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Coexpression cluster:C3960: Difference between revisions

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|ontology_enrichment_disease=DOID:8692!2.02e-09!31;DOID:1240!6.77e-07!39
|ontology_enrichment_disease=DOID:8692!2.02e-09!31;DOID:1240!6.77e-07!39
|ontology_enrichment_uberon=UBERON:0002020!6.38e-11!34;UBERON:0003528!6.38e-11!34;UBERON:0001869!1.64e-10!32;UBERON:0001893!2.40e-10!34;UBERON:0003075!2.62e-10!86;UBERON:0007284!2.62e-10!86;UBERON:0000178!3.23e-10!15;UBERON:0000179!3.23e-10!15;UBERON:0000463!3.23e-10!15;UBERON:0002791!6.69e-10!33;UBERON:0001049!6.91e-10!57;UBERON:0005068!6.91e-10!57;UBERON:0006241!6.91e-10!57;UBERON:0007135!6.91e-10!57;UBERON:0002346!9.78e-10!90;UBERON:0002616!3.26e-09!59;UBERON:0002780!4.11e-09!41;UBERON:0001890!4.11e-09!41;UBERON:0006240!4.11e-09!41;UBERON:0007023!8.89e-09!115;UBERON:0002619!9.57e-09!22;UBERON:0003080!1.30e-08!42;UBERON:0005743!1.84e-08!86;UBERON:0000073!1.94e-08!94;UBERON:0001016!1.94e-08!94;UBERON:0000956!4.01e-08!25;UBERON:0000203!4.01e-08!25;UBERON:0001950!4.63e-08!20;UBERON:0000955!6.18e-08!69;UBERON:0006238!6.18e-08!69;UBERON:0003056!7.59e-08!61;UBERON:0001017!2.57e-07!82
|ontology_enrichment_uberon=UBERON:0002020!6.38e-11!34;UBERON:0003528!6.38e-11!34;UBERON:0001869!1.64e-10!32;UBERON:0001893!2.40e-10!34;UBERON:0003075!2.62e-10!86;UBERON:0007284!2.62e-10!86;UBERON:0000178!3.23e-10!15;UBERON:0000179!3.23e-10!15;UBERON:0000463!3.23e-10!15;UBERON:0002791!6.69e-10!33;UBERON:0001049!6.91e-10!57;UBERON:0005068!6.91e-10!57;UBERON:0006241!6.91e-10!57;UBERON:0007135!6.91e-10!57;UBERON:0002346!9.78e-10!90;UBERON:0002616!3.26e-09!59;UBERON:0002780!4.11e-09!41;UBERON:0001890!4.11e-09!41;UBERON:0006240!4.11e-09!41;UBERON:0007023!8.89e-09!115;UBERON:0002619!9.57e-09!22;UBERON:0003080!1.30e-08!42;UBERON:0005743!1.84e-08!86;UBERON:0000073!1.94e-08!94;UBERON:0001016!1.94e-08!94;UBERON:0000956!4.01e-08!25;UBERON:0000203!4.01e-08!25;UBERON:0001950!4.63e-08!20;UBERON:0000955!6.18e-08!69;UBERON:0006238!6.18e-08!69;UBERON:0003056!7.59e-08!61;UBERON:0001017!2.57e-07!82
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190198111093981!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00171885757241422!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322535481946335!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320904486872689!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00762893060406779!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.0038813632555519!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108787913416931!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277055445012366!THAP1#55145;3:31.3691446028513:3.23800758564397e-05:0.000647347385599293!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329712088875094!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140329602067613
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}}
}}

Revision as of 14:24, 5 September 2012


Full id: C3960_mesothelioma_cholangiocellular_Reticulocytes_thyroid_granulosa_papillary_Whole



Phase1 CAGE Peaks

Hg19::chr1:248020569..248020580,+p6@TRIM58
Hg19::chr1:248020587..248020624,+p2@TRIM58
Hg19::chr1:248020627..248020645,+p4@TRIM58


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
mesothelial cell1.46e-1219
Uber Anatomy
Ontology termp-valuen
gray matter6.38e-1134
brain grey matter6.38e-1134
cerebral hemisphere1.64e-1032
telencephalon2.40e-1034
neural plate2.62e-1086
presumptive neural plate2.62e-1086
blood3.23e-1015
haemolymphatic fluid3.23e-1015
organism substance3.23e-1015
regional part of telencephalon6.69e-1033
neural tube6.91e-1057
neural rod6.91e-1057
future spinal cord6.91e-1057
neural keel6.91e-1057
neurectoderm9.78e-1090
regional part of brain3.26e-0959
regional part of forebrain4.11e-0941
forebrain4.11e-0941
future forebrain4.11e-0941
adult organism8.89e-09115
regional part of cerebral cortex9.57e-0922
anterior neural tube1.30e-0842
regional part of nervous system1.94e-0894
nervous system1.94e-0894
cerebral cortex4.01e-0825
pallium4.01e-0825
neocortex4.63e-0820
brain6.18e-0869
future brain6.18e-0869
pre-chordal neural plate7.59e-0861
central nervous system2.57e-0782
Disease
Ontology termp-valuen
myeloid leukemia2.02e-0931
leukemia6.77e-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
CCNT2#90536.336201576962630.003930750035764890.0190198111093981
CTCFL#140690319.74647435897440.0001298372005551160.00171885757241422
E2F6#187635.017155731697390.00791769806886330.0322535481946335
EGR1#195834.988179094810140.008056488137383440.0320904486872689
ETS1#211339.728760922202340.001085840092584840.00762893060406779
GATA1#2623313.56030814380040.0004009615963782630.0038813632555519
HMGN3#932438.178547723350590.001827766942164210.0108787913416931
SIN3A#2594235.408884726815140.006318961977991520.0277055445012366
THAP1#55145331.36914460285133.23800758564397e-050.000647347385599293
YY1#752834.911170749853860.008441455341808260.0329712088875094
ZBTB7A#5134137.35190930787590.002516255860282270.0140329602067613



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.