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Coexpression cluster:C4826: Difference between revisions

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|ontology_enrichment_disease=DOID:305!1.10e-15!106;DOID:0050687!3.17e-11!143;DOID:299!1.41e-08!25
|ontology_enrichment_disease=DOID:305!1.10e-15!106;DOID:0050687!3.17e-11!143;DOID:299!1.41e-08!25
|ontology_enrichment_uberon=UBERON:0006555!6.11e-15!17;UBERON:0005103!6.11e-15!17;UBERON:0000083!6.11e-15!17;UBERON:0009201!6.11e-15!17;UBERON:0004819!6.11e-15!17;UBERON:0006553!6.11e-15!17;UBERON:0003074!6.11e-15!17;UBERON:0003060!6.11e-15!17;UBERON:0009773!8.36e-15!12;UBERON:0001231!8.36e-15!12;UBERON:0004810!8.36e-15!12;UBERON:0000466!1.03e-14!126;UBERON:0004211!3.61e-14!16;UBERON:0001285!3.61e-14!16;UBERON:0007684!3.61e-14!16;UBERON:0003220!3.61e-14!16;UBERON:0004208!3.61e-14!16;UBERON:0000058!5.04e-14!26;UBERON:0004876!7.15e-14!20;UBERON:0000080!7.39e-14!18;UBERON:0002120!7.39e-14!18;UBERON:0004875!7.39e-14!18;UBERON:0005721!7.39e-14!18;UBERON:0005754!7.39e-14!18;UBERON:0007297!7.39e-14!18;UBERON:0003064!1.95e-13!37;UBERON:0003887!9.74e-13!21;UBERON:0006554!1.04e-12!44;UBERON:0001008!2.94e-12!45;UBERON:0002113!4.41e-12!27;UBERON:0003918!4.41e-12!27;UBERON:0005095!4.41e-12!27;UBERON:0007687!4.41e-12!27;UBERON:0003886!4.73e-12!63;UBERON:0000489!4.96e-12!32;UBERON:0000464!6.28e-12!104;UBERON:0002553!1.05e-11!70;UBERON:0004921!1.17e-11!129;UBERON:0004185!1.17e-11!129;UBERON:0005172!5.55e-11!55;UBERON:0005173!5.55e-11!55;UBERON:0005177!8.99e-11!107;UBERON:0001007!2.54e-10!155;UBERON:0001555!2.54e-10!155;UBERON:0007026!2.54e-10!155;UBERON:0001225!2.77e-10!13;UBERON:0008987!2.77e-10!13;UBERON:0003101!1.44e-09!22;UBERON:0000079!1.44e-09!22;UBERON:0003135!1.99e-09!11;UBERON:0004119!2.62e-09!169;UBERON:0000925!2.62e-09!169;UBERON:0006595!2.62e-09!169;UBERON:0002417!3.85e-09!61;UBERON:0000916!3.85e-09!61;UBERON:0005409!9.37e-09!35;UBERON:0000160!1.45e-08!27;UBERON:0004111!6.97e-08!241;UBERON:0001851!7.75e-08!16;UBERON:0000077!8.79e-08!130;UBERON:0009569!1.21e-07!113;UBERON:0005156!2.54e-07!59;UBERON:0000990!2.54e-07!59;UBERON:0000353!3.21e-07!17;UBERON:0001046!5.40e-07!19
|ontology_enrichment_uberon=UBERON:0006555!6.11e-15!17;UBERON:0005103!6.11e-15!17;UBERON:0000083!6.11e-15!17;UBERON:0009201!6.11e-15!17;UBERON:0004819!6.11e-15!17;UBERON:0006553!6.11e-15!17;UBERON:0003074!6.11e-15!17;UBERON:0003060!6.11e-15!17;UBERON:0009773!8.36e-15!12;UBERON:0001231!8.36e-15!12;UBERON:0004810!8.36e-15!12;UBERON:0000466!1.03e-14!126;UBERON:0004211!3.61e-14!16;UBERON:0001285!3.61e-14!16;UBERON:0007684!3.61e-14!16;UBERON:0003220!3.61e-14!16;UBERON:0004208!3.61e-14!16;UBERON:0000058!5.04e-14!26;UBERON:0004876!7.15e-14!20;UBERON:0000080!7.39e-14!18;UBERON:0002120!7.39e-14!18;UBERON:0004875!7.39e-14!18;UBERON:0005721!7.39e-14!18;UBERON:0005754!7.39e-14!18;UBERON:0007297!7.39e-14!18;UBERON:0003064!1.95e-13!37;UBERON:0003887!9.74e-13!21;UBERON:0006554!1.04e-12!44;UBERON:0001008!2.94e-12!45;UBERON:0002113!4.41e-12!27;UBERON:0003918!4.41e-12!27;UBERON:0005095!4.41e-12!27;UBERON:0007687!4.41e-12!27;UBERON:0003886!4.73e-12!63;UBERON:0000489!4.96e-12!32;UBERON:0000464!6.28e-12!104;UBERON:0002553!1.05e-11!70;UBERON:0004921!1.17e-11!129;UBERON:0004185!1.17e-11!129;UBERON:0005172!5.55e-11!55;UBERON:0005173!5.55e-11!55;UBERON:0005177!8.99e-11!107;UBERON:0001007!2.54e-10!155;UBERON:0001555!2.54e-10!155;UBERON:0007026!2.54e-10!155;UBERON:0001225!2.77e-10!13;UBERON:0008987!2.77e-10!13;UBERON:0003101!1.44e-09!22;UBERON:0000079!1.44e-09!22;UBERON:0003135!1.99e-09!11;UBERON:0004119!2.62e-09!169;UBERON:0000925!2.62e-09!169;UBERON:0006595!2.62e-09!169;UBERON:0002417!3.85e-09!61;UBERON:0000916!3.85e-09!61;UBERON:0005409!9.37e-09!35;UBERON:0000160!1.45e-08!27;UBERON:0004111!6.97e-08!241;UBERON:0001851!7.75e-08!16;UBERON:0000077!8.79e-08!130;UBERON:0009569!1.21e-07!113;UBERON:0005156!2.54e-07!59;UBERON:0000990!2.54e-07!59;UBERON:0000353!3.21e-07!17;UBERON:0001046!5.40e-07!19
