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Coexpression cluster:C1769: Difference between revisions

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|full_id=C1769_sacrococcigeal_rectum_leiomyoma_Prostate_smooth_small_Smooth
|full_id=C1769_sacrococcigeal_rectum_leiomyoma_Prostate_smooth_small_Smooth
|id=C1769
|id=C1769
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=CL:0002504!7.53e-09!3;CL:1000279!7.53e-09!3;CL:1000280!7.53e-09!3;CL:0002622!1.89e-08!3
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.91e-10!115;UBERON:0001017!5.32e-07!82;UBERON:0003076!5.96e-07!15;UBERON:0003057!5.96e-07!15
|ontology_enrichment_uberon=UBERON:0003076!1.34e-14!15;UBERON:0003057!1.34e-14!15;UBERON:0005409!2.28e-14!25;UBERON:0002298!5.43e-14!6;UBERON:0011216!1.02e-13!223;UBERON:0000160!4.77e-13!17;UBERON:0004921!3.01e-12!118;UBERON:0004733!4.29e-12!12;UBERON:0002028!4.29e-12!12;UBERON:0007277!4.29e-12!12;UBERON:0001046!6.40e-12!19;UBERON:0000059!3.56e-11!11;UBERON:0004732!4.76e-11!13;UBERON:0000162!9.94e-11!14;UBERON:0001353!9.94e-11!14;UBERON:0000163!9.94e-11!14;UBERON:0006866!9.94e-11!14;UBERON:0000164!9.94e-11!14;UBERON:0000931!9.94e-11!14;UBERON:0007023!2.28e-10!114;UBERON:0001155!3.37e-10!9;UBERON:0001007!4.28e-10!145;UBERON:0001555!4.28e-10!145;UBERON:0007026!4.28e-10!145;UBERON:0004122!6.55e-10!15;UBERON:0004119!6.57e-10!160;UBERON:0000925!6.57e-10!160;UBERON:0006595!6.57e-10!160;UBERON:0000077!8.60e-10!29;UBERON:0003937!1.27e-09!12;UBERON:0005399!1.27e-09!12;UBERON:0003101!1.98e-09!22;UBERON:0000079!1.98e-09!22;UBERON:0005156!2.31e-09!59;UBERON:0000990!2.31e-09!59;UBERON:0000062!1.10e-08!503;UBERON:0003064!1.13e-08!28;UBERON:0001896!1.58e-08!3;UBERON:0005290!1.58e-08!3;UBERON:0010096!1.58e-08!3;UBERON:0002367!6.16e-08!11;UBERON:0010147!6.16e-08!11;UBERON:0009846!6.16e-08!11;UBERON:0003353!6.16e-08!11;UBERON:0004902!6.16e-08!11;UBERON:0003820!6.16e-08!11;UBERON:0009847!6.16e-08!11;UBERON:0000477!3.22e-07!373;UBERON:0000988!3.61e-07!3;UBERON:0000481!4.60e-07!342
|tf_chipseq_enrich=EP300#2033;4:5.41915338097856:0.0020938692794389:0.0121173388194891!RAD21#5885;4:8.28402711636506:0.000401162263912245:0.00386646231826605
|tf_chipseq_enrich=EP300#2033;4:5.41915338097856:0.0020938692794389:0.0121173388194891!RAD21#5885;4:8.28402711636506:0.000401162263912245:0.00386646231826605
|tfbs_overrepresentation=0.23317,0.0958562,0.00591253,0.078254,0.0064802,0.43203,0.0706464,0.0130832,0.0539364,0.0424746,0.221396,0.346629,0.294377,8.83742e-05,0.00263517,0.101024,0.00224213,0.158251,0.0865245,0.173528,0.29418,0.211047,0.000434037,0.153106,0.0683222,0.332688,0.324018,0.146582,0.0282046,0.0119764,0.31768,0.182756,0.0298713,0.00735786,0.108398,0.136785,0.578129,0.070583,0.192426,0.108683,0.155571,0.0406818,0.00219687,0.0459718,0.193292,0.0596699,0.0625547,0.28382,0.178503,0.193726,0.243359,0.0886583,0.114185,0.150136,0.308837,0.0632035,0.172598,0.061176,0.127101,0.169687,0.0485674,0.236408,0.174369,0.123348,0.0892839,0.0827236,0.515105,0.0980005,0.139298,0.0379738,0.547889,0.110232,0.143944,0.190944,0.012429,0.0283664,0.0127862,0.00263851,0.0613084,0.0120583,0.154245,0.348799,0.0698251,0.183986,0.436695,0.38341,0.104918,0.323505,0.790836,0.102375,0.138802,0.0812726,0.153861,0.0777027,0.138224,0.184264,0.769004,0.242703,0.149747,0.413729,0.000148728,0.416542,0.225088,0.0610111,0.0648403,0.0672793,0.109136,0.15155,0.228612,0.097251,0.285407,0.0560173,0.23661,0.0293017,0.162943,0.0556189,0.0336673,0.0926302,0.220791,0.13579,0.262107,0.0623132,0.222452,0.0101186,0.01438,0.277102,0.000588944,0.0245339,0.136609,0.214614,0.0973103,0.121587,0.0935301,0.0376876,0.200735,0.016024,0.105753,0.0905147,0.0544577,0.0065834,0.037671,0.203496,0.316207,0.246229,0.779726,0.112838,0.159217,0.1364,0.0640569,0.193163,0.0545278,0.227801,0.282656,0.0439093,0.070163,0.188135,0.121467,0.0703645,0.00369024