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Difference between revisions of "Coexpression cluster:C576"

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|gostat_on_coexpression_clusters=GO:0042493!response to drug!0.0221113997876872!64240;55244$GO:0006855!multidrug transport!0.0363522643590524!55244$GO:0005017!platelet-derived growth factor receptor activity!0.0363522643590524!5159$GO:0004873!asialoglycoprotein receptor activity!0.0363522643590524!432$GO:0004992!platelet activating factor receptor activity!0.0387711830818315!5159$GO:0030299!cholesterol absorption!0.0458376287579303!64240$GO:0003917!DNA topoisomerase type I activity!0.0458376287579303!116447$GO:0044241!lipid digestion!0.0458376287579303!64240$GO:0050892!intestinal absorption!0.0458376287579303!64240$GO:0003918!DNA topoisomerase (ATP-hydrolyzing) activity!0.0458376287579303!116447$GO:0005160!transforming growth factor beta receptor binding!0.0458376287579303!3626$GO:0016020!membrane!0.0458376287579303!64240;5909;5159;55244;64083;432;7803$GO:0010212!response to ionizing radiation!0.0458376287579303!64240$GO:0006268!DNA unwinding during replication!0.0458376287579303!116447$GO:0006265!DNA topological change!0.0458376287579303!116447$GO:0003916!DNA topoisomerase activity!0.0458376287579303!116447$GO:0015893!drug transport!0.0458376287579303!55244$GO:0032392!DNA geometric change!0.0458376287579303!116447$GO:0032508!DNA duplex unwinding!0.0458376287579303!116447$GO:0022600!digestive system process!0.0459595450544434!64240$GO:0015238!drug transporter activity!0.0483613875409549!55244$GO:0005021!vascular endothelial growth factor receptor activity!0.0483613875409549!5159
 
|gostat_on_coexpression_clusters=GO:0042493!response to drug!0.0221113997876872!64240;55244$GO:0006855!multidrug transport!0.0363522643590524!55244$GO:0005017!platelet-derived growth factor receptor activity!0.0363522643590524!5159$GO:0004873!asialoglycoprotein receptor activity!0.0363522643590524!432$GO:0004992!platelet activating factor receptor activity!0.0387711830818315!5159$GO:0030299!cholesterol absorption!0.0458376287579303!64240$GO:0003917!DNA topoisomerase type I activity!0.0458376287579303!116447$GO:0044241!lipid digestion!0.0458376287579303!64240$GO:0050892!intestinal absorption!0.0458376287579303!64240$GO:0003918!DNA topoisomerase (ATP-hydrolyzing) activity!0.0458376287579303!116447$GO:0005160!transforming growth factor beta receptor binding!0.0458376287579303!3626$GO:0016020!membrane!0.0458376287579303!64240;5909;5159;55244;64083;432;7803$GO:0010212!response to ionizing radiation!0.0458376287579303!64240$GO:0006268!DNA unwinding during replication!0.0458376287579303!116447$GO:0006265!DNA topological change!0.0458376287579303!116447$GO:0003916!DNA topoisomerase activity!0.0458376287579303!116447$GO:0015893!drug transport!0.0458376287579303!55244$GO:0032392!DNA geometric change!0.0458376287579303!116447$GO:0032508!DNA duplex unwinding!0.0458376287579303!116447$GO:0022600!digestive system process!0.0459595450544434!64240$GO:0015238!drug transporter activity!0.0483613875409549!55244$GO:0005021!vascular endothelial growth factor receptor activity!0.0483613875409549!5159
 
|id=C576
 
|id=C576
|ontology_enrichment_celltype=CL:0000136!1.49e-11!15
+
|ontology_enrichment_celltype=CL:0000181!3.55e-46!12;CL:0000417!3.55e-46!12;CL:0000668!3.55e-46!12;CL:0000412!3.55e-46!12;CL:0000182!3.55e-46!12;CL:0000223!9.15e-10!58
 
