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Coexpression cluster:C3446: Difference between revisions

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|full_id=C3446_Hepatocyte_bronchial_gall_signet_Prostate_smallcell_hepatocellular
|full_id=C3446_Hepatocyte_bronchial_gall_signet_Prostate_smallcell_hepatocellular
|id=C3446
|id=C3446
|ontology_enrichment_celltype=CL:0000223!1.65e-28!59;CL:0002076!1.13e-20!43;CL:0000066!1.18e-15!254;CL:0002368!9.40e-13!13;CL:0002251!2.50e-10!21;CL:0000181!4.18e-08!12;CL:0000417!4.18e-08!12;CL:0000668!4.18e-08!12;CL:0000414!4.18e-08!12;CL:0000412!4.18e-08!12;CL:0000182!4.18e-08!12;CL:0002202!2.18e-07!9;CL:0002632!2.18e-07!9;CL:0002328!8.27e-07!3
|ontology_enrichment_celltype=CL:0000223!8.82e-24!58;CL:0002076!4.30e-17!42;CL:0000066!7.87e-14!253;CL:0002251!6.64e-09!20;CL:0002368!1.31e-08!13;CL:0002231!2.09e-08!3;CL:0000181!2.71e-08!12;CL:0000417!2.71e-08!12;CL:0000668!2.71e-08!12;CL:0000412!2.71e-08!12;CL:0000182!2.71e-08!12
|ontology_enrichment_disease=DOID:305!9.22e-11!106;DOID:1749!1.15e-07!14;DOID:0050687!5.71e-07!143
|ontology_enrichment_disease=DOID:305!4.49e-10!106;DOID:0050687!3.71e-07!143
|ontology_enrichment_uberon=UBERON:0004119!2.90e-37!169;UBERON:0000925!2.90e-37!169;UBERON:0006595!2.90e-37!169;UBERON:0001007!2.62e-32!155;UBERON:0001555!2.62e-32!155;UBERON:0007026!2.62e-32!155;UBERON:0004921!9.10e-30!129;UBERON:0004185!9.10e-30!129;UBERON:0000077!6.56e-22!130;UBERON:0001041!8.73e-18!98;UBERON:0001004!2.47e-17!72;UBERON:0005911!1.18e-16!82;UBERON:0000466!3.85e-15!126;UBERON:0000161!3.91e-14!35;UBERON:0000166!6.74e-12!21;UBERON:0003929!1.23e-10!54;UBERON:0000065!8.81e-10!53;UBERON:0009497!9.74e-10!25;UBERON:0000015!9.74e-10!25;UBERON:0002423!9.74e-10!25;UBERON:0006235!9.74e-10!25;UBERON:0004161!9.74e-10!25;UBERON:0005177!1.01e-09!107;UBERON:0005409!1.58e-09!35;UBERON:0000464!1.77e-09!104;UBERON:0002365!2.27e-09!31;UBERON:0002330!2.27e-09!31;UBERON:0009854!5.57e-09!23;UBERON:0005178!7.19e-09!34;UBERON:0002224!7.19e-09!34;UBERON:0005181!1.65e-08!35;UBERON:0000160!2.44e-08!27;UBERON:0003104!3.43e-08!238;UBERON:0009142!3.43e-08!238;UBERON:0000165!3.88e-08!28;UBERON:0000930!3.88e-08!28;UBERON:0008835!8.31e-08!22;UBERON:0003894!8.31e-08!22;UBERON:0009856!1.26e-07!26;UBERON:0002107!1.55e-07!19;UBERON:0006925!1.55e-07!19;UBERON:0008836!1.55e-07!19;UBERON:0007196!1.59e-07!14;UBERON:0001558!1.59e-07!14;UBERON:0000481!3.79e-07!347;UBERON:0004815!8.27e-07!3;UBERON:0002031!8.27e-07!3
|ontology_enrichment_uberon=UBERON:0004119!1.58e-26!160;UBERON:0000925!1.58e-26!160;UBERON:0006595!1.58e-26!160;UBERON:0001007!1.99e-23!145;UBERON:0001555!1.99e-23!145;UBERON:0007026!1.99e-23!145;UBERON:0004921!1.55e-20!118;UBERON:0005911!1.21e-13!82;UBERON:0001041!1.56e-12!87;UBERON:0000466!2.71e-11!117;UBERON:0001004!8.82e-11!74;UBERON:0000161!2.21e-10!36;UBERON:0003929!3.49e-10!54;UBERON:0009497!1.66e-09!25;UBERON:0000015!1.66e-09!25;UBERON:0002423!1.66e-09!25;UBERON:0006235!1.66e-09!25;UBERON:0004161!1.66e-09!25;UBERON:0009854!1.72e-08!23;UBERON:0005177!5.34e-08!101;UBERON:0000166!1.18e-07!22;UBERON:0003101!1.62e-07!22;UBERON:0000079!1.62e-07!22;UBERON:0009856!2.71e-07!26;UBERON:0008835!3.74e-07!22;UBERON:0003894!3.74e-07!22;UBERON:0000065!5.81e-07!54
|tfbs_overrepresentation=0.000598099,0.0586687,0.35968,0.0477154,0.199763,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.000504333,0.225367,0.188771,0.125978,0.000616359,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.00178278,0.0665252,0.00367271,0.324808,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.00120442,0.120917,0.0362416,0.0380166,0.18151,0.0064353,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.00153794,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.0235519,0.608896,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.21992,0.153631,0.0927458,0.27413,0.0574857,0.00442705,0.141874,0.0370665,0.00209623,0.0409286,0.0669887,0.338096,0.0109386,0.00407722,5.86349e-05,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.0101452,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,1.63831e-05,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.0128549,0.596561,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.00239446,0.0516985,0.0337251,0.00237216,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,2.7657e-06,0.00111717,0.137725,0.46397,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.0133424,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.00360981,0.27358,0.15185,0.206299,0.0169462,0.0458667,0.104357,0.121154,0.00662754,0.0549274,0.169057,0.0142864,0.100942,0.062995,0.10299,0.14193,0.0119362,0.15606,0.161026,7.1088e-05,0.126611,0.138852,0.085973,0.060453,0.059896,0.0538541,0.0859236,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.0381183,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.000292777,7.98174e-10,0.0183114,0.185743,0.00497001,0.00497632,0.159674,0.107242,0.201859,0.0695832,0.582402,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.00453939,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.584917,0.713218,0.198118,0.0821962,0.20128,0.252249,0.807281,0.0638737,0.629514,0.261553,0.446302,0.373681,0.309233,0.00510271,0.000787222,0.395854,0.329568,0.178727,0.0030348,0.0408801,0.00531795,0.405773,0.39729,0.581713,0.0139202,0.187251,0.000106625,0.00115743,0.0186051,0.109988,0.000789293,0.0257868,0.427027,0.0124294,0.463191,0.647576,0.0407001,0.03861,0.370782,0.0173702,0.484505,0.253571,0.276829,0.00591608,0.00462582,0.316882,0.223503,0.155672,0.603208,0.283727,0.00679651,0.577664,0.291709,0.120054,0.576651,0.102333,0.292835,0.137839,0.439556,0.373868,0.57762,0.608919,0.18237,0.706298,0.821217,0.400457,0.0419647,0.236471,0.185661,0.346319,0.00117453,0.0405716,0.258117,0.503058,0.513852,0.169228,0.0338468,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.0182356,0.230427,0.421596,0.581837,0.0021959,0.0267008,0.546839,0.0477082,0.448039,0.218623,0.312808,0.117923,0.0451077,0.0747529,0.0284893,0.650179,0.223844,0.50215,0.0484563,0.0671437,0.477304,0.0465597,0.0077225,0.683186,0.278044,0.490301,0.108847,0.228096,0.00847033,0.19763,0.15631,0.567452,0.0182254,0.48267,0.420626,0.165111,0.858756,0.335105,0.144809,0.145539,0.385517,0.0818086,0.447325,0.0247309,0.252232,0.0122989,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.0460163,0.00541072,0.284593,0.343734,0.00622965,0.305777,0.00257275,0.503082,0.522888,0.284629,0.00375279,0.000101021,1.15893e-08,0.0965765,0.41707,0.363685,0.464871,0.40841,0.0228979,0.171685,0.651524,0.437176,0.040018,0.339277,0.552319,0.281425,0.141758,0.455379,0.520495,0.159617,0.238587,0.372281,0.0293409,0.0192138,0.0891382,0.0595618,0.171389,0.625309,0.0688327,0.539392,0.34988,0.475069,0.0958562,0.0204872,0.630264,0.00689935,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.010955,0.223391,0.0223093,0.116981,0.441735,0.191777,0.111931,2.9178e-05,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.0842821,0.0179103,0.303939,0.0434097,0.0140073,0.0464827,0.169603,0.114583,0.104559,0.000130076,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.00872488,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.062811,0.19559,0.132201,0.188694,0.0481795,0.199971,0.0966069,0.127758,0.175785,0.0012141,0.015204,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.0419304,0.00481323,0.173708,0.141119,0.211595,0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}}
}}

