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Coexpression cluster:C3864: Difference between revisions

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|full_id=C3864_small_Intestinal_serous_choriocarcinoma_Hepatocyte_rectal_Prostate
|full_id=C3864_small_Intestinal_serous_choriocarcinoma_Hepatocyte_rectal_Prostate
|id=C3864
|id=C3864
|ontology_enrichment_celltype=CL:0000066!1.23e-18!254;CL:0000223!2.09e-11!59;CL:0002076!9.51e-10!43
|ontology_enrichment_celltype=CL:0000066!1.53e-15!253;CL:0000223!8.40e-13!58;CL:0002076!3.02e-10!42
|ontology_enrichment_disease=DOID:305!4.49e-22!106;DOID:0050687!2.83e-19!143;DOID:162!1.25e-10!235;DOID:14566!2.41e-10!239;DOID:299!4.83e-10!25
|ontology_enrichment_disease=DOID:305!1.84e-22!106;DOID:0050687!5.58e-19!143;DOID:299!1.27e-09!25;DOID:162!2.56e-09!235;DOID:14566!5.12e-09!239;DOID:1749!3.03e-07!14
|ontology_enrichment_uberon=UBERON:0004119!4.60e-17!169;UBERON:0000925!4.60e-17!169;UBERON:0006595!4.60e-17!169;UBERON:0007023!8.00e-16!115;UBERON:0004921!4.25e-15!129;UBERON:0004185!4.25e-15!129;UBERON:0001007!9.97e-15!155;UBERON:0001555!9.97e-15!155;UBERON:0007026!9.97e-15!155;UBERON:0005177!1.09e-13!107;UBERON:0000077!1.82e-13!130;UBERON:0000064!5.06e-13!219;UBERON:0000466!1.19e-12!126;UBERON:0005911!6.61e-12!82;UBERON:0000062!1.01e-11!511;UBERON:0001049!1.03e-11!57;UBERON:0005068!1.03e-11!57;UBERON:0006241!1.03e-11!57;UBERON:0007135!1.03e-11!57;UBERON:0000464!1.12e-10!104;UBERON:0004121!1.17e-10!169;UBERON:0003075!1.39e-10!86;UBERON:0007284!1.39e-10!86;UBERON:0001041!1.57e-10!98;UBERON:0005743!5.34e-10!86;UBERON:0000924!5.81e-10!173;UBERON:0006601!5.81e-10!173;UBERON:0000073!7.58e-10!94;UBERON:0001016!7.58e-10!94;UBERON:0002346!1.54e-09!90;UBERON:0001017!3.02e-09!82;UBERON:0000481!3.77e-09!347;UBERON:0002616!9.74e-09!59;UBERON:0000153!1.03e-08!129;UBERON:0007811!1.03e-08!129;UBERON:0003080!2.09e-08!42;UBERON:0003056!2.21e-08!61;UBERON:0000033!2.33e-08!123;UBERON:0009569!2.51e-08!113;UBERON:0000955!2.68e-08!69;UBERON:0006238!2.68e-08!69;UBERON:0002780!3.28e-08!41;UBERON:0001890!3.28e-08!41;UBERON:0006240!3.28e-08!41;UBERON:0005172!9.67e-08!55;UBERON:0005173!9.67e-08!55;UBERON:0002020!1.54e-07!34;UBERON:0003528!1.54e-07!34;UBERON:0000922!1.73e-07!612;UBERON:0004111!1.95e-07!241;UBERON:0001893!2.04e-07!34;UBERON:0002791!3.01e-07!33;UBERON:0002048!5.07e-07!22;UBERON:0000117!5.07e-07!22;UBERON:0000171!5.07e-07!22;UBERON:0000170!5.07e-07!22;UBERON:0005597!5.07e-07!22;UBERON:0000118!5.07e-07!22;UBERON:0005409!6.96e-07!35;UBERON:0001004!8.40e-07!72;UBERON:0001008!9.13e-07!45;UBERON:0000063!9.26e-07!97
|ontology_enrichment_uberon=UBERON:0011216!7.30e-21!223;UBERON:0004119!6.55e-20!160;UBERON:0000925!6.55e-20!160;UBERON:0006595!6.55e-20!160;UBERON:0004921!3.44e-18!118;UBERON:0001007!5.53e-18!145;UBERON:0001555!5.53e-18!145;UBERON:0007026!5.53e-18!145;UBERON:0007023!4.21e-16!114;UBERON:0005911!2.26e-15!82;UBERON:0005177!2.43e-14!101;UBERON:0000477!2.13e-12!373;UBERON:0000466!2.77e-12!117;UBERON:0001041!3.52e-12!87;UBERON:0000062!1.70e-11!503;UBERON:0000064!1.78e-11!218;UBERON:0000481!6.61e-11!342;UBERON:0009569!1.08e-09!112;UBERON:0000464!4.49e-09!95;UBERON:0001049!1.28e-08!56;UBERON:0005068!1.28e-08!56;UBERON:0006241!1.28e-08!56;UBERON:0007135!1.28e-08!56;UBERON:0005409!1.64e-08!25;UBERON:0005172!1.65e-08!54;UBERON:0005173!1.65e-08!54;UBERON:0004111!4.67e-08!240;UBERON:0000073!5.78e-08!53;UBERON:0002616!5.78e-08!53;UBERON:0003929!7.69e-08!54;UBERON:0000922!1.14e-07!592;UBERON:0002048!2.52e-07!22;UBERON:0000117!2.52e-07!22;UBERON:0000171!2.52e-07!22;UBERON:0000170!2.52e-07!22;UBERON:0005597!2.52e-07!22;UBERON:0000118!2.52e-07!22;UBERON:0004121!2.78e-07!171;UBERON:0000924!2.78e-07!171;UBERON:0006601!2.78e-07!171;UBERON:0006554!3.79e-07!47;UBERON:0001017!5.43e-07!81;UBERON:0001016!7.39e-07!89;UBERON:0000160!7.67e-07!17;UBERON:0001008!8.44e-07!48;UBERON:0010371!8.45e-07!104;UBERON:0005153!9.42e-07!37
