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Coexpression cluster:C1871

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Full id: C1871_breast_MCF7_clear_renal_amniotic_leiomyoblastoma_choriocarcinoma



Phase1 CAGE Peaks

Hg19::chr20:49347993..49348004,+p7@PARD6B
Hg19::chr20:49348006..49348019,+p5@PARD6B
Hg19::chr20:49348020..49348069,+p2@PARD6B
Hg19::chr20:49348083..49348096,+p3@PARD6B
Hg19::chr20:49367522..49367525,+p@chr20:49367522..49367525
+


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>disease_data<br>


Cell Type
Ontology termp-valuen
epithelial cell1.19e-17254
endodermal cell2.19e-0959
Disease
Ontology termp-valuen
carcinoma1.47e-31106
cell type cancer1.74e-31143
cancer7.30e-28235
disease of cellular proliferation5.98e-27239
adenocarcinoma3.25e-1125
organ system cancer4.68e-09137
disease of anatomical entity1.69e-0839


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
BHLHE40#8553217.9487254187910.004747812859838950.0223188021455966
CCNT2#90545.068961261570110.002709998091280770.0148994257030571
CEBPB#105146.376918100659850.001113944176677320.00765641433813769
CHD2#110648.275218267293490.0004028373567101730.00387866974255128
E2F1#186943.925911371903460.007214984547106360.0298792882792831
E2F6#187644.013724585357910.006632118233933880.0283015361703776
EGR1#195843.990543275848110.0067800983001440.0287696211907829
FOS#235347.198364247115530.0006947858453382510.00559811286076852
HDAC2#3066410.7324961893010.0001450965797478750.00188643616236627
HMGN3#932446.542838178680470.00100801277768350.00722155621405455
IRF1#365946.109731002851120.001315525264767990.00881170748634585
MAX#414945.16204440720570.002526309009485180.0140008058711394
MXI1#460147.969257303007440.0004668546380070170.00429584418844184
NFKB1#479044.390450739355070.004707732692524960.0222083605706949
NFYB#4801413.40783460282926.03169250119439e-050.000991725335535643
NRF1#489949.768223558168730.0002101297748106790.00244548067210302
RFX5#599349.638328661756080.000221480125815720.0024976960220352
SIN3A#2594244.327107781452110.004977052855762880.0232478385975678
SP1#666744.558705102512720.00407573565781680.01948929794271
SP2#6668420.92282439507571.03516506540382e-050.000269470598867671
TAF7#687949.146455523939130.0002720662872412990.00290327280813263
TCF12#693848.507571921749140.0003614215578492260.0036124515341387
USF1#739145.089199421766370.00266867775360040.0147210709295026
USF2#7392410.39375790805570.0001646179728687530.00202694370059417
ZEB1#6935413.51074561403515.85221769500384e-050.00096708823393751



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.