::chr11:66083457..66083472,-p7@CD248
Hg19::chr11:66083621..66083639,-p5@CD248
Hg19::chr11:66084059..66084071,-p12@CD248
Hg19::chr11:66084508..66084523,-p1@CD248


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>


Uber Anatomy
Ontology termp-valuen
dense mesenchyme tissue4.75e-1973
somite6.31e-1971
presomitic mesoderm6.31e-1971
presumptive segmental plate6.31e-1971
dermomyotome6.31e-1971
trunk paraxial mesoderm6.31e-1971
paraxial mesoderm2.24e-1872
presumptive paraxial mesoderm2.24e-1872
multilaminar epithelium4.67e-1683
muscle tissue4.78e-1664
musculature4.78e-1664
musculature of body4.78e-1664
skeletal muscle tissue1.53e-1562
striated muscle tissue1.53e-1562
myotome1.53e-1562
epithelial vesicle2.05e-1578
integument5.81e-1346
integumental system5.81e-1346
trunk mesenchyme1.33e-11122
adipose tissue2.50e-1114
surface structure6.98e-1199
mesenchyme1.13e-10160
entire embryonic mesenchyme1.13e-10160
organ component layer1.48e-1066
skin of body8.58e-1041
connective tissue3.39e-08371
mesoderm7.42e-08315
mesoderm-derived structure7.42e-08315
presumptive mesoderm7.42e-08315
tissue1.17e-07773
organism subdivision1.80e-07264
unilaminar epithelium2.79e-07148
extraembryonic membrane8.85e-0714
membranous layer8.85e-0714


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


No analysis results for this cluster

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.