,0.0555742,0.00101828,0.0124693,0.186743,0.029797,0.412853,0.183121,0.065826,0.0221909,0.0663482,0.463935,0.281162,0.218835,0.646289,0.0885874,0.129639,0.145577,0.22277,0.284267,0.0432639,0.0586816,0.0343712,0.195671,0.0452583,6.21348e-05,0.11983,0.190123,0.286036,0.0660586,0.134265,0.272191,0.172119,0.292239,0.196376,0.351465,0.18064,0.0772176,0.126988,0.0984435,0.110187,0.176022,0.144361,0.0986228,0.0508565,0.0989516,0.21691,0.393782,0.0169899,0.240045,0.319604,0.279218,0.0752697,0.167805,0.193654,0.180992,0.0256232,0.265567,0.258402,0.162511,0.102771,0.165687,0.0275026,0.540012,0.0331894,0.0033588,0.00751221,0.201982,0.220536,0.139142,0.0987108,0.09782,0.167847,0.554981,0.0687568,0.124225,0.1547,0.150448,0.0774663,0.0928873,0.257365,0.00809006,0.285222,0.511,0.158559,0.134615,0.0185225,0.217494,0.132125,0.179065,0.540443,0.187334,0.000230043,0.289141,0.289982,0.157983,0.158078,0.000233772,0.000978137,0.0551792,0.113261,0.766691,0.101058,0.0416746,0.25718,0.204241,0.0568578,0.131428,0.131579,0.148683,0.188945,0.122666,0.419402,0.00552332,0.387442,0.259312,1.91789e-05,0.0626022,0.2074,0.0613825,0.0603274,0.467941,0.0907735,0.161661,0.00975252,0.517141,0.14923,0.00161422,0.396701,0.258806,0.541514,0.0247857,0.00600163,0.0305032,0.568246,0.486439,0.0098791,0.0233572,0.410803,3.10044e-05,0.0119132,0.569955,0.426202,0.19503,0.0475794,0.528152,0.284119,0.601223,5.07614e-05,0.488132,0.336705,0.604733,0.187073,0.645432,0.0989863,0.714193,0.126184,0.537972,0.591562,0.668584,0.385794,0.102625,0.450485,0.299354,0.470142,0.344006,0.00689628,0.201404,0.107686,0.0261767,0.762263,0.0207023,0.000565999,0.174433,0.592924,0.438692,0.660225,0.619033,0.541742,0.17537,0.0740284,0.0451617,0.0565206,0.163274,0.00928443,0.415372,0.0753458,0.289863,0.507647,0.137929,0.409489,0.226746,0.0068829,0.00779982,0.036478,0.000137856,0.423719,0.02328,0.0035016,0.109234,0.11883,0.288602,0.194485,0.0115589,0.0598994,0.588284,0.553251,0.732646,0.386101,0.260733,0.337121,0.464864,0.861932,0.0740433,0.00769413,8.90189e-05,0.000469092,0.0635587,0.687274,0.000343484,0.034252,0.294103,0.111787,0.00469812,0.128,0.418989,0.759561,0.0151512,0.350461,0.495024,0.000564456,0.246694,0.165722,0.0648625,0.00540405,0.23106,0.702113,0.961692,0.493489,0.0286189,0.230597,0.00953273,0.0455037,0.0781633,0.641833,0.0132352,0.241286,0.0764074,0.217887,0.0143968,0.214395,0.158849,0.732038,0.0211405,0.10833,0.00580989,0.0241289,0.455709,0.00494219,0.00688487,0.0367334,4.88248e-10,0.398041,0.524026,0.0690809,0.0119366,0.227327,0.00740683,1.62001e-07,0.207705,0.000673614,0.711229,0.0333777,0.0165193,0.0161717,0.498776,0.387091,0.423517,0.0274367,0.0826665,0.0359783,0.251608,0.365107,0.0440487,6.96563e-06,0.295455,0.144104,0.0972855,0.129462,0.226009,0.508875,0.370345,0.0363258,0.0944328,0.0570792,0.244483,0.0870485,0.469232,0.113555,0.0910724,0.299839,0.126587,0.0940929,0.00240742,0.343849,0.0561517,0.622796,0.621499,3.49338e-05,0.179502,0.111889,0.0715061,0.023355,0.201779,0.0248508,0.171725,0.412647,0.102448,0.550877,0.029672,0.453305,0.0182061,0.561724,0.00298503,0.266371,5.99893e-05,0.168118,0.145381,0.140277,0.251925,0.172066,0.0720324,0.00647589,0.19738,0.205854,0.32541,0.0508541,0.035208,0.0818982,0.134306,0.108669,0.284804,0.178494,0.338195,0.146979,0.304235,0.210475,0.294266,0.0790025,0.0541661,0.580279,0.203728,0.275452,0.288155,0.265827,0.141761,0.153627,0.0186891,0.342497,0.171961,0.415228,0.00800917,0.272406,0.223952,0.327153,0.0496113,0.20949,0.0730994,0.0857377,0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14,0.344469,0.00121753,0.303359,0.0494743,1.90406e-06,0.00254622,0.00150414,1.57394e-05,7.96686e-05,0.151046,0.483953,0.00941969,0.00730933,0.15463,0.13907,0.0267252,0.000315243,0.250466,0.000219787,0.115686,0.408975,0.000816283,0.0090162,0.27567,0.00312626,0.33299,8.28294e-07,0.00711361,0.00721116
}}
}}

