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Coexpression cluster:C1844: Difference between revisions

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|full_id=C1844_squamous_epidermoid_bronchioalveolar_Corneal_Alveolar_Esophageal_Urothelial
|full_id=C1844_squamous_epidermoid_bronchioalveolar_Corneal_Alveolar_Esophageal_Urothelial
|id=C1844
|id=C1844
|ontology_enrichment_celltype=CL:0000066!1.41e-31!254;CL:0002076!1.68e-16!43;CL:0000223!1.63e-13!59;CL:0002368!1.00e-07!13;CL:0002251!2.39e-07!21;CL:1000497!5.69e-07!18;CL:0002518!5.69e-07!18;CL:1000449!7.74e-07!16
|ontology_enrichment_celltype=CL:0000066!5.31e-30!253;CL:0002076!7.59e-29!42;CL:0000223!1.10e-20!58;CL:0002251!3.00e-16!20;CL:0002368!1.39e-13!13;CL:1000507!1.55e-10!10;CL:1000494!1.55e-10!10;CL:0002202!4.08e-09!9;CL:0002632!4.08e-09!9;CL:0002159!1.92e-08!14;CL:1000449!9.57e-08!15;CL:1000497!1.33e-07!17;CL:0002518!1.33e-07!17
|ontology_enrichment_disease=DOID:305!1.62e-13!106;DOID:1749!9.31e-09!14;DOID:299!6.63e-07!25
|ontology_enrichment_disease=DOID:1749!1.25e-13!14;DOID:305!1.50e-12!106
|ontology_enrichment_uberon=UBERON:0004119!4.77e-18!169;UBERON:0000925!4.77e-18!169;UBERON:0006595!4.77e-18!169;UBERON:0000464!6.39e-15!104;UBERON:0000466!1.24e-14!126;UBERON:0001004!9.43e-14!72;UBERON:0001007!4.05e-13!155;UBERON:0001555!4.05e-13!155;UBERON:0007026!4.05e-13!155;UBERON:0000468!4.22e-12!659;UBERON:0000077!1.37e-11!130;UBERON:0004921!1.44e-11!129;UBERON:0004185!1.44e-11!129;UBERON:0000467!5.36e-11!625;UBERON:0000480!8.47e-11!626;UBERON:0000065!2.31e-10!53;UBERON:0002553!1.82e-09!70;UBERON:0000062!2.39e-09!511;UBERON:0005911!4.68e-09!82;UBERON:0001008!5.70e-09!45;UBERON:0006554!1.30e-08!44;UBERON:0000926!1.41e-08!448;UBERON:0004120!1.41e-08!448;UBERON:0006603!1.41e-08!448;UBERON:0009569!1.89e-08!113;UBERON:0001041!1.93e-08!98;UBERON:0000922!1.96e-08!612;UBERON:0008947!5.43e-08!38;UBERON:0003258!5.43e-08!38;UBERON:0000161!7.13e-08!35;UBERON:0000058!1.06e-07!26;UBERON:0000080!1.71e-07!18;UBERON:0002120!1.71e-07!18;UBERON:0004875!1.71e-07!18;UBERON:0005721!1.71e-07!18;UBERON:0005754!1.71e-07!18;UBERON:0007297!1.71e-07!18;UBERON:0002050!1.90e-07!605;UBERON:0005423!1.90e-07!605;UBERON:0005177!2.17e-07!107;UBERON:0005156!2.81e-07!59;UBERON:0000990!2.81e-07!59;UBERON:0003886!3.17e-07!63;UBERON:0000072!3.23e-07!46;UBERON:0000923!3.27e-07!604;UBERON:0005291!3.27e-07!604;UBERON:0006598!3.27e-07!604;UBERON:0002532!3.27e-07!604;UBERON:0006555!3.74e-07!17;UBERON:0005103!3.74e-07!17;UBERON:0000083!3.74e-07!17;UBERON:0009201!3.74e-07!17;UBERON:0004819!3.74e-07!17;UBERON:0006553!3.74e-07!17;UBERON:0003074!3.74e-07!17;UBERON:0003060!3.74e-07!17;UBERON:0004876!4.63e-07!20;UBERON:0005153!5.23e-07!37;UBERON:0004211!7.74e-07!16;UBERON:0001285!7.74e-07!16;UBERON:0007684!7.74e-07!16;UBERON:0003220!7.74e-07!16;UBERON:0004208!7.74e-07!16
