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Coexpression cluster:C3252: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3252_CD14_hepatoblastoma_pineal_CD4_pituitary_thymus_rectal
|full_id=C3252_CD14_hepatoblastoma_pineal_CD4_pituitary_thymus_rectal
|id=C3252
|id=C3252

Revision as of 16:08, 12 September 2012


Full id: C3252_CD14_hepatoblastoma_pineal_CD4_pituitary_thymus_rectal



Phase1 CAGE Peaks

Hg19::chr12:12715613..12715624,-p6@DUSP16
Hg19::chr12:12715763..12715778,-p3@DUSP16
Hg19::chr12:12715789..12715806,-p1@DUSP16


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
leukocyte2.81e-09140
CD14-positive, CD16-negative classical monocyte2.30e-0842
classical monocyte1.14e-0745
mature alpha-beta T cell2.53e-0718
alpha-beta T cell2.53e-0718
immature T cell2.53e-0718
mature T cell2.53e-0718
immature alpha-beta T cell2.53e-0718
Uber Anatomy
Ontology termp-valuen
adult organism2.05e-16115
subdivision of digestive tract1.75e-09129
endodermal part of digestive tract1.75e-09129
foregut4.96e-0898
mixed endoderm/mesoderm-derived structure5.06e-08130
digestive system6.63e-08155
digestive tract6.63e-08155
primitive gut6.63e-08155
endoderm-derived structure1.02e-07169
endoderm1.02e-07169
presumptive endoderm1.02e-07169
hemolymphoid system5.95e-07112
hematopoietic system6.22e-07102
blood island6.22e-07102
Disease
Ontology termp-valuen
carcinoma9.21e-07106


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
BCL11A#53335328.36945510360714.37778126761649e-050.000776909257108918
CCNT2#90536.336201576962630.003930750035764890.0189364639967364
CEBPB#105137.971147625824820.001974187055288560.0114992817550073
CTCF#1066435.360256373075030.0064925092527670.0278583062386908
CTCFL#140690319.74647435897440.0001298372005551160.00171321129359138
E2F1#186934.907389214879320.008460985347239390.0323968634946596
E2F6#187635.017155731697390.00791769806886330.032079624029717
EBF1#187938.9064668465690.00141523283560980.0091299958069215
EGR1#195834.988179094810140.008056488137383440.0319381880652947
ELF1#199734.258097958807540.01295179875054610.0460468719263441
EP300#203336.77394172622320.003216880500103790.0167015203097206
HMGN3#932438.178547723350590.001827766942164210.0108417192975912
HNF4A#3172323.13229036295378.07584663437677e-050.00122538623659404
JUN#3725312.51282919233630.0005103313992726250.00443304508098093
JUND#372736.994663941871030.002921845042734990.0156281150475366
MEF2C#4208341.31135449262411.41744912101957e-050.000340080332529664
NFKB1#479035.488063424193840.006049381815655430.0268778774544898
NR3C1#2908314.9730233311730.0002978331194675480.00308126727727303
POU2F2#545239.106124057742520.001324165192682130.00880127846741736
RAD21#5885310.35503389545630.0009004912073565420.00662251962573832
RFX5#5993312.04791082719510.0005717246050312580.00483406298776389
TFAP2C#7022310.80922860986020.0007916746575753130.00613638930996795
ZBTB7A#5134137.35190930787590.002516255860282270.0139732677084075
ZNF263#1012738.221841637010680.001799043925565870.0108985120964138



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.

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