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Coexpression cluster:C3793: Difference between revisions

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|full_id=C3793_iPS_testicular_Alveolar_Burkitt_transitionalcell_neuroblastoma_small
|full_id=C3793_iPS_testicular_Alveolar_Burkitt_transitionalcell_neuroblastoma_small
|id=C3793
|id=C3793
|ontology_enrichment_celltype=CL:0000066!4.15e-28!254;CL:0000012!2.70e-19!682;CL:0000548!3.10e-19!679;CL:0000004!3.10e-19!679;CL:0000255!3.10e-19!679;CL:0002321!1.27e-13!248;CL:0000220!6.49e-13!246;CL:0000003!1.32e-12!722;CL:0000063!1.02e-07!578;CL:0000076!1.68e-07!62;CL:0000221!1.81e-07!71;CL:0000144!1.83e-07!625;CL:0002319!2.45e-07!25;CL:1000449!9.19e-07!16
|ontology_enrichment_celltype=CL:0000066!3.17e-27!253;CL:0000548!4.43e-20!679;CL:0000255!4.43e-20!679;CL:0002321!9.91e-14!250;CL:0000003!2.39e-13!722;CL:1000449!5.22e-08!15;CL:0002319!2.33e-07!25;CL:1000497!4.79e-07!17;CL:0002518!4.79e-07!17;CL:0000221!4.91e-07!72;CL:0000076!6.89e-07!63
|ontology_enrichment_disease=DOID:162!7.85e-41!235;DOID:14566!3.59e-39!239;DOID:0050687!8.83e-23!143;DOID:305!2.95e-18!106;DOID:0050686!4.20e-18!137;DOID:2531!3.86e-13!51;DOID:0060083!3.86e-13!51;DOID:1240!2.57e-10!39;DOID:3095!2.27e-09!22;DOID:2994!2.27e-09!22;DOID:8692!5.02e-08!31
|ontology_enrichment_disease=DOID:162!1.92e-40!235;DOID:14566!8.39e-39!239;DOID:0050687!1.58e-22!143;DOID:0050686!3.60e-18!137;DOID:305!6.23e-18!106;DOID:2531!4.33e-13!51;DOID:0060083!4.33e-13!51;DOID:1240!1.69e-10!39;DOID:3095!9.94e-10!22;DOID:2994!9.94e-10!22;DOID:8692!3.11e-08!31
|ontology_enrichment_uberon=UBERON:0004211!9.19e-07!16;UBERON:0001285!9.19e-07!16;UBERON:0007684!9.19e-07!16;UBERON:0003220!9.19e-07!16;UBERON:0004208!9.19e-07!16
|ontology_enrichment_uberon=UBERON:0004211!5.22e-08!15;UBERON:0009773!5.22e-08!15;UBERON:0001231!5.22e-08!15;UBERON:0001285!5.22e-08!15;UBERON:0007684!5.22e-08!15;UBERON:0004208!5.22e-08!15;UBERON:0006555!2.36e-07!16;UBERON:0004819!2.36e-07!16;UBERON:0001851!4.12e-07!15
|tf_chipseq_enrich=BRCA1#672;3:20.1842306432238:0.000121570486027164:0.0016420977742099!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00660323844813677!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325352300692318!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00437094413199608!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322171063472168!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320562162671514!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0462231038035909!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00762072800413062!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154075151200005!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00433826475757615!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108688806965034!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128056735584736!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186477792725764!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00720235711860305!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294454220948416!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269593081905371!NFYA#4800;3:18.4255806998305:0.000159813550781416:0.00199602576298258!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.017289150828395!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00882205208972499!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00165226529074271!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276695346115239!SIX5#147912;3:17.086715355459:0.000200406054632501:0.00239668017173523!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246445334528674!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.010907108617918!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00375055723282591!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00542860629331397!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190247309536483!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329330278088574!ZBTB33#10009;3:31.6647250299812:3.14815888737575e-05:0.000633874235663459!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00388923269963759
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}}
}}