|ontology_enrichment_uberon=UBERON:0004119!1.25e-35!160;UBERON:0000925!1.25e-35!160;UBERON:0006595!1.25e-35!160;UBERON:0001007!2.42e-27!145;UBERON:0001555!2.42e-27!145;UBERON:0007026!2.42e-27!145;UBERON:0004921!6.61e-24!118;UBERON:0001004!6.92e-18!74;UBERON:0001008!1.81e-17!48;UBERON:0006554!1.02e-16!47;UBERON:0000161!4.97e-16!36;UBERON:0005911!1.62e-15!82;UBERON:0001041!8.44e-15!87;UBERON:0005153!1.14e-12!37;UBERON:0000065!7.16e-12!54;UBERON:0005177!7.50e-12!101;UBERON:0000464!2.34e-11!95;UBERON:0000466!2.99e-11!117;UBERON:0000062!3.98e-11!503;UBERON:0000166!7.24e-11!22;UBERON:0005157!1.03e-10!47;UBERON:0004810!1.55e-10!10;UBERON:0000475!4.19e-10!264;UBERON:0005178!8.00e-10!34;UBERON:0002224!8.00e-10!34;UBERON:0005181!2.28e-09!35;UBERON:0000922!2.68e-09!592;UBERON:0001046!1.27e-08!19;UBERON:0000344!2.14e-08!20;UBERON:0000165!2.60e-08!29;UBERON:0000930!2.60e-08!29;UBERON:0003102!3.98e-08!99;UBERON:0005423!5.60e-08!581;UBERON:0000064!5.94e-08!218;UBERON:0000481!6.77e-08!342;UBERON:0000468!9.46e-08!656;UBERON:0004211!9.57e-08!15;UBERON:0009773!9.57e-08!15;UBERON:0001231!9.57e-08!15;UBERON:0001285!9.57e-08!15;UBERON:0007684!9.57e-08!15;UBERON:0004208!9.57e-08!15;UBERON:0009569!1.29e-07!112;UBERON:0008947!1.70e-07!38;UBERON:0003258!1.70e-07!38;UBERON:0005631!2.27e-07!14;UBERON:0000158!2.27e-07!14;UBERON:0003929!2.74e-07!54;UBERON:0000365!3.39e-07!5;UBERON:0007196!4.13e-07!15;UBERON:0001558!4.13e-07!15;UBERON:0000467!4.17e-07!624;UBERON:0006555!4.41e-07!16;UBERON:0004819!4.41e-07!16;UBERON:0002530!4.78e-07!59;UBERON:0000480!4.91e-07!625;UBERON:0000072!5.05e-07!47;UBERON:0011216!6.47e-07!223;UBERON:0000153!8.55e-07!62;UBERON:0007811!8.55e-07!62
|tf_chipseq_enrich=CEBPB#1051;4:6.37691810065985:0.00111394417667732:0.00765591049407753!ELF1#1997;4:3.40647836704603:0.0123506610529955:0.0447381621016161!IRF1#3659;4:6.10973100285112:0.00131552526476799:0.00881057734558833!JUND#3727;4:5.59573115349682:0.00184959330175546:0.0109357832224886!MYC#4609;4:4.17782549728752:0.00569196903682344:0.0256865382291321!NFYA#4800;4:14.7404645598644:4.14733626928016e-05:0.000752377371247786!NFYB#4801;4:13.4078346028292:6.03169250119439e-05:0.00099156923206712!SP1#6667;4:4.55870510251272:0.0040757356578168:0.0194884056572992!TBP#6908;5:3.70677068709639:0.00142875510672112:0.0091933802347882
|tf_chipseq_enrich=CEBPB#1051;4:6.37691810065985:0.00111394417667732:0.00765591049407753!ELF1#1997;4:3.40647836704603:0.0123506610529955:0.0447381621016161!IRF1#3659;4:6.10973100285112:0.00131552526476799:0.00881057734558833!JUND#3727;4:5.59573115349682:0.00184959330175546:0.0109357832224886!MYC#4609;4:4.17782549728752:0.00569196903682344:0.0256865382291321!NFYA#4800;4:14.7404645598644:4.14733626928016e-05:0.000752377371247786!NFYB#4801;4:13.4078346028292:6.03169250119439e-05:0.00099156923206712!SP1#6667;4:4.55870510251272:0.0040757356578168:0.0194884056572992!TBP#6908;5:3.70677068709639:0.00142875510672112:0.0091933802347882