Revision as of 11:40, 19 October 2012


Full id: C1769_sacrococcigeal_rectum_leiomyoma_Prostate_smooth_small_Smooth



Phase1 CAGE Peaks

Hg19::chr16:86229728..86229756,+p@chr16:86229728..86229756
+
Hg19::chr9:128246769..128246778,-p@chr9:128246769..128246778
-
Hg19::chr9:128246806..128246820,-p9@MAPKAP1
Hg19::chr9:128246863..128246905,-p7@MAPKAP1
Hg19::chr9:128246911..128246949,-p4@MAPKAP1


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><br>

Uber Anatomy
Ontology termp-valuen
posterior neural tube1.34e-1415
chordal neural plate1.34e-1415
gastrointestinal system2.28e-1425
brainstem5.43e-146
organ system subdivision1.02e-13223
intestine4.77e-1317
subdivision of digestive tract3.01e-12118
segmental subdivision of hindbrain4.29e-1212
hindbrain4.29e-1212
presumptive hindbrain4.29e-1212
hindgut6.40e-1219
large intestine3.56e-1111
segmental subdivision of nervous system4.76e-1113
cloaca9.94e-1114
anal region9.94e-1114
embryonic cloaca9.94e-1114
terminal part of digestive tract9.94e-1114
primitive urogenital sinus9.94e-1114
proctodeum9.94e-1114
adult organism2.28e-10114
colon3.37e-109
digestive system4.28e-10145
digestive tract4.28e-10145
primitive gut4.28e-10145
genitourinary system6.55e-1015
endoderm-derived structure6.57e-10160
endoderm6.57e-10160
presumptive endoderm6.57e-10160
mixed endoderm/mesoderm-derived structure8.60e-1029
sex gland1.27e-0912
male reproductive gland1.27e-0912
male organism1.98e-0922
male reproductive system1.98e-0922
reproductive structure2.31e-0959
reproductive system2.31e-0959
organ1.10e-08503
intermediate mesoderm1.13e-0828
medulla oblongata1.58e-083
myelencephalon1.58e-083
future myelencephalon1.58e-083
prostate gland6.16e-0811
male accessory sex gland6.16e-0811
embryonic cloacal epithelium6.16e-0811
epithelium of hindgut6.16e-0811
urogenital sinus epithelium6.16e-0811
prostate bud6.16e-0811
prostate field6.16e-0811
anatomical cluster3.22e-07373
pons3.61e-073
multi-tissue structure4.60e-07342


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
EP300#203345.419153380978560.00209386927943890.0121173388194891
RAD21#588548.284027116365060.0004011622639122450.00386646231826605



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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