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Coexpression cluster:C1527: Difference between revisions

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|full_id=C1527_glioblastoma_Lens_mesothelioma_mesenchymal_granulosa_Ciliary_Smooth
|full_id=C1527_glioblastoma_Lens_mesothelioma_mesenchymal_granulosa_Ciliary_Smooth
|id=C1527
|id=C1527
|ontology_enrichment_celltype=CL:0000055!2.37e-37!180;CL:0000393!1.18e-17!60;CL:0000211!1.18e-17!60;CL:0000222!1.73e-17!119;CL:0000192!4.71e-17!42;CL:0000514!4.71e-17!42;CL:0000183!6.36e-17!59;CL:0000359!1.45e-16!32;CL:0000187!2.19e-16!54;CL:0000680!1.94e-15!57;CL:0000056!1.94e-15!57;CL:0000355!1.94e-15!57;CL:0000057!1.57e-14!75;CL:0002321!4.52e-14!248;CL:0000220!6.89e-14!246;CL:0002319!5.64e-09!25;CL:0000133!7.10e-09!59;CL:0002494!1.75e-07!16;CL:0000243!4.62e-07!15;CL:0000125!4.62e-07!15;CL:0000030!4.62e-07!15;CL:0000339!4.62e-07!15;CL:0000095!8.18e-07!17;CL:0000123!8.18e-07!17;CL:0002539!8.79e-07!10
|ontology_enrichment_celltype=CL:0000055!1.26e-19!106;CL:0000222!2.03e-17!121;CL:0000393!1.76e-16!61;CL:0000211!1.76e-16!61;CL:0000183!4.56e-16!59;CL:0000192!6.92e-16!43;CL:0000514!6.92e-16!43;CL:0000359!9.72e-16!32;CL:0000187!1.59e-15!55;CL:0000057!3.61e-15!76;CL:0000680!1.40e-14!58;CL:0000056!1.40e-14!58;CL:0000355!1.40e-14!58;CL:0002321!2.75e-13!250;CL:0000133!4.11e-08!59;CL:0002319!4.76e-08!25;CL:0002494!4.49e-07!16
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004872!1.39e-27!84;UBERON:0001981!4.99e-25!60;UBERON:0007500!4.99e-25!60;UBERON:0004537!4.99e-25!60;UBERON:0006965!4.99e-25!60;UBERON:0002049!5.27e-25!79;UBERON:0007798!5.27e-25!79;UBERON:0003914!3.51e-23!118;UBERON:0000119!7.63e-23!312;UBERON:0000483!9.38e-23!309;UBERON:0001637!3.52e-22!42;UBERON:0003509!3.52e-22!42;UBERON:0004572!3.52e-22!42;UBERON:0000055!1.52e-21!69;UBERON:0000468!4.14e-21!659;UBERON:0000477!4.76e-21!286;UBERON:0004111!3.65e-20!241;UBERON:0000025!5.46e-20!194;UBERON:0004535!1.22e-19!110;UBERON:0000475!2.65e-19!365;UBERON:0001009!3.73e-19!113;UBERON:0000467!1.78e-18!625;UBERON:0000480!3.77e-18!626;UBERON:0000481!5.94e-18!347;UBERON:0004573!8.35e-18!33;UBERON:0004571!8.35e-18!33;UBERON:0000914!2.92e-16!83;UBERON:0002329!2.92e-16!83;UBERON:0003077!2.92e-16!83;UBERON:0003059!2.92e-16!83;UBERON:0007282!2.92e-16!83;UBERON:0009618!2.92e-16!83;UBERON:0007285!2.92e-16!83;UBERON:0004290!5.09e-16!70;UBERON:0002385!6.48e-16!63;UBERON:0001015!6.48e-16!63;UBERON:0000383!6.48e-16!63;UBERON:0000922!6.60e-16!612;UBERON:0005256!7.94e-16!143;UBERON:0001134!1.69e-15!61;UBERON:0002036!1.69e-15!61;UBERON:0003082!1.69e-15!61;UBERON:0000490!1.43e-14!138;UBERON:0002050!1.99e-14!605;UBERON:0005423!1.99e-14!605;UBERON:0000923!4.02e-14!604;UBERON:0005291!4.02e-14!604;UBERON:0006598!4.02e-14!604;UBERON:0002532!4.02e-14!604;UBERON:0000486!1.86e-13!82;UBERON:0000947!1.39e-11!21;UBERON:0010191!1.39e-11!21;UBERON:0004121!1.43e-10!169;UBERON:0000924!5.72e-10!173;UBERON:0006601!5.72e-10!173;UBERON:0002100!2.36e-09!216;UBERON:0000948!4.93e-