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Coexpression cluster:C617: Difference between revisions

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|ontology_enrichment_disease=DOID:305!1.17e-18!106;DOID:0050687!2.33e-17!143;DOID:162!3.27e-10!235;DOID:14566!7.51e-10!239;DOID:1749!2.80e-08!14
|ontology_enrichment_disease=DOID:305!1.17e-18!106;DOID:0050687!2.33e-17!143;DOID:162!3.27e-10!235;DOID:14566!7.51e-10!239;DOID:1749!2.80e-08!14
|ontology_enrichment_uberon=UBERON:0004119!6.04e-12!169;UBERON:0000925!6.04e-12!169;UBERON:0006595!6.04e-12!169;UBERON:0000065!9.64e-12!53;UBERON:0001004!2.16e-10!72;UBERON:0001007!3.18e-10!155;UBERON:0001555!3.18e-10!155;UBERON:0007026!3.18e-10!155;UBERON:0000077!4.87e-10!130;UBERON:0004807!8.44e-10!28;UBERON:0001041!2.09e-09!98;UBERON:0004921!2.20e-09!129;UBERON:0004185!2.20e-09!129;UBERON:0000072!7.29e-09!46;UBERON:0000464!8.18e-09!104;UBERON:0005178!1.19e-08!34;UBERON:0002224!1.19e-08!34;UBERON:0002048!1.61e-08!22;UBERON:0000117!1.61e-08!22;UBERON:0000171!1.61e-08!22;UBERON:0000170!1.61e-08!22;UBERON:0005597!1.61e-08!22;UBERON:0000118!1.61e-08!22;UBERON:0005911!2.16e-08!82;UBERON:0005181!3.95e-08!35;UBERON:0005153!5.24e-08!37;UBERON:0005177!7.69e-08!107;UBERON:0000466!1.13e-07!126;UBERON:0004802!1.24e-07!19;UBERON:0000115!1.24e-07!19;UBERON:0008947!2.01e-07!38;UBERON:0003258!2.01e-07!38
|ontology_enrichment_uberon=UBERON:0004119!6.04e-12!169;UBERON:0000925!6.04e-12!169;UBERON:0006595!6.04e-12!169;UBERON:0000065!9.64e-12!53;UBERON:0001004!2.16e-10!72;UBERON:0001007!3.18e-10!155;UBERON:0001555!3.18e-10!155;UBERON:0007026!3.18e-10!155;UBERON:0000077!4.87e-10!130;UBERON:0004807!8.44e-10!28;UBERON:0001041!2.09e-09!98;UBERON:0004921!2.20e-09!129;UBERON:0004185!2.20e-09!129;UBERON:0000072!7.29e-09!46;UBERON:0000464!8.18e-09!104;UBERON:0005178!1.19e-08!34;UBERON:0002224!1.19e-08!34;UBERON:0002048!1.61e-08!22;UBERON:0000117!1.61e-08!22;UBERON:0000171!1.61e-08!22;UBERON:0000170!1.61e-08!22;UBERON:0005597!1.61e-08!22;UBERON:0000118!1.61e-08!22;UBERON:0005911!2.16e-08!82;UBERON:0005181!3.95e-08!35;UBERON:0005153!5.24e-08!37;UBERON:0005177!7.69e-08!107;UBERON:0000466!1.13e-07!126;UBERON:0004802!1.24e-07!19;UBERON:0000115!1.24e-07!19;UBERON:0008947!2.01e-07!38;UBERON:0003258!2.01e-07!38
|tf_chipseq_enrich=NR3C1#2908;4:4.27800666604944:0.0115683845516382:0.0422873023061334
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93,0.145253,0.0527796,0.685519,0.171324,0.249488,0.920828,0.456489,0.416036,0.419538,0.756891,0.126655,0.885586,0.517459,0.168817,0.34758,0.232128,0.516141,0.396218,0.680814,0.626053,0.480937,0.903474,0.359991,0.793723,0.308916,0.586693,0.328776,0.609958,0.851067,0.525647,0.509234,0.574376,0.506986,0.352594,0.82251,0.793887,0.202394,0.372,0.297421,0.48593,0.313489,0.417019,0.473863,0.481952,0.789744,0.937933,0.219957,0.0867583,0.213016,0.257581,0.306778,0.368009,0.516161,0.149154,0.302107,0.780017,0.598376,0.993059,0.681197,0.796833,0.447,0.631254,0.599302,0.975381,0.241724,0.203517,0.675898,0.254032,0.593244,0.496898,0.291991,0.693556,0.476881,0.15556,0.465476,0.592725,0.875447,0.735078,0.660112,0.682946,0.414214,0.277745,0.415655,0.210578,0.375129,0.658666,0.307018,0.19593,0.420132,0.288264,0.697766,0.54045,0.16414,0.485192,0.193367,0.227897,0.432278,0.365739,0.58654,0.403936,0.326264,0.24021,0.712296,0.308426,0.793553,0.537664,0.63648,0.683095,0.393482,0.842529,0.587836,0.857112,0.535687,0.260698,0.628818,0.527918,0.962287,0.546377,0.294013,0.362292,0.251684,0.516765,0.533214,0.380058,0.544392,0.58155,0.633758,0.497808