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Difference between revisions of "Coexpression cluster:C366"

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|ontology_enrichment_uberon=UBERON:0007023!2.14e-54!114;UBERON:0001049!4.06e-18!56;UBERON:0005068!4.06e-18!56;UBERON:0006241!4.06e-18!56;UBERON:0007135!4.06e-18!56;UBERON:0002346!6.81e-18!86;UBERON:0003075!2.23e-17!82;UBERON:0007284!2.23e-17!82;UBERON:0002298!3.39e-15!6;UBERON:0000073!3.48e-15!53;UBERON:0002616!3.48e-15!53;UBERON:0010314!4.10e-13!132;UBERON:0003978!9.86e-13!3;UBERON:0009751!9.86e-13!3;UBERON:0000946!9.86e-13!3;UBERON:0002523!9.86e-13!3;UBERON:0005983!9.86e-13!3;UBERON:0002165!9.86e-13!3;UBERON:0002062!9.86e-13!3;UBERON:0007280!9.86e-13!3;UBERON:0010371!1.53e-12!104;UBERON:0006947!4.59e-12!3;UBERON:0004054!4.59e-12!3;UBERON:0001896!2.35e-11!3;UBERON:0005290!2.35e-11!3;UBERON:0010096!2.35e-11!3;UBERON:0003076!5.33e-11!15;UBERON:0003057!5.33e-11!15;UBERON:0001017!5.39e-11!81;UBERON:0000955!8.65e-11!68;UBERON:0006238!8.65e-11!68;UBERON:0003528!2.50e-10!34;UBERON:0002020!2.50e-10!34;UBERON:0000477!6.79e-10!373;UBERON:0002780!9.48e-10!41;UBERON:0001890!9.48e-10!41;UBERON:0003080!9.48e-10!41;UBERON:0006240!9.48e-10!41;UBERON:0000125!9.87e-10!9;UBERON:0002308!9.87e-10!9;UBERON:0001016!1.74e-09!89;UBERON:0004111!3.33e-09!240;UBERON:0005904!3.79e-09!4;UBERON:0002133!4.31e-09!2;UBERON:0011216!4.63e-09!223;UBERON:0003127!8.23e-09!2;UBERON:0003103!8.50e-09!68;UBERON:0000025!1.05e-08!192;UBERON:0002148!1.15e-08!2;UBERON:0006331!1.15e-08!2;UBERON:0009662!1.15e-08!2;UBERON:0001893!2.69e-08!34;UBERON:0000481!4.94e-08!342;UBERON:0004733!1.99e-07!12;UBERON:0002028!1.99e-07!12;UBERON:0007277!1.99e-07!12;UBERON:0002791!2.92e-07!32;UBERON:0003056!6.84e-07!61;UBERON:0004732!7.89e-07!13;UBERON:0004121!7.93e-07!171;UBERON:0000924!7.93e-07!171;UBERON:0006601!7.93e-07!171
 