09!24;UBERON:0005498!4.93e-09!24;UBERON:0004140!4.93e-09!24;UBERON:0009881!4.93e-09!24;UBERON:0004141!4.93e-09!24;UBERON:0003084!4.93e-09!24;UBERON:0007005!4.93e-09!24;UBERON:0004139!4.93e-09!24;UBERON:0004291!4.93e-09!24;UBERON:0003104!2.40e-08!238;UBERON:0009142!2.40e-08!238;UBERON:0007100!3.82e-08!27;UBERON:0003103!7.64e-08!69;UBERON:0000064!9.03e-08!219;UBERON:0000033!1.25e-07!123;UBERON:0001135!2.94e-07!15;UBERON:0000153!4.65e-07!129;UBERON:0007811!4.65e-07!129;UBERON:0003075!7.76e-07!86;UBERON:0007284!7.76e-07!86;UBERON:0004237!8.79e-07!10;UBERON:0004695!8.79e-07!10;UBERON:0002111!8.79e-07!10;UBERON:0004178!8.79e-07!10
|ontology_enrichment_uberon=UBERON:0000477!2.30e-29!373;UBERON:0004872!2.18e-26!83;UBERON:0002049!2.37e-24!78;UBERON:0007798!2.37e-24!78;UBERON:0007500!3.56e-24!59;UBERON:0001981!3.56e-24!59;UBERON:0004537!3.56e-24!59;UBERON:0006965!3.56e-24!59;UBERON:0003914!4.25e-23!117;UBERON:0000119!8.12e-23!309;UBERON:0000483!1.05e-22!306;UBERON:0001637!1.00e-21!42;UBERON:0003509!1.00e-21!42;UBERON:0004572!1.00e-21!42;UBERON:0000468!1.27e-21!656;UBERON:0000055!5.46e-21!68;UBERON:0004111!2.28e-20!240;UBERON:0000025!9.30e-20!192;UBERON:0000481!1.08e-19!342;UBERON:0000467!2.71e-19!624;UBERON:0000480!5.72e-19!625;UBERON:0004535!1.10e-18!109;UBERON:0001009!2.89e-18!112;UBERON:0004573!2.78e-17!33;UBERON:0004571!2.78e-17!33;UBERON:0007503!9.98e-17!78;UBERON:0007524!8.18e-16!73;UBERON:0000490!1.77e-15!148;UBERON:0003077!2.42e-15!72;UBERON:0007285!2.42e-15!72;UBERON:0002329!2.48e-15!71;UBERON:0003059!2.48e-15!71;UBERON:0007282!2.48e-15!71;UBERON:0004290!2.48e-15!71;UBERON:0009618!2.48e-15!71;UBERON:0000922!3.09e-15!592;UBERON:0002385!3.28e-15!64;UBERON:0001015!3.28e-15!64;UBERON:0000383!3.28e-15!64;UBERON:0003104!7.07e-15!160;UBERON:0009142!7.07e-15!160;UBERON:0001134!8.93e-15!62;UBERON:0002036!8.93e-15!62;UBERON:0003082!8.93e-15!62;UBERON:0005256!1.48e-14!122;UBERON:0005423!3.82e-14!581;UBERON:0002050!5.30e-14!564;UBERON:0000923!6.12e-14!560;UBERON:0010316!6.12e-14!560;UBERON:0005291!6.12e-14!560;UBERON:0006598!6.12e-14!560;UBERON:0010317!6.12e-14!560;UBERON:0002532!6.12e-14!560;UBERON:0000486!4.19e-13!83;UBERON:0010314!7.31e-13!132;UBERON:0000475!2.33e-12!264;UBERON:0000947!2.49e-11!21;UBERON:0010191!2.49e-11!21;UBERON:0004121!8.74e-10!171;UBERON:0000924!8.74e-10!171;UBERON:0006601!8.74e-10!171;UBERON:0000948!1.75e-08!24;UBERON:0005498!1.75e-08!24;UBERON:0004140!1.75e-08!24;UBERON:0009881!1.75e-08!24;UBERON:0004141!1.75e-08!24;UBERON:0003084!1.75e-08!24;UBERON:0007005!1.75e-08!24;UBERON:0004139!1.75e-08!24;UBERON:0004291!1.75e-08!24;UBERON:0002100!2.76e-08!199;UBERON:0000064!9.44e-08!218;UBERON:0003103!1.01e-07!68;UBERON:0007100!1.04e-07!27;UBERON:0003075!4.06e-07!82;UBERON:0007284!4.06e-07!82;UBERON:0001135!5.18e-07!15;UBERON:0000479!8.89e-07!773