Revision as of 15:24, 19 October 2012


Full id: C3793_iPS_testicular_Alveolar_Burkitt_transitionalcell_neuroblastoma_small



Phase1 CAGE Peaks

Hg19::chr19:41257160..41257167,+p6@SNRPA
Hg19::chr19:41257173..41257187,+p4@SNRPA
Hg19::chr19:41257196..41257214,+p5@SNRPA


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
epithelial cell3.17e-27253
animal cell4.43e-20679
eukaryotic cell4.43e-20679
embryonic cell9.91e-14250
native cell2.39e-13722
epithelial cell of nephron5.22e-0815
neural cell2.33e-0725
kidney cell4.79e-0717
kidney epithelial cell4.79e-0717
ectodermal cell4.91e-0772
squamous epithelial cell6.89e-0763
Uber Anatomy
Ontology termp-valuen
nephron epithelium5.22e-0815
renal tubule5.22e-0815
nephron tubule5.22e-0815
nephron5.22e-0815
uriniferous tubule5.22e-0815
nephrogenic mesenchyme5.22e-0815
excretory tube2.36e-0716
kidney epithelium2.36e-0716
cortex4.12e-0715
Disease
Ontology termp-valuen
cancer1.92e-40235
disease of cellular proliferation8.39e-39239
cell type cancer1.58e-22143
organ system cancer3.60e-18137
carcinoma6.23e-18106
hematologic cancer4.33e-1351
immune system cancer4.33e-1351
leukemia1.69e-1039
germ cell and embryonal cancer9.94e-1022
germ cell cancer9.94e-1022
myeloid leukemia3.11e-0831


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
BRCA1#672320.18423064322380.0001215704860271640.0016420977742099
CHD2#1106310.34402283411690.0009033701102746880.00660323844813677
E2F1#186934.907389214879320.008460985347239390.0325352300692318
E2F4#1874312.66806031528440.0004917987006298980.00437094413199608
E2F6#187635.017155731697390.00791769806886330.0322171063472168
EGR1#195834.988179094810140.008056488137383440.0320562162671514
ELF1#199734.258097958807540.01295179875054610.0462231038035909
ETS1#211339.728760922202340.001085840092584840.00762072800413062
GABPB1#255337.067683836182170.002832212825417420.0154075151200005
GTF2F1#2962312.73966087675770.0004835525047438590.00433826475757615
HMGN3#932438.178547723350590.001827766942164210.0108688806965034
IRF1#365937.63716375356390.002244692747297240.0128056735584736
MAX#414936.452555509007120.003721913834265510.0186477792725764
MXI1#460139.96157162875930.001011470541259020.00720235711860305
MYC#460935.22228187160940.007020843755740150.0294454220948416
NFKB1#479035.488063424193840.006049381815655430.0269593081905371
NFYA#4800318.42558069983050.0001598135507814160.00199602576298258
PAX5#507936.669565531177830.003370290999677260.017289150828395
POU2F2#545239.106124057742520.001324165192682130.00882205208972499
RXRA#6256320.07461713913330.0001235730348432220.00165226529074271
SIN3A#2594235.408884726815140.006318961977991520.0276695346115239
SIX5#147912317.0867153554590.0002004060546325010.00239668017173523
SP1#666735.69838137814090.005403962701712170.0246445334528674
SPI1#668838.204323508522730.001810593189410520.010907108617918
SRF#6722313.79717826216780.0003806615025800190.00375055723282591
TAF7#6879311.43306940492390.0006690181981945830.00542860629331397
USF1#739136.361499277207960.00388404057290560.0190247309536483
YY1#752834.911170749853860.008441455341808260.0329330278088574
ZBTB33#10009331.66472502998123.14815888737575e-050.000633874235663459
ZNF143#7702313.50087655222790.0004062804962997170.00388923269963759



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.