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398,0.197279,0.146467,0.0912686,0.425114,0.7034,0.218241,0.0242146,0.00594938,0.327369,0.339826,0.12998,0.123097,0.254847,0.0506165,0.0898207,0.0083677,0.0918749,0.0686325,0.0569043,0.0639461,0.387306,0.267408,0.312064,0.080156,0.274185,0.53753,0.0545112,0.510703,0.33844,0.0649137,0.0974216,0.595767,0.195675,0.174786,0.176557,0.396547,0.0472148,0.735114,0.229138,0.0639045,0.141461,0.0900204,0.228387,0.0016009,0.334921,0.296227,0.208788,0.00169887,0.36304,2.75722e-05,0.123626,0.270619,0.132705,0.285556,0.493429,0.233835,0.224471,0.262929,0.0270029,0.143824,0.460679,0.431098,0.0775891,0.153079,0.0179567,0.211515,0.125701,0.175283,0.204954,0.209341,0.0144211,0.0789618,0.084895,0.160115,0.0819954,0.10091,0.122658,0.151161,0.228398,0.056055,0.120552,0.41771,0.0270276,0.00238059,0.000837059,0.00278609,0.190688,0.299739,0.278645,0.733648,0.0940982,0.0780533,0.564811,0.0993772,0.274769,0.448923,0.11602,0.344528,0.0028606,0.0585992,0.20045,0.274438,0.76735,0.0940748,0.319826,2.71283e-07,0.173868,0.109708,0.174594,0.0809806,0.154589,0.318794,0.122767,0.0749261,0.176858,0.00680381,0.347759,0.242462,0.0620267,0.211111,0.0738743,0.0882327,0.183058,0.150073,0.270522,0.16872,0.341388,0.000146263,0.359135,0.123404,0.430769,0.240825,0.000533273,0.336623,0.163542,0.483244,0.00417724,0.500871,0.239667,0.10226,0.29809,0.235147,0.689826,0.000211407,0.116923,0.148426,0.0983658,0.228743,0.238223,0.156976,0.244789,0.267391,0.301441,0.21807,0.350528,0.382904,0.432408,0.190404,0.135865,0.488841,0.18137,0.180609,0.291283,0.273972,0.153023,0.0935746,0.0834173,0.22307,0.160699,0.391307,0.166736,0.181253,0.0422294,0.263877,0.146486,0.0171018,0.262486,0.0482841,0.131936,0.288826,0.246621,0.463617,0.697373,0.0965376,0.377203,0.279263,0.00849138,0.0720023,0.581771,0.800557,0.0594155,0.0605031,0.0234962,0.0713793,0.212621,0.594469,1.28824e-07,0.629713,0.581874,0.355154,0.377285,0.000494303,0.180545,0.603804,0.629445,0.306963,0.569605,0.526495,0.580285,0.0473662,0.764863,0.820986,0.24322,7.90608e-05,0.561689,0.0269405,0.321844,0.0175443,8.3213e-09,0.000273281,0.663441,0.349068,0.70429,4.60789e-05,0.196345,0.427789,0.689998,7.83077e-05,0.0238314,0.433702,0.258394,0.00423004,0.432123,0.759415,0.09639,0.494975,0.651196,0.392155,0.077743,0.371758,0.00115147,0.562417,0.025506,0.128028,0.254547,0.000678098,0.51445,0.0063379,4.90708e-06,0.541378,0.00134841,0.00506703,0.253789,0.0294574,0.914902,0.315485,0.311289,0.318577,0.4488,0.0139453,0.0147352,0.511254,0.553178,0.246387,0.224252,0.0603905,2.93518e-05,5.04095e-05,0.00665694,0.257848