|tf_chipseq_enrich=CTCF#10664;6:5.36025637307503:4.21437267579784e-05:0.000756002864801873!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380704118399273!RAD21#5885;6:10.3550338954563:8.10515055094479e-07:3.54329769104279e-05!TAF1#6872;6:3.34304628574529:0.000716247428463562:0.0057369556853521!TBP#6908;6:3.70677068709639:0.00038541647290796:0.00378099859233838!ZNF263#10127;6:8.22184163701068:3.23542093046082e-06:0.000108825805654234
|tf_chipseq_enrich=CTCF#10664;6:5.36025637307503:4.21437267579784e-05:0.000756002864801873!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380704118399273!RAD21#5885;6:10.3550338954563:8.10515055094479e-07:3.54329769104279e-05!TAF1#6872;6:3.34304628574529:0.000716247428463562:0.0057369556853521!TBP#6908;6:3.70677068709639:0.00038541647290796:0.00378099859233838!ZNF263#10127;6:8.22184163701068:3.23542093046082e-06:0.000108825805654234
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49099,0.106792,0.149864,0.109211,0.081783,0.0678906,0.076236,0.444489,0.31161,0.361651,0.0953991,0.0574586,0.0671053,0.0650516,0.575882,0.390908,0.0773818,0.115736,0.096963,0.229952,0.205891,0.207936,0.454529,0.0563868,0.023361,0.268235,0.0761868,0.167255,0.107028,0.267379,0.443026,0.387018,0.343977,0.244992,0.632847,0.417985,0.491614,0.146453,0.0559261,0.157053,0.332022,0.557852,0.273582,0.262915,0.306556,0.26147,0.170005,0.0001223,0.491788,0.092369,0.18076,0.692556,0.248113,0.148878,0.022954,0.240599,0.245625,0.205821,0.696152,0.100989,0.188919,0.0975693,0.119835,0.145322,0.178533,0.267392,0.0668831,0.142859,0.477403,0.932252,0.881177,0.387334,0.494914,0.224219,0.347904,0.324262,0.0771032,0.111827,0.0929171,0.63152,0.118035,0.0577116,0.510835,0.137556,0.397628,0.49748,0.0699003,0.235435,0.31953,0.954017,0.799035,0.370285,0.0138101,0.204831,0.130161,0.205669,0.0963721,0.0177725,0.369139,0.145449,0.0892237,0.208284,0.135613,0.401189,0.283386,0.0739625,0.247651,0.0879809,0.104922,0.215434,0.177269,0.31512,0.198881,0.0144746,0.111068,0.4137,0.146194,0.491435,0.0439802,0.35188,0.3889,0.192889,0.547162,0.316041,0.565635,0.280212,0.121421,0.346061,0.275075,1.67221e-05,0.287361,0.138613,0.175356,0.116846,0.267784,0.278571,0.185281,0.286026,0.00657377,0.349805,0.255609,0.404239,0.439697,0.493192,0.223892,0.160738,0.553042,0.213489,0.212611,0.338443,0.319005,0.180695,0.126288,0.436073,0.261316,0.189596,0.448839,0.196587,0.213353,0.0504588,0.307626,4.67345e-05,0.828194,0.306056,0.341713,0.156156,0.33569,0.288104,0.526446,0.761719,0.114697,2.88032e-05,0.324956,0.00165725,0.408751,0.281184,0.305648,0.070868,0.0921869,0.245,0.0850317,0.249379,0.661446,0.00259511,0.696439,0.648789,0.409327,0.005593,0.685907,0.603176,0.305003,0.00144666,0.355968,0.636386,0.592254,0.27962,0.616927,0.0988178,0.873099,0.677416,0.255628,0.628346,0.737948,0.750579,0.689958,0.772379,0.984603,0.230665,0.402631,0.768239,0.302735,0.0176172,0.488239,0.167812,0.799242,0.48468,0.494578,0.301433,0.129825,0.492887,0.0302301,0.727698,0.559471,0.717449,0.449761,0.6937,0.427531,0.801496,0.26122,0.275995,0.403716,0.297082,0.526245,0.059179,0.0504529,0.622334,0.607585,0.811787,0.72684,0.195513,0.518149,0.177522,0.36546,0.360788,0.368898,0.510705