|ontology_enrichment_disease=
 
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.53e-10!115;UBERON:0009856!6.54e-08!26;UBERON:0007499!1.67e-07!25;UBERON:0009854!2.07e-07!23;UBERON:0000475!2.71e-07!365;UBERON:0002107!3.11e-07!19;UBERON:0006925!3.11e-07!19;UBERON:0008836!3.11e-07!19;UBERON:0008835!5.31e-07!22;UBERON:0003894!5.31e-07!22;UBERON:0002417!5.32e-07!61;UBERON:0000916!5.32e-07!61;UBERON:0009497!7.68e-07!25;UBERON:0000015!7.68e-07!25;UBERON:0002423!7.68e-07!25;UBERON:0006235!7.68e-07!25;UBERON:0004161!7.68e-07!25
+
|ontology_enrichment_uberon=UBERON:0002107!1.67e-56!19;UBERON:0006925!1.67e-56!19;UBERON:0008836!1.67e-56!19;UBERON:0008835!7.93e-49!22;UBERON:0003894!7.93e-49!22;UBERON:0009854!1.03e-46!23;UBERON:0007499!5.45e-43!25;UBERON:0009497!5.45e-43!25;UBERON:0000015!5.45e-43!25;UBERON:0002423!5.45e-43!25;UBERON:0006235!5.45e-43!25;UBERON:0004161!5.45e-43!25;UBERON:0009856!2.42e-41!26;UBERON:0002365!1.07e-34!31;UBERON:0002330!1.07e-34!31;UBERON:0002368!9.61e-31!35;UBERON:0000949!6.32e-24!45;UBERON:0003929!6.12e-20!54;UBERON:0005172!6.12e-20!54;UBERON:0005173!6.12e-20!54;UBERON:0002530!3.01e-18!59;UBERON:0002417!6.06e-18!60;UBERON:0000916!6.06e-18!60;UBERON:0005911!4.14e-13!82;UBERON:0001041!2.38e-12!87;UBERON:0005177!1.29e-10!101;UBERON:0009569!1.48e-09!112;UBERON:0000466!3.86e-09!117;UBERON:0003914!3.86e-09!117;UBERON:0004921!5.54e-09!118;UBERON:0005256!9.32e-09!122;UBERON:0001007!2.81e-07!145;UBERON:0001555!2.81e-07!145;UBERON:0007026!2.81e-07!145;UBERON:0000490!3.55e-07!148
 
|tf_chipseq_enrich=CEBPB#1051;6:3.18845905032993:0.00708661775802942:0.02955157804076!EP300#2033;8:3.61276892065237:0.000545267193917108:0.00470949061077645!FOXA1#3169;5:3.69380658312848:0.00829376303603737:0.0326741726790157!FOXA2#3170;5:8.21015458422175:0.000234934965228373:0.00256442023761351!HDAC2#3066;5:4.47187341220875:0.00365865752308656:0.0184753182986963!HEY1#23462;12:3.23208883448457:1.10567306413993e-05:0.00028597174132172!HNF4A#3172;9:13.8793742177722:2.07194282394466e-09:1.78393764707301e-07!HNF4G#3174;10:19.1689483509645:6.57815993221828e-12:8.41931918089393e-10!RXRA#6256;6:8.0298468556533:5.16480117100425e-05:0.000878941941499939!SP1#6667;9:3.41902882688454:0.000283012712846588:0.00301085512040184!TCF7L2#6934;5:3.59005885437911:0.00934660680353175:0.0353038071592786
 
|tf_chipseq_enrich=CEBPB#1051;6:3.18845905032993:0.00708661775802942:0.02955157804076!EP300#2033;8:3.61276892065237:0.000545267193917108:0.00470949061077645!FOXA1#3169;5:3.69380658312848:0.00829376303603737:0.0326741726790157!FOXA2#3170;5:8.21015458422175:0.000234934965228373:0.00256442023761351!HDAC2#3066;5:4.47187341220875:0.00365865752308656:0.0184753182986963!HEY1#23462;12:3.23208883448457:1.10567306413993e-05:0.00028597174132172!HNF4A#3172;9:13.8793742177722:2.07194282394466e-09:1.78393764707301e-07!HNF4G#3174;10:19.1689483509645:6.57815993221828e-12:8.41931918089393e-10!RXRA#6256;6:8.0298468556533:5.16480117100425e-05:0.000878941941499939!SP1#6667;9:3.41902882688454:0.000283012712846588:0.00301085512040184!TCF7L2#6934;5:3.59005885437911:0.00934660680353175:0.0353038071592786
 