|ontology_enrichment_uberon=UBERON:0007023!2.14e-54!114;UBERON:0001049!4.06e-18!56;UBERON:0005068!4.06e-18!56;UBERON:0006241!4.06e-18!56;UBERON:0007135!4.06e-18!56;UBERON:0002346!6.81e-18!86;UBERON:0003075!2.23e-17!82;UBERON:0007284!2.23e-17!82;UBERON:0002298!3.39e-15!6;UBERON:0000073!3.48e-15!53;UBERON:0002616!3.48e-15!53;UBERON:0010314!4.10e-13!132;UBERON:0003978!9.86e-13!3;UBERON:0009751!9.86e-13!3;UBERON:0000946!9.86e-13!3;UBERON:0002523!9.86e-13!3;UBERON:0005983!9.86e-13!3;UBERON:0002165!9.86e-13!3;UBERON:0002062!9.86e-13!3;UBERON:0007280!9.86e-13!3;UBERON:0010371!1.53e-12!104;UBERON:0006947!4.59e-12!3;UBERON:0004054!4.59e-12!3;UBERON:0001896!2.35e-11!3;UBERON:0005290!2.35e-11!3;UBERON:0010096!2.35e-11!3;UBERON:0003076!5.33e-11!15;UBERON:0003057!5.33e-11!15;UBERON:0001017!5.39e-11!81;UBERON:0000955!8.65e-11!68;UBERON:0006238!8.65e-11!68;UBERON:0003528!2.50e-10!34;UBERON:0002020!2.50e-10!34;UBERON:0000477!6.79e-10!373;UBERON:0002780!9.48e-10!41;UBERON:0001890!9.48e-10!41;UBERON:0003080!9.48e-10!41;UBERON:0006240!9.48e-10!41;UBERON:0000125!9.87e-10!9;UBERON:0002308!9.87e-10!9;UBERON:0001016!1.74e-09!89;UBERON:0004111!3.33e-09!240;UBERON:0005904!3.79e-09!4;UBERON:0002133!4.31e-09!2;UBERON:0011216!4.63e-09!223;UBERON:0003127!8.23e-09!2;UBERON:0003103!8.50e-09!68;UBERON:0000025!1.05e-08!192;UBERON:0002148!1.15e-08!2;UBERON:0006331!1.15e-08!2;UBERON:0009662!1.15e-08!2;UBERON:0001893!2.69e-08!34;UBERON:0000481!4.94e-08!342;UBERON:0004733!1.99e-07!12;UBERON:0002028!1.99e-07!12;UBERON:0007277!1.99e-07!12;UBERON:0002791!2.92e-07!32;UBERON:0003056!6.84e-07!61;UBERON:0004732!7.89e-07!13;UBERON:0004121!7.93e-07!171;UBERON:0000924!7.93e-07!171;UBERON:0006601!7.93e-07!171
 