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8058,0.28262,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.0306378,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.118532,0.132886,0.0774373,0.109194,0.128564,0.131452,0.112518,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.739716,0.655293,0.21727,0.289306,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.0899568,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.43617,0.519327,0.00173453,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.000243212,6.10604e-05,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.0203723,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,0.0718905,0.0919008,3.81507e-05,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.0622625,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.511859,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,0.0743925,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.418146,0.36927,0.449036,0.407369,0.231447,0.18653,0.43956,0.37006,0.42622,0.448797,0.197484,0.396996,0.36145,0.0160226,0.381071,0.580441,0.0863135,0.432035,0.722159,0.390366,0.145312,0.50058,0.443185,0.522904,0.158867,0.60734,0.227104,0.518585,0.250246,0.38649,0.284625,0.504757,0.55194,0.144318,0.28907,0.164197,0.462688,0.0461094,0.574635,0.478174,0.00846715,0.468444,0.258219,0.446557,0.243383,0.0186777,0.0889613,0.382874,0.109758,0.161598,0.164332,0.644754,0.496032,0.21803,0.37357,0.0203982,0.138234,0.452741,0.0508568,0.771991,0.20342,0.200493,0.20558,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.181415,0.0442318,0.0674279,0.616388,0.408413,0.516511,0.322213,0.0931134,0.33942,0.61031,0.387276,0.522605,0.802166,0.537348,0.222037,0.416621,0.416292,0.128937,0.734551,0.579431,0.204817,0.452428,0.138871,0.673493,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.00818864,0.373557,0.523625,0.408861,0.365487,0.534741,0.39088,0.0109626,0.00266072,0.203486,0.273398,0.0816179,0.4466,0.351067,0.275347,0.637444,0.305885,0.241132,0.0795725,0.30666,0.00604105,0.495883,0.386538,0.508064,0.250964,0.383276,0.457886,0.504711,0.0262575,0.159791,0.196976,0.191517,0.463751,0.0663581,0.307334,0.459728,0.283463,0.563586,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.47795,0.359231,0.339729,0.197805,0.24107,0.0870376,0.332774,0.000131919,0.299887,0.266492,0.205413,0.17639,0.00311629,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.0186488,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.00241368,0.000916623,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.000701257,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.0331281,0.173026,0.200432,0.139785,0.00149718,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.0219648,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.00132285,0.0812887,0.0981146,0.064145,0.0077532,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.0381402,0.0359756,0.0215087,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.0597546,0.000283503,0.218052,0.223831,0.11528,0.194982,0.190993,0.00472154,0.283218,0.0342254,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.0406636,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.21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}}
}}