,0.353942,0.192234,0.427276,0.400353,0.466967,0.283682,2.47386e-05,2.63571e-06,0.474058,0.583101,0.0015715,0.138015,0.263776,0.498956,0.0748236,0.55798,0.708394,0.00662882,0.723248,0.34194,0.000339901,0.062406,0.27725,0.0254154,0.0587619,0.317485,0.265627,0.220564,0.845182,0.262394,0.307462,0.135076,0.0266179,0.664443,0.274593,0.490712,0.183857,0.709432,0.218812,0.531474,0.720644,0.562305,0.528646,0.361524,0.31558,0.00219357,0.0453518,0.62698,0.00636153,0.415367,0.000374479,0.0239664,0.011528,0.00122072,0.0241542,0.453004,3.68666e-07,0.00964276,0.001393,0.382214,0.553161,0.0202686,0.68995,0.339393,0.694478,0.306231,0.0497423,0.646049,0.0701109,0.457741,0.0851712,0.0189513,0.748909,0.289012,0.209347,0.412586,0.00116135,0.0172799,0.55475,0.294859,0.523749,0.0331565,0.307426,0.462582,0.049727,0.490527,0.714189,0.44799,6.46678e-05,0.0070566,0.276338,0.126433,0.0176264,0.318174,0.0555558,0.295666,0.00174232,0.00540731,0.116969,1.63206e-05,0.255983,0.297663,0.256708,0.0086349,0.322052,0.145568,0.153833,0.261242,0.38389,0.0463258,0.00164979,0.321362,0.00347751,0.280757,0.301366,0.340343,0.00093263,0.501812,0.128553,0.000849,0.053444,0.291523,0.19697,0.00645096,0.0537285,0.15063,0.198077,0.281455,8.47082e-05,0.00237959,0.138495,0.208834,0.32256,0.082459,0.342366,0.109684,1.92576e-07,0.0952935,0.181288,0.230841,0.352328,0.0357989,0.351665,0.265112,0.0633313,0.10772,0.0854747,0.0747609,0.406458,0.312881,0.512825,0.244656,0.192188,0.158985,0.174153,0.0972854,0.00822058,0.249919,0.339517,0.303699,0.198326,0.394084,0.458518,0.282501,0.252005,0.390891,0.238377,0.334983,0.197875,0.287909,0.289389,0.117618,0.392533,0.396962,0.0562195,0.330317,0.321404,0.225079,0.050521,0.379651,0.185715,0.345505,0.375521,0.271405,0.311201,0.221943,0.306427,0.367733,0.246925,0.208775,0.390438,0.343014,0.270094,0.276922,0.156279,1.5282e-07,0.461742,0.422872,0.336468,0.13327,0.313545,0.17149,0.0877361,0.0880065,0.238969,0.126615,0.0669467,0.0879453,0.474066,0.00182507,0.326779,0.292869,0.358198,0.29552,0.131776,0.158116,0.104606,0.194814,0.104167,0.168186,0.108081,0.123829,0.205215,0.175247,0.0724304,0.109077,0.144842,0.0604892,0.214671,0.316879,0.442567,0.430541,0.000838419,0.224871,0.398887,0.0138446,0.0542381,0.00101402,0.445995,0.385709,0.278202,0.00256269,0.400591,0.209809,0.253154,0.319519,0.309489,0.430805,0.362154,0.480785,0.185476,0.336314,0.344469,0.184651,0.303359,0.000489902,0.42392,0.00254622,0.380826,0.259046,0.345068,0.151046,0.483953,0.347171,0.321735,0.15463,0.13907,0.0267252,0.269432,0.250466,0.409882,0.115686,0.408975,0.162633,0.342661,0.27567,0.248127,0.33299,0.384731,0.0574076,0.00721116
}}
}}

Revision as of 11:45, 19 October 2012


Full id: C1844_squamous_epidermoid_bronchioalveolar_Corneal_Alveolar_Esophageal_Urothelial



Phase1 CAGE Peaks