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262,0.853797,0.990216,0.285605,0.927426,0.708351,0.331486,0.126864,0.971926,0.729237,0.110416,0.688254,0.95171,0.251882,0.999655,0.790174,0.327146,0.59954,0.432207,0.788944,0.789552,0.231178,0.0207759,0.0543061,0.959904,0.287295,0.656887,0.546959,0.564359,0.5744,0.867013,0.582106,0.474471,0.782435,0.546154,0.447338,0.606107,0.975392,0.657218,0.384048,0.630974,0.93329,0.759696,0.553359,0.685348,0.399899,0.755693,0.99015,0.70903,0.0169555,0.0891349,0.401493,0.471774,0.185881,0.625931,0.205264,0.0477186,0.53734,0.961021,0.99927,0.620401,0.913678,0.854866,0.719006,0.630013,0.859106,0.996809,0.447304,0.385906,0.382608,0.0259729,0.57404,0.871858,0.52285,0.113465,0.857699,0.303939,0.73874,0.0140019,0.999989,1,0.672005,0.704703,0.317775,0.50204,0.0296967,0.397512,0.634903,0.900076,0.186147,0.373302,0.688937,0.517452,0.472508,0.811015,0.319006,0.758956,0.369014,0.10707,0.12337,0.255277,0.849314,0.670022,0.918384,0.444936,0.0543218,0.546271,0.656545,0.808551,0.368801,0.914776,0.657496,0.980958,0.296087,0.40421,0.228071,0.0280395,0.0214532,0.799799,0.992855,0.504858,0.171962,0.618642,0.128957,0.461527,0.225101,0.641046,0.50194,0.845391,0.364501,0.771437,0.730596,0.5532,0.255468,0.361555,0.583621,0.57168,0.33764,0.335625,0.15494,0.572189,0.0796573,0.0907519,0.545697,0.780066,0.283036,0.347983,0.66527,0.0337584,0.228086,0.279614,0.613399,0.387173,0.839075,0.347823,0.572131,0.870624,0.506481,0.887178,0.97397,0.124915,0.941645,0.584406,0.704802,0.927748,0.966658,0.986889,0.307552,0.612688,0.754679,0.358746,0.761711,0.971466,0.990036,0.387412,0.893565,0.127207,0.99661,0.520082,0.677756,0.914969,0.709082,0.377295,0.394269,0.294604,0.891889,0.523313,0.502251,0.888876,0.815461,0.626969,0.375085,0.962785,0.263518,0.931251,0.608089,0.998796,0.999989,0.0472991,0.447411,0.493655,0.865376,0.430569,0.702735,0.81134,0.903045,0.258015,0.833643,0.587707,0.659315,0.927737,0.7768,0.776031,0.986818,0.949562,0.540728,0.305612,0.999961,0.729163,0.85157,0.989219,0.00943601,0.984969,0.976706,0.966887,0.998668,0.686709,0.999972,0.775037,0.997761,0.983354,0.95813,0.897128,0.38735,0.0839187,0.692613,0.56885,0.109988,0.428687,0.116577,0.242053,0.45003,0.968798,0.268249,0.088585,0.44532,0.832907,0.736681,0.0412132,0.649354,0.21122,0.890478,0.594477,0.643946,0.99923,0.170502,0.602138,0.30636,0.099454,0.381917,0.126475,0.72338,0.541503,0.323547,0.996494,0.882371,0.714903,0.785423,0.784751,0.427741,0.850886,0.862152,0.401793,0.850802,0.0043873,0.986746,0.838955,0.378452,0.581333,0.893011,0.891664,0.30334,0.76891,0.686677,0.610197,0.429045,0.6659,0.642255,0.376565,0.659871,0.932256,0.663364,0.618794,0.948694,0.540855,0.929488,0.831471,0.938232,0.706212,0.520783,0.841861,0.0785306,0.297367,0.527628,0.718659,0.835418,0.783757,0.953567,0.573835,0.970942,0.710143,0.837192,0.17941,0.880681,0.430839,0.95172,0.0339564,0.418869,0.121157,0.834044,0.881394,0.0356434,0.395733,0.484921,0.623646,0.713985,0.208417,0.0825943,0.783204,0.646413,0.9563,0.0614569,0.768598,0.477491,0.0110189,0.214279,0.200516,0.132318,0.555598,0.406739,0.668658,0.290328,0.0624255,0.183993,0.346531,0.525917,0.370075,0.104591,0.625515,0.831361,0.013565,0.902909,0.243617,0.265063,0.273857,0.55542,0.853037,0.341711,0.20596,0.842191,0.587826,0.364327,0.917604,0.111896,0.787191,0.885652,0.445661,0.381072,0.612042,0.378898,0.65143,0.282049,0.624525,0.381817,0.139851,0.923699,0.96189,0.591165,0.754752,0.208136,0.0690777,0.919108,0.501958,0.903468,0.59881,0.698848,0.792939,0.733815,0.527908,0.481592,0.842483,0.32467,0.495332,0.414975,0.37263,0.38184,0.657805,0.265799,0.0907351,0.366274,0.646148,0.682753,0.126564,0.912189,0.514614,0.710376,0.638514,0.148991,0.578171,0.309053,0.863565,0.824857,0.571083,0.225417,0.701791,0.733651,0.86962,0.0572565,0.0406095,0.350694,0.805967,0.897594,0.43178,0.902351,0.198712,0.362422,0.322518,0.708487,0.721483,0.313635,0.566201,0.0765399,0.778145,0.888685,0.760387,0.507233,0.409905,0.79634,0.716895,0.848783,0.857075,0.271452,0.659388,0.8853,0.963048,0.914656,0.57606,0.895366,0.676566,0.106031,0.424626,0.805726,0.195627,0.34016,0.424394,0.739946,0.805928,0.685876,0.344759,0.744149,0.87776,0.0545446,0.643948,0.00476448,0.727493,0.483153,0.668749,0.496554,0.547588,0.400584,0.685267,0.0757621,0.49992,0.608908,0.312282,0.425274,0.400378,0.68035,0.126743,0.0302405,0.783108,0.588762,0.0796011,0.187126,0.476818,0.971088,0.946266,0.858585,0.647724,0.592499,0.75656,0.256396,0.671383,0.383163,0.656619,0.932657,0.358003,0.707973,0.704327,0.464841,0.34633,0.637786,0.165055,0.8425,0.242863,0.548513,0.269085,0.0153127,0.0771106,0.365174,0.471137,0.902637,0.635009,0.592801,0.334225,0.0427613,0.515958,0.824124,0.521768,0.610707,0.0926297,0.246134,0.30575,0.510203,0.0996296,0.333546,0.40559,0.167072
 +
|tfbs_overrepresentation_for_novel_motifs=0.414688,0.0139597,0.177713,0.354094,0.581353,1.17637,0.150903,0.130777,0.263726,0.00830226,0.311591,1.00861,0.0261228,0.144149,0.577363,0.15742,0.302324,0.427834,0.199922,0.280338,0.39993,0.213592,0.104721,0.894914,0.228519,0.560796,0.139006,0.338447,0.138982,0.11384,0.28353,0.330539,0.173875,0.326925,0.0247493,0.367771,0.0239955,0.109281,1.37613,0.225483,1.12625,0.263233,0.261829,0.572945,0.16995,0.211277,0.15155,0.297545,0.487586,0.325193,0.201351,0.158611,0.131669,0.391649,1.29305,0.14586,0.143142,0.127237,0.218929,0.126682,0.362777,0.152958,0.264825,0.28158,0.163803,0.256459,0.598376,0.940287,0.322501,0.786982,0.247246,0.138154,0.00084636,0.518722,0.0751876,0.0636748,0.391211,0.741579,0.319998,0.481486,0.0975543,1.4039,0.163587,0.134389,0.474452,0.00041772,1.62401,0.533842,0.218841,1.03562,0.682835,0.451575,0.343662,0.362002,0.136766,0.080127,0.353518,0.37755,0.221992,0.169479,0.0855436,0.89974,0.373064,0.305101,0.248225,0.0914534,0.293159,0.438102,0.0638422,0.0294273,0.422457,1.72408,0.171939,0.0982118,0.63916,0.758227,0.0097733,0.282017,0.708511,2.62631,1.27406,0.620753,1.16689,0.980472,0.740513,0.742852,0.450707,0.34759,0.548727,0.205977,0.452157,0.287152,0.561391,0.972022,0.694633,1.59126,0.0806627,1.14426,0.655888,1.48038,1.08626,0.62213,0.887594,0.374712,0.249475,0.388204,0.668871,1.32355,0.259159,0.0146617,0.00473725,0.000113697,0.452479,0.246299,0.464485,0.815647,0.207907,0.0299572,0.851598,0.0529349,0.621036,0.436936,0.319392,0.199524,0.261021,0.490363,0.162163,0.458109,0.00111136
 