Revision as of 12:08, 5 September 2012


Full id: C4826_hepatocellular_Renal_kidney_adenocarcinoma_Intestinal_small_Prostate



Phase1 CAGE Peaks

Hg19::chr9:71735882..71735896,+p6@TJP2
Hg19::chr9:71735910..71735923,+p16@TJP2
Hg19::chr9:71735943..71735948,+p26@TJP2


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>

Uber Anatomy
Ontology termp-valuen
excretory tube6.11e-1517
mesonephric epithelium6.11e-1517
mesonephric tubule6.11e-1517
nephric duct6.11e-1517
kidney epithelium6.11e-1517
renal duct6.11e-1517
mesonephric duct6.11e-1517
pronephric duct6.11e-1517
renal tubule8.36e-1512
nephron tubule8.36e-1512
nephron tubule epithelium8.36e-1512
immaterial anatomical entity1.03e-14126
nephron epithelium3.61e-1416
nephron3.61e-1416
uriniferous tubule3.61e-1416
metanephric mesenchyme3.61e-1416
nephrogenic mesenchyme3.61e-1416
duct5.04e-1426
urogenital ridge7.15e-1420
mesonephros7.39e-1418
pronephros7.39e-1418
nephrogenic cord7.39e-1418
pronephric mesoderm7.39e-1418
rostral part of nephrogenic cord7.39e-1418
presumptive pronephric mesoderm7.39e-1418
intermediate mesoderm1.95e-1337
intraembryonic coelom9.74e-1321
urinary system structure1.04e-1244
renal system2.94e-1245
kidney4.41e-1227
kidney mesenchyme4.41e-1227
kidney rudiment4.41e-1227
kidney field4.41e-1227
body cavity precursor4.73e-1263
cavitated compound organ4.96e-1232
anatomical space6.28e-12104
anatomical cavity1.05e-1170
subdivision of digestive tract1.17e-11129
endodermal part of digestive tract1.17e-11129
abdomen element5.55e-1155
abdominal segment element5.55e-1155
trunk region element8.99e-11107
digestive system2.54e-10155
digestive tract2.54e-10155
primitive gut2.54e-10155
cortex of kidney2.77e-1013
renal parenchyma2.77e-1013
male organism1.44e-0922
male reproductive system1.44e-0922
male reproductive organ1.99e-0911
endoderm-derived structure2.62e-09169
endoderm2.62e-09169
presumptive endoderm2.62e-09169
abdominal segment of trunk3.85e-0961
abdomen3.85e-0961
gastrointestinal system9.37e-0935
intestine1.45e-0827
anatomical conduit6.97e-08241
cortex7.75e-0816
mixed endoderm/mesoderm-derived structure8.79e-08130
subdivision of trunk1.21e-07113
reproductive structure2.54e-0759
reproductive system2.54e-0759
parenchyma3.21e-0717
hindgut5.40e-0719
Disease
Ontology termp-valuen
carcinoma1.10e-15106
cell type cancer3.17e-11143
adenocarcinoma1.41e-0825


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
BCL11A#53335328.36945510360714.37778126761649e-050.00077982448884291
E2F1#186934.907389214879320.008460985347239390.0328252915557331
ELF1#199734.258097958807540.01295179875054610.0465411818644468
ELK4#2005316.2356816584680.0002336043955745990.00256571768528926
EP300#203336.77394172622320.003216880500103790.0168658525376677
FOS#235338.99795530889440.001372499272417130.00902660274004865
FOSL2#2355316.93020060456170.0002060162053171620.00244223909955949
GATA3#2625327.2365163572064.94721007899563e-050.000856000121670352
HDAC2#3066313.41562023662630.0004140761399857210.00394038250423405
HNF4A#3172323.13229036295378.07584663437677e-050.00123579977530795
JUND#372736.994663941871030.002921845042734990.0157824967374295
MYC#460935.22228187160940.007020843755740150.0296490194899416
NANOG#79923329.24477848101273.99627955670032e-050.000742118493282762
NR3C1#2908314.9730233311730.0002978331194675480.00310650086528226
POU5F1#54603335.4392014519062.63510205045339e-081.82498291145426e-06
RXRA#6256320.07461713913330.0001235730348432220.00166141145545717
SIN3A#2594235.408884726815140.006318961977991520.0278622844726613
SP1#666735.69838137814090.005403962701712170.0248179262391327
TAF7#6879311.43306940492390.0006690181981945830.00546298605170008
TCF12#6938310.63446490218640.0008313523990202070.00632563115264981
USF1#739136.361499277207960.00388404057290560.0191378238060808
YY1#752834.911170749853860.008441455341808260.0331597079190248
ZNF263#1012738.221841637010680.001799043925565870.0110277232387706



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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