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7635,0.901088,0.154781,0.882857,0.710461,0.182373,0.264717,0.75446,0.13973,0.438047,0.441658,0.44727,0.135062,0.981414,0.541932,0.179723,0.367181,0.24648,0.540592,0.429747,0.705816,0.651424,0.504688,0.713716,0.741574,0.815718,0.326917,0.611971,0.34762,0.267461,0.604786,0.550255,0.533561,0.233089,0.176102,0.372391,0.843129,0.815875,0.215174,0.392525,0.565209,0.509791,0.331688,0.439061,0.497452,0.505726,0.979645,0.949109,0.233675,0.407539,0.226368,0.273208,0.324685,0.388388,0.540612,0.158915,0.319809,0.482262,0.800914,0.61462,0.125943,0.509101,0.469911,0.656617,0.624641,0.981104,0.256564,0.216359,0.91758,0.269486,0.618557,0.533476,0.30924,0.718381,0.820988,0.165697,0.488864,0.618035,0.999525,0.983598,0.321495,0.707921,0.436169,0.294337,0.437654,0.223799,0.395767,0.683892,0.324936,0.208357,0.44227,0.305343,0.722525,0.565276,0.174777,0.509038,0.205654,0.24203,0.454777,0.386034,0.244488,0.425563,0.356389,0.254974,0.736792,0.326406,0.815556,0.200788,0.661828,0.708068,0.414762,0.588704,0.613121,0.875652,0.560447,0.276477,0.286981,0.552561,0.970159,0.57128,0.311354,0.0847977,0.267022,0.541227,0.557937,0.400873,0.56927,0.606796,0.29225,0.521917,0.726044,0.765005,0.817144,0.469353,0.354726,0.597562,0.451391,0.44986,0.644026,0.617298,0.392405,0.453212,0.41919,0.531029,0.408774,0.774474,0.0182221,0.451155,0.121414,0.601112,0.378227,0.81527,0.598846,0.648409,0.345883,0.640311,0.572397,0.287843,0.872903,0.262554,0.415259,0.625604,0.707991,0.146076,0.926845,0.953696,0.167866,0.929823,0.504701,0.199217,0.511852,0.138237,0.90018,0.572412,0.735674,0.731856,0.980451,0.784636,0.900804,0.937809,0.797581,0.300977,0.718633,0.893837,0.73349,0.909175,0.630484,0.888259,0.537307,0.881337,0.449625,0.847152,0.968931,0.789776,0.714598,0.595053,0.975131,0.724192,0.706894,0.99185,0.441432,0.812644,0.970208,0.763961,0.890267,0.818392,0.592132,0.600109,0.242131,0.986075,0.835475,0.871194,0.388507,0.189525,0.343354,0.752041,0.868723,0.708463,0.897255,0.824822,0.585751,0.915858,0.965065,0.665289,0.811212,0.677947,0.881035,0.629253,0.94674,0.814904,0.977993,0.679264,0.673328,0.68359,0.0354723,0.436246,0.764683,0.632508,0.0979855,0.571999,0.533166,0.4952,0.396764,0.848562,0.643204,0.59123,0.376927,0.472945,0.812139,0.235876,0.123171,0.632449,0.493733,0.766198,0.522032,0.927541,0.49191,0.856957,0.901021,0.874215,0.692204,0.913638,0.714069,0.987297,0.897112,0.715032,0.750356,0.749842,0.816149,0.896895,0.929859,0.682067,0.802534,0.526477,0.917409,0.598696,0.301767,0.352955,0.125692,0.962217,0.61828,0.867904,0.903526,0.715877,0.738074,0.195487,0.531781,0.708303,0.392377,0.153611,0.0286049,0.474062,0.681926,0.17779,0.636102,0.219311,0.745057,0.112855,0.74833,0.674053,0.839774,0.540114,0.85594,0.913116,0.473482,0.764216,0.224769,0.953177,0.970195,0.130144,0.689604,0.0989502,0.654574,0.817491,0.83789,0.547799,0.953968,0.233994,0.782494,0.959326,0.722917,0.79731,0.402657,0.799819,0.697468,0.408583,0.651586,0.874509,0.0258912,0.502587,0.701762,0.329585,0.724132,0.531956,0.877902,0.683257,0.074919,0.333365,0.48177,0.318846,0.15758,0.650589,0.776375,0.647568,0.311463,0.455022,0.222792,0.653553,0.589343,0.710222,0.688406,0.376218,0.394146,0.230576,0.76613,0.686514,0.433881,0.687453,0.94837,0.627929,0.659004,0.712952,0.359451,0.617892,0.844359,0.70758,0.669472,0.644388,0.482161,0.671228,0.15268,0.38724,0.484299,0.62901,0.723773,0.804782,0.360598,0.504775,0.689106,0.415859,0.715585,0.294279,0.689303,0.787739,0.451227,0.544961,0.728315,0.0127094,0.373192,0.236351,0.178215,0.2896,0.235131,0.207933,0.7909,0.675589,0.884374,0.569042,0.472855,0.405145,0.436753,0.264384,0.703671,0.213909,0.711872,0.66241,0.143106,0.777547,0.280203,0.630628,0.581499,0.437906,0.558205,0.705897,0.48391,0.638918,0.641165,0.31298,0.775835,0.780702,0.67999,0.699663,0.687511,0.534658,0.657796,0.419307,0.460081,0.719638,0.75647,0.613225,0.673203,0.528985,0.666362,0.747244,0.572915,0.504664,0.773508,0.359041,0.611134,0.621945,0.399385,0.676673,0.844055,0.490774,0.707863,0.348894,0.676528,0.431288,0.240791,0.241466,0.559235,0.333781,0.187694,0.241313,0.854523,0.780673,0.694879,0.64641,0.383919,0.282953,0.345521,0.403299,0.282135,0.477978,0.281079,0.424456,0.29046,0.327384,0.497947,0.438989,0.201933,0.292836,0.374626,0.170712,0.515655,0.681219,0.826788,0.815334,0.881301,0.534283,0.197939,0.771969,0.306962,0.369827,0.829964,0.768195,0.623948,0.234336,0.0701683,0.506604,0.583424,0.6849,0.304985,0.503829,0.740494,0.584799,0.459605,0.70766,0.361416,0.457962,0.661914,0.286206,0.808817,0.49578,0.762623,0.593207,0.719076,0.388139,0.862574,0.721773,0.687969,0.395855,0.361878,0.851225,0.610074,0.57891,0.469331,0.308457,0.793549,0.412853,0.715967,0.619978,0.574957,0.703245,0.767086,0.684335,0.893824
 