}}
 
}}

Revision as of 05:09, 26 November 2012


Full id: C366_heart_vagina_adipose_diaphragm_left_aorta_breast



Phase1 CAGE Peaks

Hg19::chr10:15647768..15647794,-p@chr10:15647768..15647794
-
Hg19::chr10:92678409..92678410,-p@chr10:92678409..92678410
-
Hg19::chr11:123340107..123340127,+p@chr11:123340107..123340127
+
Hg19::chr12:2386467..2386484,+p@chr12:2386467..2386484
+
Hg19::chr12:2468720..2468724,+p@chr12:2468720..2468724
+
Hg19::chr13:31729140..31729163,-p@chr13:31729140..31729163
-
Hg19::chr14:102550059..102550072,-p@chr14:102550059..102550072
-
Hg19::chr14:102551390..102551436,-p10@HSP90AA1
Hg19::chr14:102551456..102551467,-p27@HSP90AA1
Hg19::chr14:92349687..92349698,-p@chr14:92349687..92349698
-
Hg19::chr15:35082449..35082469,-p@chr15:35082449..35082469
-
Hg19::chr15:86272097..86272099,+p@chr15:86272097..86272099
+
Hg19::chr16:10783399..10783401,+p@chr16:10783399..10783401
+
Hg19::chr17:77026478..77026512,+p@chr17:77026478..77026512
+
Hg19::chr19:14628234..14628252,-p@chr19:14628234..14628252
-
Hg19::chr19:2716727..2716731,-p10@DIRAS1
Hg19::chr1:159174559..159174571,+p3@DARC
Hg19::chr22:47045714..47045722,+p@chr22:47045714..47045722
+
Hg19::chr3:46505091..46505110,-p5@LTF
Hg19::chr3:64517143..64517146,-p@chr3:64517143..64517146
-
Hg19::chr3:64673668..64673684,-p1@ADAMTS9
Hg19::chr4:95332178..95332184,+p@chr4:95332178..95332184
+
Hg19::chr5:99385820..99385831,-p@chr5:99385820..99385831
-
Hg19::chr5:99390735..99390743,-p@chr5:99390735..99390743
-
Hg19::chr6:31785440..31785544,+p@chr6:31785440..31785544
+
Hg19::chr6:31785565..31785576,+p@chr6:31785565..31785576
+
Hg19::chr6:31797870..31797898,+p6@HSPA1B
Hg19::chr7:105926145..105926185,-p7@NAMPT
Hg19::chr7:105926216..105926230,-p10@NAMPT
Hg19::chr9:124095011..124095025,+p@chr9:124095011..124095025
+