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325436175995409!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322296631957756!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320708783572263!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186558340822065!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294560680113183!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172950973720172!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190309788127463!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00421657145651973!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329477970865951!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140232254958388
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325436175995409!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322296631957756!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320708783572263!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186558340822065!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294560680113183!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172950973720172!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190309788127463!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00421657145651973!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329477970865951!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140232254958388
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475,0.0558058,0.28262,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,8.47333e-05,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.00896808,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.00501606,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.022113,0.132886,0.0774373,0.109194,0.128564,0.131452,0.112518,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.00264443,0.0232393,0.21727,0.289306,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,2.90292e-07,0.000581378,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.000125914,0.101607,0.00771936,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.15663,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.00102368,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.0597157,0.000886556,0.188651,0.0813902,0.184948,0.156261,0.311847,0.511859,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,0.000500398,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.418146,0.36927,0.449036,0.407369,0.231447,0.544776,0.43956,0.37006,0.42622,0.448797,0.197484,0.396996,0.0107863,0.00202987,0.381071,0.057779,0.643768,0.432035,0.0411943,0.390366,0.0305485,0.50058,0.443185,0.522904,0.000322406,0.00516504,0.227104,0.518585,0.617852,0.38649,0.284625,0.0344717,0.192225,0.729153,0.28907,0.164197,0.462688,0.287881,0.0556235,0.478174,0.336276,0.468444,0.00355636,0.446557,0.243383,0.000171205,0.390974,0.73485,0.319063,0.161598,0.405056,0.00422412,0.150692,0.00613559,0.37357,5.07251e-06,0.477353,6.7495e-07,0.399222,3.61308e-06,1.5821e-07,0.200493,0.20558,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.0168417,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.181415,0.282286,0.000976922,0.0165273,0.408413,0.516511,0.322213,0.656109,0.33942,0.61031,0.387276,0.522605,1.90459e-08,0.180745,0.222037,0.416621,0.416292,0.462712,0.734551,0.579431,0.204817,0.452428,0.138871,0.308032,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.373557,0.523625,0.408861,0.0768488,0.534741,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.00438156,0.0830022,0.305885,0.241132,0.371414,0.0527347,0.303709,0.0323359,0.386538,0.00602464,0.250964,0.383276,0.457886,0.504711,0.220231,0.159791,0.196976,0.191517,0.129584,0.0145214,0.307334,0.459728,0.283463,0.563586,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.47795,0.359231,0.339729,0.197805,0.0153645,0.387069,0.332774,0.52832,0.299887,0.266492,0.205413,0.17639,8.36739e-05,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.00386277,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.00111175,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.0159159,0.200432,0.139785,0.197112,0.0315594,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.0257454,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.00132285,0.0812887,0.0981146,0.064145,0.121913,4.56072e-05,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.00335066,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.00144649,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604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}}
}}

