Personal tools

Coexpression cluster:C3508

From FANTOM5_SSTAR

Revision as of 04:00, 5 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3508_hepatoblastoma_non_neuroepithelioma_fibrous_Reticulocytes_myxofibrosarcoma_Fibroblast



Phase1 CAGE Peaks

Hg19::chr15:69706617..69706641,+p3@KIF23
Hg19::chr1:68962744..68962772,-p1@DEPDC1
Hg19::chr1:68962782..68962801,-p3@DEPDC1


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:0051231spindle elongation0.00359113989022636
GO:0000022mitotic spindle elongation0.00359113989022636
GO:0007052mitotic spindle organization and biogenesis0.0131657686583527
GO:0007051spindle organization and biogenesis0.0170536462966801
GO:0005871kinesin complex0.020102687443671
GO:0005819spindle0.0466325961121085



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><br>disease_data<br>


Cell Type
Ontology termp-valuen
epithelial cell9.48e-14254
animal cell1.45e-12679
eukaryotic cell1.45e-12679
non-terminally differentiated cell6.26e-11180
embryonic cell5.15e-08248
neurectodermal cell2.91e-0759
migratory neural crest cell4.78e-0741
Disease
Ontology termp-valuen
cancer1.51e-56235
disease of cellular proliferation4.14e-56239
cell type cancer4.43e-32143
organ system cancer9.03e-24137
carcinoma7.82e-21106
hematologic cancer9.85e-1551
immune system cancer9.85e-1551
leukemia4.25e-1239
myeloid leukemia9.10e-1031
germ cell and embryonal cancer5.13e-0822
germ cell cancer5.13e-0822
sarcoma5.93e-0820
disease of anatomical entity2.07e-0739


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
ATF3#467214.97544968400580.005768294540793880.0259524797977845
E2F1#186934.907389214879320.008460985347239390.0324587440743585
E2F4#1874312.66806031528440.0004917987006298980.00436425902753726
E2F6#187635.017155731697390.00791769806886330.0321432196460396
ELF1#199734.258097958807540.01295179875054610.0461253805397355
ETS1#211339.728760922202340.001085840092584840.00761049952549948
FOS#235338.99795530889440.001372499272417130.00896450603577064
MAX#414936.452555509007120.003721913834265510.0186227642857689
NFE2#4778251.4695071010860.0004987653528392110.00440586608180448
NFYA#4800318.42558069983050.0001598135507814160.00199292745433556
NFYB#4801316.75979325353650.0002123649923296180.00245426440565597
SETDB1#9869226.8800174520070.001814468907964410.0108921323300894
SIN3A#2594235.408884726815140.006318961977991520.0276058759315426
SP1#666735.69838137814090.005403962701712170.0246015631665628
TAF7#6879311.43306940492390.0006690181981945830.00541766237119052



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.