,0.701346,0.741186,0.212975,0.446456,0.335602,0.847259,0.428988,0.427501,0.61865,0.591991,0.371883,0.760919,0.737264,0.506747,0.387692,0.750933,0.399946,0.428759,0.113799,0.575907,0.358215,0.983591,0.573659,0.623034,0.327109,0.614937,0.54748,0.825205,0.846996,0.247428,0.734435,0.600262,0.683016,0.706597,0.700344,0.470597,0.157609,0.708494,0.14058,0.187268,0.487947,0.920115,0.883605,0.526182,0.23,0.707263,0.500094,0.932939,0.884283,0.925158,0.937944,0.641807,0.905631,0.876715,0.912043,0.893425,0.912245,0.526797,0.740229,0.93698,0.900691,0.380712,0.833958,0.141957,0.859115,0.384261,0.96139,0.699462,0.444144,0.938353,0.89771,0.790513,0.636398,0.9764,0.984016,0.472538,0.567003,0.785221,0.212614,0.564398,0.584672,0.852336,0.947613,0.16504,0.936758,0.727883,0.970588,0.407716,0.865352,0.970216,0.560684,0.988639,0.710257,0.619637,0.979614,0.177253,0.926921,0.189456,0.717807,0.98784,0.8176,0.0919205,0.648031,0.658362,0.811346,0.402463,0.121206,0.143699,0.895196,0.547086,0.159636,0.916061,0.376091,0.259157,0.0567885,0.566109,0.70572,0.449954,0.789986,0.192911,0.259141,0.607087,0.458064,0.993114,0.462429,0.702235,0.25422,0.541603,0.556228,0.855571,0.814606,0.89832,0.858796,0.872361,0.874013,0.114432,0.715756,0.91892,0.944923,0.985256,0.767989,0.656826,0.770712,0.50228,0.892947,0.21007,0.642527,0.333901,0.830598,0.589568,0.592968,0.848819,0.887251,0.859885,0.702981,0.880311,0.151878,0.901081,0.621927,0.715288,0.654138,0.774723,0.889111,0.762222,0.59884,0.191897,0.94962,0.50796,0.368799,0.637226,0.509574,0.815347,0.828331,0.664579,0.642691,0.740375,0.658769,0.942576,0.962329,0.323185,0.843827,0.0847171,0.261339,0.786693,0.986404,0.510977,0.547806,0.78892,0.898374,0.949646,0.907496,0.774553,0.882589,0.442609,0.896226,0.80577,0.614452,0.855887,0.642475,0.932203,0.89816,0.848665,0.864828,0.810569,0.947952,0.658026,0.595703,0.315097,0.779701,0.657795,0.147894,0.625216,0.752893,0.622192,0.294118,0.762137,0.56305,0.628185,0.56424,0.685278,0.663217,0.356279,0.373564,0.571642,0.742343,0.649921,0.747657,0.662256,0.14708,0.602579,0.0810678,0.688046,0.6919,0.13414,0.823809,0.682601,0.276474,0.619012,0.458936,0.64592,0.14327,0.366902,0.461022,0.603657,0.699036,0.197385,0.341247,0.481022,0.663924,0.382899,0.690717,0.277689,0.664123,0.424149,0.428828,0.520437,0.343234,0.56202,0.702807,0.577896,0.167392,0.27322,0.22134,0.195528,0.767906,0.650305,0.866489,0.544167,0.449866,0.384185,0.414781,0.249171,0.678642,0.553004,0.686951,0.637063,0.46149,0.409147,0.820512,0.605271,0.556477,0.750457,0.533477,0.680896,0.460642,0.613545,0.61579,0.295569,0.752335,0.757358,0.654735,0.674587,0.662315,0.51031,0.264557,0.737348,0.437434,0.694833,0.732422,0.587939,0.647906,0.504741,0.084866,0.367371,0.547991,0.480913,0.749937,0.69157,0.58586,0.596617,0.378621,0.651396,0.517352,0.455187,0.682887,0.329999,0.65125,0.409482,0.226719,0.227361,0.534493,0.315496,0.176359,0.227215,0.834572,0.757328,0.303866,0.621034,0.711117,0.624999,0.326761,0.382401,0.266095,0.454858,0.265087,0.402864,0.274042,0.309364,0.474347,0.416949,0.189841,0.276311,0.354746,0.160298,0.491672,0.655972,0.083904,0.793321,0.86318,0.509942,0.759521,0.748352,0.647234,0.700164,0.808646,0.744466,0.598612,0.789177,0.761425,0.482811,0.558381,0.659682,0.64545,0.210944,0.133562,0.840422,0.436971,0.682681,0.693478,0.435373,0.636566,0.628086,0.786522,0.788583,0.738739,0.568069,0.694262,0.367768,0.843134,0.697002,0.662776,0.375214,0.342479,0.831075,0.584807,0.553916,0.0627657,0.291242,0.770651,0.391636,0.691105,0.594658,0.550009,0.678211,0.00278078,0.659112,0.876701
}}
}}

