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Coexpression cluster:C4769: Difference between revisions

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|full_id=C4769_Nucleus_normal_Urothelial_Prostate_Mesenchymal_lung_Fibroblast
|full_id=C4769_Nucleus_normal_Urothelial_Prostate_Mesenchymal_lung_Fibroblast
|id=C4769
|id=C4769
|ontology_enrichment_celltype=CL:0000548!5.07e-09!679;CL:0000004!5.07e-09!679;CL:0000255!5.07e-09!679;CL:0000012!8.03e-09!682;CL:0000063!2.06e-08!578;CL:0002320!4.59e-07!365
|ontology_enrichment_celltype=CL:0000548!9.65e-10!679;CL:0000255!9.65e-10!679;CL:0000057!5.60e-07!76
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004119!4.82e-12!169;UBERON:0000925!4.82e-12!169;UBERON:0006595!4.82e-12!169;UBERON:0001007!8.49e-12!155;UBERON:0001555!8.49e-12!155;UBERON:0007026!8.49e-12!155;UBERON:0003929!2.15e-10!54;UBERON:0004921!4.99e-08!129;UBERON:0004185!4.99e-08!129;UBERON:0005911!5.61e-08!82;UBERON:0000161!1.39e-07!35;UBERON:0002384!3.15e-07!375;UBERON:0000926!4.85e-07!448;UBERON:0004120!4.85e-07!448;UBERON:0006603!4.85e-07!448;UBERON:0000077!8.13e-07!130
|ontology_enrichment_uberon=UBERON:0004119!5.29e-12!160;UBERON:0000925!5.29e-12!160;UBERON:0006595!5.29e-12!160;UBERON:0001007!1.43e-11!145;UBERON:0001555!1.43e-11!145;UBERON:0007026!1.43e-11!145;UBERON:0003929!2.78e-10!54;UBERON:0005911!8.97e-09!82;UBERON:0000161!1.04e-07!36;UBERON:0004921!1.22e-07!118;UBERON:0002384!7.64e-07!371
|tf_chipseq_enrich=ATF3#467;3:22.4631745260087:8.81932387510763e-05:0.00130096238162763!BCLAF1#9774;3:21.6526476101218:9.8473954032885e-05:0.00139602569366641!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0191341693304707!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281544250892598!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00172432189582602!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327997048617473!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00439300072657253!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0324624688342172!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.032273850814322!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0465251740286264!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00902319347299336!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.0058453005970973!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00389689448763721!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00393894689716447!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109329983775881!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157759693128367!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187503236185835!MEF2A#4205;3:18.7432309096441:0.000151824390562247:0.00195492387201707!MEF2C#4208;3:41.3113544926241:1.41744912101957e-05:0.000340784918853966!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0296274556954118!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270957407661894!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00473851295654795!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173762068280246!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00669083673912278!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00166098380772089!SETDB1#9869;3:40.3200261780105:1.52461559299059e-05:0.000360247348227023!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0278481757962468!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0248059274175509!SP2#6668;3:26.1535304938446:5.58768218891694e-05:0.00094307036219828!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109462542465323!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00155428924861846!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00546085123886237!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00632286725904976!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00617816728230785!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00249702749243673!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00619385044291768!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0191306033481271!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0331435020467336!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00390677918727982
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445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.00662343,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.000943525,0.201033,0.0488949,0.016278,0.00132287,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.419264,0.00782667,0.108872,0.11002,0.26144,0.0286025,0.00896808,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.0178107,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.000584633,0.28711,0.0473033,0.094881,0.118532,0.132886,0.0774373,0.109194,0.128564,0.131452,0.00681584,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.739716,0.655293,0.21727,0.289306,0.119215,0.0198413,0.177967,9.55576e-10,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.0987169,0.000581378,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.0457643,0.152372,0.0203723,0.0257725,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.15663,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.000166026,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.0622625,0.113145,0.112651,0.186638,0.174776,0.0948451,0.0384217,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,0.00340589,0.184948,0.156261,0.311847,0.0001026,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,0.0170505,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.418146,0.000118274,0.449036,0.0973145,0.231447,0.18653,3.19513e-05,0.37006,0.42622,0.448797,0.197484,0.396996,0.36145,0.0966095,0.381071,0.580441,1.28363e-05,0.0198622,0.138468,0.0140037,0.145312,0.50058,0.0217093,0.00696618,0.875915,0.000283689,0.227104,0.166658,0.0734371,0.38649,0.0450114,0.156746,0.04783,0.144318,0.0465139,0.164197,0.462688,1.59145e-06,3.31949e-06,0.000566617,0.336276,0.468444,0.258219,0.446557,0.243383,0.191695,0.0889613,0.149257,0.029557,0.161598,0.0527155,0.000102726,0.150692,0.0239796,0.0013757,0.200632,0.138234,0.199161,0.160298,0.771991,0.20342,0.200493,0.20558,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.181415,0.282286,0.194707,0.616388,0.408413,0.165147,0.322213,0.0931134,0.33942,5.7752e-05,0.387276,0.522605,0.000283063,0.537348,0.222037,0.416621,0.416292,0.0252635,1.06909e-05,0.000280804,0.204817,0.452428,0.138871,0.000165333,0.0147755,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.373557,0.0393909,0.00209775,0.0111982,0.178743,0.0140668,0.363192,0.236011,0.00165643,0.273398,0.375787,0.4466,0.351067,0.275347,0.00388821,0.0524515,0.241132,0.0118241,0.30666,0.303709,0.495883,0.0867777,0.508064,0.250964,0.0131557,0.457886,0.504711,0.220231,0.159791,0.196976,0.00136659,0.463751,0.235208,0.307334,0.0246928,0.283463,0.201728,0.135386,0.0932845,0.273281,0.368095,0.275089,0.384593,0.0283414,0.359231,0.339729,0.197805,0.608187,0.0136044,0.332774,0.173874,0.299887,0.266492,0.205413,0.17639,0.0779009,0.0424553,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.119514,0.179412,0.193601,0.00215229,0.00221755,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.000350724,0.179889,0.226869,0.27872,0.0855609,0.131118,0.0233967,0.247588,0.00219731,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.00972162,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.0135229,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.0367308,0.261744,0.203781,0.00193951,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.0159159,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.036274,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.0437875,0.218161,0.0822373,0.0219487,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.0488311,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.00236454,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.0271615,0.11528,0.194982,0.00135479,0.0440463,0.283218,0.249955,0.1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}}
}}

