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Coexpression cluster:C2591: Difference between revisions

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|id=C2591
|id=C2591
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=DOID:162!1.62e-19!235;DOID:14566!1.11e-18!239;DOID:2531!1.13e-18!51;DOID:0060083!1.13e-18!51;DOID:1240!2.90e-15!39;DOID:8692!2.30e-14!31;DOID:0050686!6.09e-11!137
|ontology_enrichment_disease=DOID:162!2.25e-19!235;DOID:14566!2.63e-18!239;DOID:2531!5.03e-18!51;DOID:0060083!5.03e-18!51;DOID:1240!6.18e-15!39;DOID:8692!7.13e-14!31;DOID:0050686!7.24e-11!137
|ontology_enrichment_uberon=UBERON:0001737!9.90e-07!9
|ontology_enrichment_uberon=UBERON:0001737!8.76e-07!9
|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.0051253609353498!CHD2#1106;4:10.3440228341169:8.73193255208051e-05:0.00129135415435675!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106560437344208!E2F4#1874;4:12.6680603152844:3.88145892637771e-05:0.000727261730914894!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00997440130976996!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101492379840209!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160992290590759!ETS1#2113;4:9.72876092220234:0.000111595531741814:0.00154636138245765!GABPB1#2553;3:5.30076287713663:0.0101267882423427:0.0378658707973947!GATA1#2623;4:13.5603081438004:2.95627390049268e-05:0.000614183986261298!GTF2B#2959;4:31.9438299343242:9.59435337635006e-07:4.08989662152091e-05!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186215216756506!HMGN3#9324;4:8.17854772335059:0.000223457028444047:0.00248246235439505!IRF1#3659;4:7.6371637535639:0.000293885399618549:0.00307761929717854!REST#5978;4:9.65002871612802:0.000115282561421917:0.00157159580111521!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.0079688279363175!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00684702637484386!STAT3#6774;4:10.5194649971542:8.16377768286615e-05:0.0012322832452968!SUZ12#23512;4:50.1157809110629:1.5827390373096e-07:8.81128370562782e-06!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322508635045517!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244485481811387!YY1#7528;4:4.91117074985386:0.0017187183805544:0.010692871206691!ZBTB7A#51341;4:7.3519093078759:0.00034222354001599:0.00346836334747501!ZNF263#10127;3:6.16638122775801:0.00653981434797598:0.0279773756067777
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}}
}}

Revision as of 14:12, 19 October 2012


Full id: C2591_acute_Hodgkin_Reticulocytes_merkel_Chondrocyte_chronic_NK



Phase1 CAGE Peaks

Hg19::chr1:51434441..51434456,+p5@CDKN2C
Hg19::chr1:51434469..51434489,+p2@CDKN2C
Hg19::chr1:51434497..51434515,+p7@CDKN2C
Hg19::chr1:51434648..51434692,+p3@CDKN2C


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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
larynx8.76e-079
Disease
Ontology termp-valuen
cancer2.25e-19235
disease of cellular proliferation2.63e-18239
hematologic cancer5.03e-1851
immune system cancer5.03e-1851
leukemia6.18e-1539
myeloid leukemia7.13e-1431
organ system cancer7.24e-11137


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#90546.336201576962630.0006203100587215640.0051253609353498
CHD2#1106410.34402283411698.73193255208051e-050.00129135415435675
E2F1#186944.907389214879320.001724022357361790.0106560437344208
E2F4#1874412.66806031528443.88145892637771e-050.000727261730914894
E2F6#187645.017155731697390.00157802193473060.00997440130976996
EGR1#195844.988179094810140.001615011500076050.0101492379840209
ELF1#199744.258097958807540.003041525565781240.0160992290590759
ETS1#211349.728760922202340.0001115955317418140.00154636138245765
GABPB1#255335.300762877136630.01012678824234270.0378658707973947
GATA1#2623413.56030814380042.95627390049268e-050.000614183986261298
GTF2B#2959431.94382993432429.59435337635006e-074.08989662152091e-05
HEY1#2346244.040111043105710.00375304636917980.0186215216756506
HMGN3#932448.178547723350590.0002234570284440470.00248246235439505
IRF1#365947.63716375356390.0002938853996185490.00307761929717854
REST#597849.650028716128020.0001152825614219170.00157159580111521
SIN3A#2594245.408884726815140.001168172384885160.0079688279363175
SP1#666745.69838137814090.0009482606065333980.00684702637484386
STAT3#6774410.51946499715428.16377768286615e-050.0012322832452968
SUZ12#23512450.11578091106291.5827390373096e-078.81128370562782e-06
TAF1#687243.343046285745290.008005664898701650.0322508635045517
TBP#690843.706770687096390.005296377814784350.0244485481811387
YY1#752844.911170749853860.00171871838055440.010692871206691
ZBTB7A#5134147.35190930787590.000342223540015990.00346836334747501
ZNF263#1012736.166381227758010.006539814347975980.0279773756067777



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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