}}
 
}}

Revision as of 07:26, 19 October 2012


Full id: C576_Hepatocyte_hepatocellular_liver_Intestinal_mature_breast_Prostate



Phase1 CAGE Peaks

  Short description
Hg19::chr10:113987378..113987454,- p@chr10:113987378..113987454
-
Hg19::chr10:7755243..7755254,- p@chr10:7755243..7755254
-
Hg19::chr10:7773844..7773851,+ p@chr10:7773844..7773851
+
Hg19::chr12:57828432..57828442,+ p7@INHBC
Hg19::chr12:57828463..57828472,+ p9@INHBC
Hg19::chr16:85570675..85570678,+ p@chr16:85570675..85570678
+
Hg19::chr17:19437692..19437704,- p1@AK127534
Hg19::chr17:7082861..7082882,- p9@ASGR1
Hg19::chr1:21996247..21996270,- p6@RAP1GAP
Hg19::chr2:20793103..20793113,- p@chr2:20793103..20793113
-
Hg19::chr2:44066386..44066398,- p6@ABCG5
Hg19::chr5:149516966..149516977,- p8@PDGFRB
Hg19::chr5:32174797..32174803,- p17@GOLPH3
Hg19::chr6:64231645..64231678,+ p6@PTP4A1
Hg19::chr8:144417558..144417572,- p7@TOP1MT


