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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3556_immature_Basophils_CD8_Natural_Peripheral_adult_CD4
|full_id=C3556_immature_Basophils_CD8_Natural_Peripheral_adult_CD4
|gostat_on_coexpression_clusters=GO:0006369!transcription termination from RNA polymerase II promoter!0.00153067231837984!4150$GO:0006353!transcription termination!0.00535735311432945!4150$GO:0043624!cellular protein complex disassembly!0.00857176498292712!4150$GO:0043241!protein complex disassembly!0.00857176498292712!4150$GO:0032984!macromolecular complex disassembly!0.00857176498292712!4150$GO:0022411!cellular component disassembly!0.0111520411767674!4150$GO:0006367!transcription initiation from RNA polymerase II promoter!0.0111520411767674!4150$GO:0006352!transcription initiation!0.0174113976215707!4150$GO:0003702!RNA polymerase II transcription factor activity!0.0431649593783116!4150$GO:0065004!protein-DNA complex assembly!0.0431649593783116!4150
|gostat_on_coexpression_clusters=GO:0006369!transcription termination from RNA polymerase II promoter!0.00153067231837984!4150$GO:0006353!transcription termination!0.00535735311432945!4150$GO:0043624!cellular protein complex disassembly!0.00857176498292712!4150$GO:0043241!protein complex disassembly!0.00857176498292712!4150$GO:0032984!macromolecular complex disassembly!0.00857176498292712!4150$GO:0022411!cellular component disassembly!0.0111520411767674!4150$GO:0006367!transcription initiation from RNA polymerase II promoter!0.0111520411767674!4150$GO:0006352!transcription initiation!0.0174113976215707!4150$GO:0003702!RNA polymerase II transcription factor activity!0.0431649593783116!4150$GO:0065004!protein-DNA complex assembly!0.0431649593783116!4150

Revision as of 16:30, 12 September 2012


Full id: C3556_immature_Basophils_CD8_Natural_Peripheral_adult_CD4



Phase1 CAGE Peaks

Hg19::chr16:29819579..29819591,+p32@MAZ
Hg19::chr16:29819630..29819645,+p37@MAZ
Hg19::chr5:14664931..14664942,+p6@FAM105B


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:0006369transcription termination from RNA polymerase II promoter0.00153067231837984
GO:0006353transcription termination0.00535735311432945
GO:0043624cellular protein complex disassembly0.00857176498292712
GO:0043241protein complex disassembly0.00857176498292712
GO:0032984macromolecular complex disassembly0.00857176498292712
GO:0022411cellular component disassembly0.0111520411767674
GO:0006367transcription initiation from RNA polymerase II promoter0.0111520411767674
GO:0006352transcription initiation0.0174113976215707
GO:0003702RNA polymerase II transcription factor activity0.0431649593783116
GO:0065004protein-DNA complex assembly0.0431649593783116



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>


Disease
Ontology termp-valuen
hematologic cancer3.19e-0751
immune system cancer3.19e-0751


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
CCNT2#90536.336201576962630.003930750035764890.0189740988623243
CTCFL#140690213.16431623931620.007433367036996010.0306766278095715
EGR1#195834.988179094810140.008056488137383440.0320050043583183
ELF1#199734.258097958807540.01295179875054610.0461379667681385
HMGN3#932438.178547723350590.001827766942164210.0108577527827023
IRF1#365937.63716375356390.002244692747297240.0127868149795449
SMC3#9126210.02995522995520.0126656379767470.045731601198046
ZNF263#1012738.221841637010680.001799043925565870.0109238574733822



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.