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Coexpression cluster:C4256: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0007049!cell cycle!0.0353349536749479!2177;1871
|gostat_on_coexpression_clusters=GO:0007049!cell cycle!0.0353349536749479!2177;1871
|id=C4256
|id=C4256
|ontology_enrichment_celltype=CL:0000066!1.11e-17!254;CL:0000012!2.79e-17!682;CL:0000548!6.32e-17!679;CL:0000004!6.32e-17!679;CL:0000255!6.32e-17!679;CL:0000003!3.35e-11!722;CL:0000063!7.60e-09!578;CL:0002321!2.58e-07!248;CL:0002319!2.95e-07!25;CL:0000133!4.93e-07!59;CL:0000220!7.94e-07!246
|ontology_enrichment_celltype=CL:0000066!1.87e-16!253;CL:0000548!6.48e-15!679;CL:0000255!6.48e-15!679;CL:0000003!1.19e-10!722;CL:0002319!3.45e-07!25;CL:0000133!4.96e-07!59
|ontology_enrichment_disease=DOID:162!2.87e-58!235;DOID:14566!5.89e-57!239;DOID:0050687!2.81e-30!143;DOID:0050686!4.33e-28!137;DOID:305!3.31e-24!106;DOID:2531!3.44e-24!51;DOID:0060083!3.44e-24!51;DOID:1240!3.12e-20!39;DOID:8692!2.80e-16!31;DOID:3095!6.69e-07!22;DOID:2994!6.69e-07!22
|ontology_enrichment_disease=DOID:162!2.49e-56!235;DOID:14566!2.76e-55!239;DOID:0050687!8.12e-30!143;DOID:0050686!5.82e-26!137;DOID:305!1.14e-23!106;DOID:2531!3.15e-23!51;DOID:0060083!3.15e-23!51;DOID:1240!1.91e-19!39;DOID:8692!1.35e-15!31
|ontology_enrichment_uberon=
|ontology_enrichment_uberon=
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.01905689364893!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00661806053219544!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326446063275457!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00437988952801961!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323292074679026!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.046367288578764!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00763869415529218!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00582577484350845!FOXA2#3170;2:16.4203091684435:0.00481068235210548:0.0225980683745578!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154517826502518!GTF2B#2959;2:21.2958866228828:0.00287818058991141:0.0155869485418593!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00434947377856721!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00392429201306431!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108936912442326!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.012842854488604!IRF3#3661;2:31.3213014743264:0.00133951467332011:0.00887787618776999!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157150362765578!KAT2A#2648;2:410.726666666667:7.8689746933917e-06:0.000222416197023853!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00721514731634116!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295308055177505!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270227282910709!NFYA#4800;2:12.2837204665537:0.00851601140372443:0.0324837003284724!NFYB#4801;2:11.1731955023576:0.0102546713505453:0.0381433015592135!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173317160724454!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00883840279660823!RDBP#7936;2:102.425602660017:0.000126437939273122:0.00168345894183397!REST#5978;3:9.65002871612802:0.00111263624711459:0.00769502794599037!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00485686888115012!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00165565672687509!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277603192705782!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247190110636001!SP2#6668;2:17.4356869958964:0.00427356848176974:0.0203245545841325!SREBF1#6720;2:31.3372329603255:0.0013381626513618:0.00887680190203095!STAT2#6773;2:43.5091807909604:0.000696899089886823:0.0056095139921919!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00544510533052089!THAP1#55145;2:20.9127630685675:0.00298344741373694:0.0158722563518553!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330267908310149
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.01905689364893!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00661806053219544!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326446063275457!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00437988952801961!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323292074679026!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.046367288578764!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00763869415529218!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00582577484350845!FOXA2#3170;2:16.4203091684435:0.00481068235210548:0.0225980683745578!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154517826502518!GTF2B#2959;2:21.2958866228828:0.00287818058991141:0.0155869485418593!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00434947377856721!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00392429201306431!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108936912442326!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.012842854488604!IRF3#3661;2:31.3213014743264:0.00133951467332011:0.00887787618776999!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157150362765578!KAT2A#2648;2:410.726666666667:7.8689746933917e-06:0.000222416197023853!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00721514731634116!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295308055177505!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270227282910709!NFYA#4800;2:12.2837204665537:0.00851601140372443:0.0324837003284724!NFYB#4801;2:11.1731955023576:0.0102546713505453:0.0381433015592135!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173317160724454!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00883840279660823!RDBP#7936;2:102.425602660017:0.000126437939273122:0.00168345894183397!REST#5978;3:9.65002871612802:0.00111263624711459:0.00769502794599037!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00485686888115012!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00165565672687509!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277603192705782!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247190110636001!SP2#6668;2:17.4356869958964:0.00427356848176974:0.0203245545841325!SREBF1#6720;2:31.3372329603255:0.0013381626513618:0.00887680190203095!STAT2#6773;2:43.5091807909604:0.000696899089886823:0.0056095139921919!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00544510533052089!THAP1#55145;2:20.9127630685675:0.00298344741373694:0.0158722563518553!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330267908310149
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}}
}}