Revision as of 15:28, 19 October 2012


Full id: C3864_small_Intestinal_serous_choriocarcinoma_Hepatocyte_rectal_Prostate



Phase1 CAGE Peaks

Hg19::chr1:151483855..151483871,+p2@CGN
Hg19::chr1:151483881..151483912,+p1@CGN
Hg19::chr1:151483924..151483940,+p3@CGN


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 cell1.53e-15253
endodermal cell8.40e-1358
endo-epithelial cell3.02e-1042
Uber Anatomy
Ontology termp-valuen
organ system subdivision7.30e-21223
endoderm-derived structure6.55e-20160
endoderm6.55e-20160
presumptive endoderm6.55e-20160
subdivision of digestive tract3.44e-18118
digestive system5.53e-18145
digestive tract5.53e-18145
primitive gut5.53e-18145
adult organism4.21e-16114
endo-epithelium2.26e-1582
trunk region element2.43e-14101
anatomical cluster2.13e-12373
immaterial anatomical entity2.77e-12117
foregut3.52e-1287
organ1.70e-11503
organ part1.78e-11218
multi-tissue structure6.61e-11342
subdivision of trunk1.08e-09112
anatomical space4.49e-0995
neural tube1.28e-0856
neural rod1.28e-0856
future spinal cord1.28e-0856
neural keel1.28e-0856
gastrointestinal system1.64e-0825
abdomen element1.65e-0854
abdominal segment element1.65e-0854
anatomical conduit4.67e-08240
regional part of nervous system5.78e-0853
regional part of brain5.78e-0853
gut epithelium7.69e-0854
embryo1.14e-07592
lung2.52e-0722
respiratory tube2.52e-0722
respiration organ2.52e-0722
pair of lungs2.52e-0722
lung primordium2.52e-0722
lung bud2.52e-0722
ectoderm-derived structure2.78e-07171
ectoderm2.78e-07171
presumptive ectoderm2.78e-07171
urinary system structure3.79e-0747
central nervous system5.43e-0781
nervous system7.39e-0789
intestine7.67e-0717
renal system8.44e-0748
ecto-epithelium8.45e-07104
epithelial bud9.42e-0737
Disease
Ontology termp-valuen
carcinoma1.84e-22106
cell type cancer5.58e-19143
adenocarcinoma1.27e-0925
cancer2.56e-09235
disease of cellular proliferation5.12e-09239
squamous cell carcinoma3.03e-0714


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
E2F1#186934.907389214879320.008460985347239390.0325436175995409
E2F6#187635.017155731697390.00791769806886330.0322296631957756
EGR1#195834.988179094810140.008056488137383440.0320708783572263
MAX#414936.452555509007120.003721913834265510.0186558340822065
MYC#460935.22228187160940.007020843755740150.0294560680113183
PAX5#507936.669565531177830.003370290999677260.0172950973720172
USF1#739136.361499277207960.00388404057290560.0190309788127463
USF2#7392312.99219738506960.0004558979393427810.00421657145651973
YY1#752834.911170749853860.008441455341808260.0329477970865951
ZBTB7A#5134137.35190930787590.002516255860282270.0140232254958388



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.