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:0042493response to drug0.0221113997876872
GO:0006855multidrug transport0.0363522643590524
GO:0005017platelet-derived growth factor receptor activity0.0363522643590524
GO:0004873asialoglycoprotein receptor activity0.0363522643590524
GO:0004992platelet activating factor receptor activity0.0387711830818315
GO:0030299cholesterol absorption0.0458376287579303
GO:0003917DNA topoisomerase type I activity0.0458376287579303
GO:0044241lipid digestion0.0458376287579303
GO:0050892intestinal absorption0.0458376287579303
GO:0003918DNA topoisomerase (ATP-hydrolyzing) activity0.0458376287579303
GO:0005160transforming growth factor beta receptor binding0.0458376287579303
GO:0016020membrane0.0458376287579303
GO:0010212response to ionizing radiation0.0458376287579303
GO:0006268DNA unwinding during replication0.0458376287579303
GO:0006265DNA topological change0.0458376287579303
GO:0003916DNA topoisomerase activity0.0458376287579303
GO:0015893drug transport0.0458376287579303
GO:0032392DNA geometric change0.0458376287579303
GO:0032508DNA duplex unwinding0.0458376287579303
GO:0022600digestive system process0.0459595450544434
GO:0015238drug transporter activity0.0483613875409549
GO:0005021vascular endothelial growth factor receptor activity0.0483613875409549



Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Cell Type
Ontology termp-valuen
metabolising cell3.55e-4612
endopolyploid cell3.55e-4612
parenchymal cell3.55e-4612
polyploid cell3.55e-4612
hepatocyte3.55e-4612
endodermal cell9.15e-1058
Uber Anatomy
Ontology termp-valuen
liver1.67e-5619
digestive gland1.67e-5619
liver bud1.67e-5619
hepatic diverticulum7.93e-4922
liver primordium7.93e-4922
digestive tract diverticulum1.03e-4623
epithelial sac5.45e-4325
epithelium of foregut-midgut junction5.45e-4325
anatomical boundary5.45e-4325
hepatobiliary system5.45e-4325
foregut-midgut junction5.45e-4325
septum transversum5.45e-4325
sac2.42e-4126
exocrine gland1.07e-3431
exocrine system1.07e-3431
endocrine gland9.61e-3135
endocrine system6.32e-2445
gut epithelium6.12e-2054
abdomen element6.12e-2054
abdominal segment element6.12e-2054
gland3.01e-1859
abdominal segment of trunk6.06e-1860
abdomen6.06e-1860
endo-epithelium4.14e-1382
foregut2.38e-1287
trunk region element1.29e-10101
subdivision of trunk1.48e-09112
immaterial anatomical entity3.86e-09117
epithelial tube3.86e-09117
subdivision of digestive tract5.54e-09118
trunk mesenchyme9.32e-09122
digestive system2.81e-07145
digestive tract2.81e-07145
primitive gut2.81e-07145
unilaminar epithelium3.55e-07148


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CEBPB#105163.188459050329930.007086617758029420.02955157804076
EP300#203383.612768920652370.0005452671939171080.00470949061077645
FOXA1#316953.693806583128480.008293763036037370.0326741726790157
FOXA2#317058.210154584221750.0002349349652283730.00256442023761351
HDAC2#306654.471873412208750.003658657523086560.0184753182986963
HEY1#23462123.232088834484571.10567306413993e-050.00028597174132172
HNF4A#3172913.87937421777222.07194282394466e-091.78393764707301e-07
HNF4G#31741019.16894835096456.57815993221828e-128.41931918089393e-10
RXRA#625668.02984685565335.16480117100425e-050.000878941941499939
SP1#666793.419028826884540.0002830127128465880.00301085512040184
TCF7L2#693453.590058854379110.009346606803531750.0353038071592786



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.