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:0042026protein refolding0.0216354645001766
GO:0030911TPR domain binding0.0260593848696238
GO:0030235nitric-oxide synthase regulator activity0.0260593848696238
GO:0009607response to biotic stimulus0.0260593848696238
GO:0045429positive regulation of nitric oxide biosynthetic process0.0346024795986266
GO:0045428regulation of nitric oxide biosynthetic process0.0360400055870461
GO:0006516glycoprotein catabolic process0.0475392087874602
GO:0006952defense response0.0475392087874602
GO:0046209nitric oxide metabolic process0.0475392087874602
GO:0006809nitric oxide biosynthetic process0.0475392087874602



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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism2.14e-54114
neural tube4.06e-1856
neural rod4.06e-1856
future spinal cord4.06e-1856
neural keel4.06e-1856
neurectoderm6.81e-1886
neural plate2.23e-1782
presumptive neural plate2.23e-1782
brainstem3.39e-156
regional part of nervous system3.48e-1553
regional part of brain3.48e-1553
structure with developmental contribution from neural crest4.10e-13132
valve9.86e-133
cardiac mesenchyme9.86e-133
cardial valve9.86e-133
tunica intima9.86e-133
heart layer9.86e-133
endocardium9.86e-133
endocardial cushion9.86e-133
presumptive endocardium9.86e-133
ecto-epithelium1.53e-12104
male genital duct4.59e-123
internal male genitalia4.59e-123
medulla oblongata2.35e-113
myelencephalon2.35e-113
future myelencephalon2.35e-113
posterior neural tube5.33e-1115
chordal neural plate5.33e-1115
central nervous system5.39e-1181
brain8.65e-1168
future brain8.65e-1168
brain grey matter2.50e-1034
gray matter2.50e-1034
anatomical cluster6.79e-10373
regional part of forebrain9.48e-1041
forebrain9.48e-1041
anterior neural tube9.48e-1041
future forebrain9.48e-1041
neural nucleus9.87e-109
nucleus of brain9.87e-109
nervous system1.74e-0989
anatomical conduit3.33e-09240
duct of male reproductive system3.79e-094
atrioventricular valve4.31e-092
organ system subdivision4.63e-09223
open tracheal system trachea8.23e-092
compound organ8.50e-0968
tube1.05e-08192
locus ceruleus1.15e-082
brainstem nucleus1.15e-082
hindbrain nucleus1.15e-082
telencephalon2.69e-0834
multi-tissue structure4.94e-08342
segmental subdivision of hindbrain1.99e-0712
hindbrain1.99e-0712
presumptive hindbrain1.99e-0712
regional part of telencephalon2.92e-0732
pre-chordal neural plate6.84e-0761
segmental subdivision of nervous system7.89e-0713
ectoderm-derived structure7.93e-07171
ectoderm7.93e-07171
presumptive ectoderm7.93e-07171


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)

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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.