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Coexpression cluster:C3434: Difference between revisions

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|full_id=C3434_prostate_Reticulocytes_mucinous_epidermoid_testis_teratocarcinoma_chronic
|full_id=C3434_prostate_Reticulocytes_mucinous_epidermoid_testis_teratocarcinoma_chronic
|id=C3434
|id=C3434
|ontology_enrichment_celltype=CL:0000548!3.73e-16!679;CL:0000004!3.73e-16!679;CL:0000255!3.73e-16!679;CL:0000012!7.18e-16!682;CL:0000066!1.10e-14!254;CL:0000063!6.76e-09!578;CL:0000003!1.98e-08!722;CL:0000055!1.85e-07!180
|ontology_enrichment_celltype=CL:0000548!3.10e-19!679;CL:0000255!3.10e-19!679;CL:0000066!6.20e-16!253;CL:0000003!6.88e-11!722
|ontology_enrichment_disease=DOID:162!6.01e-49!235;DOID:14566!2.06e-47!239;DOID:0050686!7.03e-25!137;DOID:0050687!1.57e-24!143;DOID:305!5.29e-21!106;DOID:2531!2.08e-16!51;DOID:0060083!2.08e-16!51;DOID:1240!5.18e-12!39;DOID:8692!1.52e-08!31;DOID:7!5.94e-07!39
|ontology_enrichment_disease=DOID:162!1.20e-49!235;DOID:14566!3.75e-48!239;DOID:0050686!3.44e-25!137;DOID:0050687!5.13e-25!143;DOID:305!5.92e-22!106;DOID:2531!3.63e-16!51;DOID:0060083!3.63e-16!51;DOID:1240!8.11e-12!39;DOID:8692!1.76e-08!31;DOID:7!1.38e-07!39
|ontology_enrichment_uberon=UBERON:0001737!7.59e-07!9
|ontology_enrichment_uberon=UBERON:0001737!5.37e-07!9
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.018961829237194!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00659400831331969!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278869493666351!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.032436106474336!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00436314683104706!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321257369313914!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319758138093862!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.04610494255797!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00896114350537463!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108515804486776!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127819347819081!IRF3#3661;3:46.9819522114896:9.63568551583244e-06:0.000253358851860026!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293840627156266!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000736357516976403!NFYA#4800;3:18.4255806998305:0.000159813550781416:0.00199197606278319!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.0024526360095005!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00136359942107243!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00880856615022477!REST#5978;3:9.65002871612802:0.00111263624711459:0.00766255305060341!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00483797974597793!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0275943330832688!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245951305444771!SP2#6668;3:26.1535304938446:5.58768218891694e-05:0.000938822297503693!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00374419915878269!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00612564493677852!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328618292248066
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}}
}}

Revision as of 15:06, 19 October 2012


Full id: C3434_prostate_Reticulocytes_mucinous_epidermoid_testis_teratocarcinoma_chronic



Phase1 CAGE Peaks

Hg19::chr14:54863667..54863678,+p3@CDKN3
Hg19::chr14:54863682..54863738,+p1@CDKN3
Hg19::chr14:54863739..54863769,+p2@CDKN3


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
animal cell3.10e-19679
eukaryotic cell3.10e-19679
epithelial cell6.20e-16253
native cell6.88e-11722
Uber Anatomy
Ontology termp-valuen
larynx5.37e-079
Disease
Ontology termp-valuen
cancer1.20e-49235
disease of cellular proliferation3.75e-48239
organ system cancer3.44e-25137
cell type cancer5.13e-25143
carcinoma5.92e-22106
hematologic cancer3.63e-1651
immune system cancer3.63e-1651
leukemia8.11e-1239
myeloid leukemia1.76e-0831
disease of anatomical entity1.38e-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#90536.336201576962630.003930750035764890.018961829237194
CHD2#1106310.34402283411690.0009033701102746880.00659400831331969
CTCF#1066435.360256373075030.0064925092527670.0278869493666351
E2F1#186934.907389214879320.008460985347239390.032436106474336
E2F4#1874312.66806031528440.0004917987006298980.00436314683104706
E2F6#187635.017155731697390.00791769806886330.0321257369313914
EGR1#195834.988179094810140.008056488137383440.0319758138093862
ELF1#199734.258097958807540.01295179875054610.04610494255797
FOS#235338.99795530889440.001372499272417130.00896114350537463
HMGN3#932438.178547723350590.001827766942164210.0108515804486776
IRF1#365937.63716375356390.002244692747297240.0127819347819081
IRF3#3661346.98195221148969.63568551583244e-060.000253358851860026
MYC#460935.22228187160940.007020843755740150.0293840627156266
NANOG#79923329.24477848101273.99627955670032e-050.000736357516976403
NFYA#4800318.42558069983050.0001598135507814160.00199197606278319
NFYB#4801316.75979325353650.0002123649923296180.0024526360095005
PBX3#5090321.91451268674419.49854535978121e-050.00136359942107243
POU2F2#545239.106124057742520.001324165192682130.00880856615022477
REST#597839.650028716128020.001112636247114590.00766255305060341
RFX5#5993312.04791082719510.0005717246050312580.00483797974597793
SIN3A#2594235.408884726815140.006318961977991520.0275943330832688
SP1#666735.69838137814090.005403962701712170.0245951305444771
SP2#6668326.15353049384465.58768218891694e-050.000938822297503693
SRF#6722313.79717826216780.0003806615025800190.00374419915878269
TCF7L2#6934310.77017656313730.0008003181298398380.00612564493677852
YY1#752834.911170749853860.008441455341808260.0328618292248066



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C3434&oldid=2249657"