Personal tools

Coexpression cluster:C3610

From FANTOM5_SSTAR

Revision as of 15:15, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3610_osteosarcoma_Mesenchymal_Renal_thyroid_Adipocyte_Fibroblast_Melanocyte



Phase1 CAGE Peaks

Hg19::chr17:17494903..17494943,-p2@PEMT
Hg19::chr17:17494948..17494966,-p3@PEMT
Hg19::chr17:17494972..17495037,-p1@PEMT


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
non-terminally differentiated cell3.95e-11106
epithelial cell3.81e-10253
embryonic cell1.16e-09250
fibroblast3.42e-0876
fat cell3.57e-0715
contractile cell3.67e-0759
Uber Anatomy
Ontology termp-valuen
multi-tissue structure2.21e-11342
cell layer4.43e-10309
organism subdivision4.62e-10264
epithelium1.01e-09306
anatomical cluster2.83e-09373
organ part5.82e-09218
multi-cellular organism1.98e-08656
trunk2.46e-08199
epithelial vesicle3.35e-0778
primordium9.57e-07160


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
BCLAF1#9774321.65264761012189.8473954032885e-050.0013911160943109
CHD2#1106310.34402283411690.0009033701102746880.00659862015295693
CTCFL#140690319.74647435897440.0001298372005551160.00171559557044228
E2F1#186934.907389214879320.008460985347239390.0324814132946273
E2F6#187635.017155731697390.00791769806886330.0321632232055237
EGR1#195834.988179094810140.008056488137383440.0320159645591944
ELF1#199734.258097958807540.01295179875054610.0461600092038044
ELK4#2005316.2356816584680.0002336043955745990.00255577304309821
ESR1#2099330.76860329615453.43136389821584e-050.000675401835970154
ETS1#211339.728760922202340.001085840092584840.0076140763683005
GABPB1#255337.067683836182170.002832212825417420.0153930826016741
GATA1#2623313.56030814380040.0004009615963782630.00387561574864872
IRF1#365937.63716375356390.002244692747297240.0127910009731
JUND#372736.994663941871030.002921845042734990.0156537690785985
MAX#414936.452555509007120.003721913834265510.0186316905016946
MYC#460935.22228187160940.007020843755740150.0294135304667554
NFKB1#479035.488063424193840.006049381815655430.0269305791749888
NR2C2#7182332.61461090524092.88098172333076e-050.000604676145906233
PAX5#507936.669565531177830.003370290999677260.017274726232592
POU2F2#545239.106124057742520.001324165192682130.00881361854302014
SIN3A#2594235.408884726815140.006318961977991520.0276278339690818
SIX5#147912317.0867153554590.0002004060546325010.00239503466526648
SMARCC2#6601394.15537442689761.19621075407887e-064.84980803358862e-05
SP1#666735.69838137814090.005403962701712170.0246155120640316
SRF#6722313.79717826216780.0003806615025800190.00374702230612202
TCF7L2#6934310.77017656313730.0008003181298398380.00612833969956323
TFAP2C#7022310.80922860986020.0007916746575753130.00614871046051224
TRIM28#10155318.59052504526250.0001555969297255280.00196902795875492
USF1#739136.361499277207960.00388404057290560.0190051215045768
YY1#752834.911170749853860.008441455341808260.0328875724416426
ZBTB7A#5134137.35190930787590.002516255860282270.0139978292208384
ZEB1#6935316.88843201754390.0002075486917327580.00242544229784911
ZNF143#7702313.50087655222790.0004062804962997170.00388673891664799



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.