Revision as of 16:14, 19 October 2012


Full id: C4769_Nucleus_normal_Urothelial_Prostate_Mesenchymal_lung_Fibroblast



Phase1 CAGE Peaks

Hg19::chr8:71520450..71520484,-p3@TRAM1
Hg19::chr8:71520485..71520511,-p4@TRAM1
Hg19::chr8:71520513..71520614,-p1@TRAM1


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><br>

Cell Type
Ontology termp-valuen
animal cell9.65e-10679
eukaryotic cell9.65e-10679
fibroblast5.60e-0776
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure5.29e-12160
endoderm5.29e-12160
presumptive endoderm5.29e-12160
digestive system1.43e-11145
digestive tract1.43e-11145
primitive gut1.43e-11145
gut epithelium2.78e-1054
endo-epithelium8.97e-0982
orifice1.04e-0736
subdivision of digestive tract1.22e-07118
connective tissue7.64e-07371


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
ATF3#467322.46317452600878.81932387510763e-050.00130096238162763
BCLAF1#9774321.65264761012189.8473954032885e-050.00139602569366641
CCNT2#90536.336201576962630.003930750035764890.0191341693304707
CTCF#1066435.360256373075030.0064925092527670.0281544250892598
CTCFL#140690319.74647435897440.0001298372005551160.00172432189582602
E2F1#186934.907389214879320.008460985347239390.0327997048617473
E2F4#1874312.66806031528440.0004917987006298980.00439300072657253
E2F6#187635.017155731697390.00791769806886330.0324624688342172
EGR1#195834.988179094810140.008056488137383440.032273850814322
ELF1#199734.258097958807540.01295179875054610.0465251740286264
FOS#235338.99795530889440.001372499272417130.00902319347299336
FOXA1#3169311.08141974938550.000734755275698670.0058453005970973
GATA1#2623313.56030814380040.0004009615963782630.00389689448763721
HDAC2#3066313.41562023662630.0004140761399857210.00393894689716447
HMGN3#932438.178547723350590.001827766942164210.0109329983775881
JUND#372736.994663941871030.002921845042734990.0157759693128367
MAX#414936.452555509007120.003721913834265510.0187503236185835
MEF2A#4205318.74323090964410.0001518243905622470.00195492387201707
MEF2C#4208341.31135449262411.41744912101957e-050.000340784918853966
MYC#460935.22228187160940.007020843755740150.0296274556954118
NFKB1#479035.488063424193840.006049381815655430.0270957407661894
NRF1#4899312.21027944771090.0005492172401020010.00473851295654795
PAX5#507936.669565531177830.003370290999677260.0173762068280246
RAD21#5885310.35503389545630.0009004912073565420.00669083673912278
RXRA#6256320.07461713913330.0001235730348432220.00166098380772089
SETDB1#9869340.32002617801051.52461559299059e-050.000360247348227023
SIN3A#2594235.408884726815140.006318961977991520.0278481757962468
SP1#666735.69838137814090.005403962701712170.0248059274175509
SP2#6668326.15353049384465.58768218891694e-050.00094307036219828
SPI1#668838.204323508522730.001810593189410520.0109462542465323
STAT1#6772320.70658749719920.0001125992441046670.00155428924861846
TAF7#6879311.43306940492390.0006690181981945830.00546085123886237
TCF12#6938310.63446490218640.0008313523990202070.00632286725904976
TCF7L2#6934310.77017656313730.0008003181298398380.00617816728230785
TFAP2A#7020316.5186343730450.0002218033880766340.00249702749243673
TFAP2C#7022310.80922860986020.0007916746575753130.00619385044291768
USF1#739136.361499277207960.00388404057290560.0191306033481271
YY1#752834.911170749853860.008441455341808260.0331435020467336
ZNF143#7702313.50087655222790.0004062804962997170.00390677918727982



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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