,0.447298,0.670481,0.576455,0.000498731,0.287839,0.262665,0.654187,0.183051,0.530004,0.583703,0.300816,0.407994,0.225997,0.00491301,0.808511,0.529993,0.329919,0.484887,0.583109,0.852842,0.000763116,0.766238,0.540605,0.881739,0.563634,0.00330009,0.624569,0.435062,0.110095,0.785953,0.00177896,0.292847,0.659285,0.0375679,0.0530046,0.823122,0.367684,0.00152867,0.258457,0.0081577,0.305952,0.356524,0.159817,0.00113431,0.145279,0.319704,0.555004,0.00276207,0.773067,0.000768764,0.00245485,0.783534,0.261107,0.594475,0.416321,0.365565,0.47205,0.610358,0.693748,0.578885,0.474879,0.0176389,0.518205,0.424119,0.60488,0.519279,0.515179,9.1927e-05,0.623664,0.757999,0.438945,0.619652,0.706112,0.167767,0.39196,0.758981,0.355152,8.14058e-05,0.712437,0.841498,0.520214,0.0365537,0.486574,0.809543,0.722202,0.639482,0.471879,0.600697,0.474504,0.621275,0.727464,0.589415,0.564042,0.0102952,0.846483,0.256519,0.55481,0.191884,0.509842,0.00468286,0.368631,0.0583945,0.149733,0.477082,0.368449,0.066291,0.0671598,0.450702,0.341084,0.138667,0.459605,0.298707,0.345583,0.299527,0.0140455,0.372757,0.172033,0.181635,0.006103,0.440771,0.613566,0.445744,0.371991,0.694395,0.0603409,0.349721,0.39301,0.396235,0.566617,0.524829,0.388491,0.357781,0.338712,0.231439,0.359148,0.0641227,0.177916,0.232711,0.327419,0.402268,0.479755,0.163801,0.0328293,0.373321,0.111784,0.395243,0.130132,0.373481,0.462042,0.213394,0.270174,0.406219,0.298,0.40549,0.30902,0.0755079,0.12783,0.101672,0.0890286,0.465261,0.362561,0.578088,0.285875,0.225945,0.18761,0.20516,0.115576,0.385234,0.291842,0.392097,0.352327,0.232997,0.451856,0.00684119,0.328594,0.294205,0.448388,0.278746,0.387086,0.232479,0.334662,0.336321,0.139427,0.450171,4.13838e-05,0.366035,0.381922,0.372037,0.263608,0.3488,0.43615,0.218495,0.398705,0.00030062,0.316114,0.360691,0.26003,0.35537,0.423126,0.0463025,0.244977,0.447896,0.395958,0.314638,0.322324,0.184473,0.363414,0.524458,0.482957,0.388728,0.157712,0.3633,0.202084,0.104337,0.104656,0.279419,0.149946,0.0797883,0.104584,0.537494,0.454949,0.378002,0.340219,0.412672,0.343186,0.155969,0.186603,0.124175,0.228962,0.12366,0.198264,0.128253,0.14669,0.240899,0.206424,0.0862744,0.129421,0.171188,0.0721407,0.251724,0.36701,0.156256,0.491191,0.573638,0.263371,0.457065,0.446399,0.360168,0.403229,0.507716,0.442751,0.323763,0.486842,0.458912,0.246162,0.295506,0.369944,0.358783,0.491474,0.417013,0.544575,0.21822,0.388558,0.397562,0.21727,0.351946,0.345508,0.484083,0.486223,0.437432,0.302171,0.398223,0.178399,0.547908,0.400541,0.372405,0.182559,0.164471,0.533328,0.313891,0.292462,0.46896,0.137165,0.467981,0.191837,0.395568,0.320916,0.289812,0.384881,0.441686,0.369492,0.592234
}}
}}

Revision as of 11:23, 19 October 2012


Full id: C1527_glioblastoma_Lens_mesothelioma_mesenchymal_granulosa_Ciliary_Smooth



Phase1 CAGE Peaks

Hg19::chr5:146889496..146889529,-p2@DPYSL3
Hg19::chr5:146889532..146889549,-p6@DPYSL3
Hg19::chr5:146889596..146889607,-p13@DPYSL3
Hg19::chr5:146889619..146889639,-p3@DPYSL3