Hg19::chr1:207205989..207206000,-p4@C1orf116
Hg19::chr1:207206001..207206012,-p5@C1orf116
Hg19::chr1:207206020..207206050,-p1@C1orf116
Hg19::chr1:207206095..207206121,-p2@C1orf116
Hg19::chr1:59042917..59042931,-p1@TACSTD2


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
endoderm-derived structure1.25e-35160
endoderm1.25e-35160
presumptive endoderm1.25e-35160
digestive system2.42e-27145
digestive tract2.42e-27145
primitive gut2.42e-27145
subdivision of digestive tract6.61e-24118
respiratory system6.92e-1874
renal system1.81e-1748
urinary system structure1.02e-1647
orifice4.97e-1636
endo-epithelium1.62e-1582
foregut8.44e-1587
epithelial bud1.14e-1237
respiratory tract7.16e-1254
trunk region element7.50e-12101
anatomical space2.34e-1195
immaterial anatomical entity2.99e-11117
organ3.98e-11503
oral opening7.24e-1122
epithelial fold1.03e-1047
nephron tubule epithelium1.55e-1010
organism subdivision4.19e-10264
thoracic cavity element8.00e-1034
thoracic cavity8.00e-1034
thoracic segment organ2.28e-0935
embryo2.68e-09592
hindgut1.27e-0819
mucosa2.14e-0820
mouth2.60e-0829
stomodeum2.60e-0829
surface structure3.98e-0899
developing anatomical structure5.60e-08581
organ part5.94e-08218
multi-tissue structure6.77e-08342
multi-cellular organism9.46e-08656
nephron epithelium9.57e-0815
renal tubule9.57e-0815
nephron tubule9.57e-0815
nephron9.57e-0815
uriniferous tubule9.57e-0815
nephrogenic mesenchyme9.57e-0815
subdivision of trunk1.29e-07112
respiratory primordium1.70e-0738
endoderm of foregut1.70e-0738
extraembryonic membrane2.27e-0714
membranous layer2.27e-0714
gut epithelium2.74e-0754
urothelium3.39e-075
tracheobronchial tree4.13e-0715
lower respiratory tract4.13e-0715
anatomical system4.17e-07624
excretory tube4.41e-0716
kidney epithelium4.41e-0716
gland4.78e-0759
anatomical group4.91e-07625
segment of respiratory tract5.05e-0747
organ system subdivision6.47e-07223
anterior region of body8.55e-0762
craniocervical region8.55e-0762
Disease
Ontology termp-valuen
squamous cell carcinoma1.25e-1314
carcinoma1.50e-12106


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
CEBPB#105146.376918100659850.001113944176677320.00765591049407753
ELF1#199743.406478367046030.01235066105299550.0447381621016161
IRF1#365946.109731002851120.001315525264767990.00881057734558833
JUND#372745.595731153496820.001849593301755460.0109357832224886
MYC#460944.177825497287520.005691969036823440.0256865382291321
NFYA#4800414.74046455986444.14733626928016e-050.000752377371247786
NFYB#4801413.40783460282926.03169250119439e-050.00099156923206712
SP1#666744.558705102512720.00407573565781680.0194884056572992
TBP#690853.706770687096390.001428755106721120.0091933802347882



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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