Revision as of 15:48, 19 October 2012


Full id: C4256_transitionalcell_embryonic_acute_retinoblastoma_iPS_Hodgkin_chronic



Phase1 CAGE Peaks

Hg19::chr3:10068095..10068170,+p1@FANCD2
Hg19::chr6:20402070..20402082,+p5@E2F3
Hg19::chr6:20402102..20402152,+p1@E2F3


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:0007049cell cycle0.0353349536749479



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>

Cell Type
Ontology termp-valuen
epithelial cell1.87e-16253
animal cell6.48e-15679
eukaryotic cell6.48e-15679
native cell1.19e-10722
neural cell3.45e-0725
neurectodermal cell4.96e-0759
Disease
Ontology termp-valuen
cancer2.49e-56235
disease of cellular proliferation2.76e-55239
cell type cancer8.12e-30143
organ system cancer5.82e-26137
carcinoma1.14e-23106
hematologic cancer3.15e-2351
immune system cancer3.15e-2351
leukemia1.91e-1939
myeloid leukemia1.35e-1531


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#90536.336201576962630.003930750035764890.01905689364893
CHD2#1106310.34402283411690.0009033701102746880.00661806053219544
E2F1#186934.907389214879320.008460985347239390.0326446063275457
E2F4#1874312.66806031528440.0004917987006298980.00437988952801961
E2F6#187635.017155731697390.00791769806886330.0323292074679026
ELF1#199734.258097958807540.01295179875054610.046367288578764
ETS1#211339.728760922202340.001085840092584840.00763869415529218
FOXA1#3169311.08141974938550.000734755275698670.00582577484350845
FOXA2#3170216.42030916844350.004810682352105480.0225980683745578
GABPB1#255337.067683836182170.002832212825417420.0154517826502518
GTF2B#2959221.29588662288280.002878180589911410.0155869485418593
GTF2F1#2962312.73966087675770.0004835525047438590.00434947377856721
HDAC2#3066313.41562023662630.0004140761399857210.00392429201306431
HMGN3#932438.178547723350590.001827766942164210.0108936912442326
IRF1#365937.63716375356390.002244692747297240.012842854488604
IRF3#3661231.32130147432640.001339514673320110.00887787618776999
JUND#372736.994663941871030.002921845042734990.0157150362765578
KAT2A#26482410.7266666666677.8689746933917e-060.000222416197023853
MXI1#460139.96157162875930.001011470541259020.00721514731634116
MYC#460935.22228187160940.007020843755740150.0295308055177505
NFKB1#479035.488063424193840.006049381815655430.0270227282910709
NFYA#4800212.28372046655370.008516011403724430.0324837003284724
NFYB#4801211.17319550235760.01025467135054530.0381433015592135
PAX5#507936.669565531177830.003370290999677260.0173317160724454
POU2F2#545239.106124057742520.001324165192682130.00883840279660823
RDBP#79362102.4256026600170.0001264379392731220.00168345894183397
REST#597839.650028716128020.001112636247114590.00769502794599037
RFX5#5993312.04791082719510.0005717246050312580.00485686888115012
RXRA#6256320.07461713913330.0001235730348432220.00165565672687509
SIN3A#2594235.408884726815140.006318961977991520.0277603192705782
SP1#666735.69838137814090.005403962701712170.0247190110636001
SP2#6668217.43568699589640.004273568481769740.0203245545841325
SREBF1#6720231.33723296032550.00133816265136180.00887680190203095
STAT2#6773243.50918079096040.0006968990898868230.0056095139921919
TAF7#6879311.43306940492390.0006690181981945830.00544510533052089
THAP1#55145220.91276306856750.002983447413736940.0158722563518553
YY1#752834.911170749853860.008441455341808260.0330267908310149



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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