Revision as of 15:07, 19 October 2012


Full id: C3446_Hepatocyte_bronchial_gall_signet_Prostate_smallcell_hepatocellular



Phase1 CAGE Peaks

Hg19::chr14:65406261..65406292,-p@chr14:65406261..65406292
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Hg19::chr14:65406411..65406422,-p@chr14:65406411..65406422
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Hg19::chr14:65406492..65406508,-p@chr14:65406492..65406508
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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
endodermal cell8.82e-2458
endo-epithelial cell4.30e-1742
epithelial cell7.87e-14253
epithelial cell of alimentary canal6.64e-0920
respiratory epithelial cell1.31e-0813
epithelial cell of prostate2.09e-083
metabolising cell2.71e-0812
endopolyploid cell2.71e-0812
parenchymal cell2.71e-0812
polyploid cell2.71e-0812
hepatocyte2.71e-0812
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.58e-26160
endoderm1.58e-26160
presumptive endoderm1.58e-26160
digestive system1.99e-23145
digestive tract1.99e-23145
primitive gut1.99e-23145
subdivision of digestive tract1.55e-20118
endo-epithelium1.21e-1382
foregut1.56e-1287
immaterial anatomical entity2.71e-11117
respiratory system8.82e-1174
orifice2.21e-1036
gut epithelium3.49e-1054
epithelium of foregut-midgut junction1.66e-0925
anatomical boundary1.66e-0925
hepatobiliary system1.66e-0925
foregut-midgut junction1.66e-0925
septum transversum1.66e-0925
digestive tract diverticulum1.72e-0823
trunk region element5.34e-08101
oral opening1.18e-0722
male organism1.62e-0722
male reproductive system1.62e-0722
sac2.71e-0726
hepatic diverticulum3.74e-0722
liver primordium3.74e-0722
respiratory tract5.81e-0754
Disease
Ontology termp-valuen
carcinoma4.49e-10106
cell type cancer3.71e-07143


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


No analysis results for this cluster

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.