Hg19::chr5:146889643..146889652,-p11@DPYSL3
Hg19::chr5:146889655..146889679,-p4@DPYSL3


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
anatomical cluster2.30e-29373
splanchnic layer of lateral plate mesoderm2.18e-2683
vasculature2.37e-2478
vascular system2.37e-2478
epithelial tube open at both ends3.56e-2459
blood vessel3.56e-2459
blood vasculature3.56e-2459
vascular cord3.56e-2459
epithelial tube4.25e-23117
cell layer8.12e-23309
epithelium1.05e-22306
artery1.00e-2142
arterial blood vessel1.00e-2142
arterial system1.00e-2142
multi-cellular organism1.27e-21656
vessel5.46e-2168
anatomical conduit2.28e-20240
tube9.30e-20192
multi-tissue structure1.08e-19342
anatomical system2.71e-19624
anatomical group5.72e-19625
cardiovascular system1.10e-18109
circulatory system2.89e-18112
systemic artery2.78e-1733
systemic arterial system2.78e-1733
epithelial vesicle9.98e-1778
dense mesenchyme tissue8.18e-1673
unilaminar epithelium1.77e-15148
paraxial mesoderm2.42e-1572
presumptive paraxial mesoderm2.42e-1572
somite2.48e-1571
presomitic mesoderm2.48e-1571
presumptive segmental plate2.48e-1571
dermomyotome2.48e-1571
trunk paraxial mesoderm2.48e-1571
embryo3.09e-15592
muscle tissue3.28e-1564
musculature3.28e-1564
musculature of body3.28e-1564
mesenchyme7.07e-15160
entire embryonic mesenchyme7.07e-15160
skeletal muscle tissue8.93e-1562
striated muscle tissue8.93e-1562
myotome8.93e-1562
trunk mesenchyme1.48e-14122
developing anatomical structure3.82e-14581
embryonic structure5.30e-14564
germ layer6.12e-14560
germ layer / neural crest6.12e-14560
embryonic tissue6.12e-14560
presumptive structure6.12e-14560
germ layer / neural crest derived structure6.12e-14560
epiblast (generic)6.12e-14560
multilaminar epithelium4.19e-1383
structure with developmental contribution from neural crest7.31e-13132
organism subdivision2.33e-12264
aorta2.49e-1121
aortic system2.49e-1121
ectoderm-derived structure8.74e-10171
ectoderm8.74e-10171
presumptive ectoderm8.74e-10171
heart1.75e-0824
primitive heart tube1.75e-0824
primary heart field1.75e-0824
anterior lateral plate mesoderm1.75e-0824
heart tube1.75e-0824
heart primordium1.75e-0824
cardiac mesoderm1.75e-0824
cardiogenic plate1.75e-0824
heart rudiment1.75e-0824
trunk2.76e-08199
organ part9.44e-08218
compound organ1.01e-0768
primary circulatory organ1.04e-0727
neural plate4.06e-0782
presumptive neural plate4.06e-0782
smooth muscle tissue5.18e-0715
tissue8.89e-07773


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
CTCF#1066465.360256373075034.21437267579784e-050.000756002864801873
POLR2A#543062.147453176558070.01019570676818780.0380704118399273
RAD21#5885610.35503389545638.10515055094479e-073.54329769104279e-05
TAF1#687263.343046285745290.0007162474284635620.0057369556853521
TBP#690863.706770687096390.000385416472907960.00378099859233838
ZNF263#1012768.221841637010683.23542093046082e-060.000108825805654234



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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