Personal tools

Coexpression cluster:C2011

From FANTOM5_SSTAR

Revision as of 11:58, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2011_mucinous_mesothelioma_squamous_glioblastoma_anaplastic_Mallassezderived_amniotic



Phase1 CAGE Peaks

Hg19::chr8:38261817..38261833,+p4@LETM2
Hg19::chr8:38261837..38261848,+p6@LETM2
Hg19::chr8:38261849..38261864,+p2@LETM2
Hg19::chr8:38261866..38261877,+p5@LETM2
Hg19::chr8:38261880..38261914,+p3@LETM2


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
epithelial cell2.16e-29253
embryonic cell1.27e-22250
animal cell6.52e-21679
eukaryotic cell6.52e-21679
mesodermal cell4.97e-15121
squamous epithelial cell5.19e-1563
native cell6.58e-15722
lining cell7.15e-1158
barrier cell7.15e-1158
mesothelial cell1.81e-1019
endo-epithelial cell1.58e-0942
somatic cell1.42e-08588
respiratory epithelial cell1.51e-0713
endodermal cell2.73e-0758
Uber Anatomy
Ontology termp-valuen
unilaminar epithelium1.31e-08148
surface structure7.26e-0899
epithelial tube8.16e-08117
organism subdivision1.67e-07264
vasculature1.97e-0778
vascular system1.97e-0778
cell layer5.46e-07309
vessel6.82e-0768
multilaminar epithelium8.96e-0783
splanchnic layer of lateral plate mesoderm9.99e-0783


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
BCL3#602534.54710280373832.02839878970325e-081.44801053450319e-06
EGR1#195854.988179094810140.0003237398000590710.00331188764603481
FOS#235358.99795530889441.69470025615156e-050.000390023799145467
FOSL1#8061539.7135797163731.01017090471068e-087.65611314347454e-07
FOSL2#2355516.93020060456177.18315284751475e-073.21147816884244e-05
JUN#3725512.51282919233633.25800591331781e-060.000109303848243174
JUND#372756.994663941871035.97069468343598e-050.00098573092324276



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.