Revision as of 12:54, 5 September 2012


Full id: C617_mucinous_gall_signet_bile_maxillary_keratoacanthoma_Alveolar



Phase1 CAGE Peaks

Hg19::chr10:88106150..88106156,+p@chr10:88106150..88106156
+
Hg19::chr11:70781237..70781270,-p@chr11:70781237..70781270
-
Hg19::chr13:99644885..99644901,+p@chr13:99644885..99644901
+
Hg19::chr14:102196739..102196744,+p1@LINC00239
Hg19::chr16:16011740..16011741,-p@chr16:16011740..16011741
-
Hg19::chr16:52028463..52028468,-p@chr16:52028463..52028468
-
Hg19::chr16:52028472..52028487,-p@chr16:52028472..52028487
-
Hg19::chr16:52028503..52028515,-p@chr16:52028503..52028515
-
Hg19::chr1:240996509..240996525,-p@chr1:240996509..240996525
-
Hg19::chr20:62321640..62321645,+p1@BC131817
Hg19::chr5:172722414..172722417,-p@chr5:172722414..172722417
-
Hg19::chr6:31080343..31080359,-p1@C6orf15
Hg19::chr7:55757275..55757282,-p1@FKBP9L
Hg19::chr7:73118172..73118185,-p3@STX1A


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


GO IDGO nameFDR corrected p-value
GO:0050796regulation of insulin secretion0.0214651323421493
GO:0030073insulin secretion0.0214651323421493
GO:0046883regulation of hormone secretion0.0214651323421493
GO:0030072peptide hormone secretion0.0214651323421493
GO:0002790peptide secretion0.0214651323421493
GO:0005484SNAP receptor activity0.0274245201189629
GO:0046879hormone secretion0.0274245201189629
GO:0015833peptide transport0.0275212931074951
GO:0051046regulation of secretion0.0369868979872323
GO:0003001generation of a signal involved in cell-cell signaling0.0394816897354447
GO:0006836neurotransmitter transport0.0399850147348268



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 cell4.30e-23254
endo-epithelial cell5.04e-1443
endodermal cell3.82e-1259
respiratory epithelial cell1.73e-0813
epithelial cell of lung1.24e-0719
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure6.04e-12169
endoderm6.04e-12169
presumptive endoderm6.04e-12169
respiratory tract9.64e-1253
respiratory system2.16e-1072
digestive system3.18e-10155
digestive tract3.18e-10155
primitive gut3.18e-10155
mixed endoderm/mesoderm-derived structure4.87e-10130
respiratory system epithelium8.44e-1028
foregut2.09e-0998
subdivision of digestive tract2.20e-09129
endodermal part of digestive tract2.20e-09129
segment of respiratory tract7.29e-0946
anatomical space8.18e-09104
thoracic cavity element1.19e-0834
thoracic cavity1.19e-0834
lung1.61e-0822
respiratory tube1.61e-0822
respiration organ1.61e-0822
pair of lungs1.61e-0822
lung primordium1.61e-0822
lung bud1.61e-0822
endo-epithelium2.16e-0882
thoracic segment organ3.95e-0835
epithelial bud5.24e-0837
trunk region element7.69e-08107
immaterial anatomical entity1.13e-07126
respiratory tract epithelium1.24e-0719
lung epithelium1.24e-0719
respiratory primordium2.01e-0738
endoderm of foregut2.01e-0738
Disease
Ontology termp-valuen
carcinoma1.17e-18106
cell type cancer2.33e-17143
cancer3.27e-10235
disease of cellular proliferation7.51e-10239
squamous cell carcinoma2.80e-0814


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
NR3C1#290844.278006666049440.01156838455163820.0422873023061334



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.