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Coexpression cluster:C1962: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!4.25e-23!365;UBERON:0007023!6.35e-23!115;UBERON:0000481!2.27e-18!347;UBERON:0000468!1.33e-17!659;UBERON:0004111!2.38e-16!241;UBERON:0000477!2.60e-16!286;UBERON:0000483!1.51e-12!309;UBERON:0000119!1.91e-12!312;UBERON:0000025!3.61e-12!194;UBERON:0000467!4.90e-12!625;UBERON:0000480!4.94e-12!626;UBERON:0001049!8.60e-11!57;UBERON:0005068!8.60e-11!57;UBERON:0006241!8.60e-11!57;UBERON:0007135!8.60e-11!57;UBERON:0002616!2.64e-10!59;UBERON:0000062!1.26e-09!511;UBERON:0002100!3.19e-09!216;UBERON:0000955!3.93e-09!69;UBERON:0006238!3.93e-09!69;UBERON:0001017!1.18e-08!82;UBERON:0000033!1.35e-08!123;UBERON:0007100!1.71e-08!27;UBERON:0000153!1.81e-08!129;UBERON:0007811!1.81e-08!129;UBERON:0005743!2.36e-08!86;UBERON:0003075!3.00e-08!86;UBERON:0007284!3.00e-08!86;UBERON:0000914!5.83e-08!83;UBERON:0002329!5.83e-08!83;UBERON:0003077!5.83e-08!83;UBERON:0003059!5.83e-08!83;UBERON:0007282!5.83e-08!83;UBERON:0009618!5.83e-08!83;UBERON:0007285!5.83e-08!83;UBERON:0005256!1.03e-07!143;UBERON:0003080!1.10e-07!42;UBERON:0000922!1.15e-07!612;UBERON:0000948!2.48e-07!24;UBERON:0005498!2.48e-07!24;UBERON:0004140!2.48e-07!24;UBERON:0009881!2.48e-07!24;UBERON:0004141!2.48e-07!24;UBERON:0003084!2.48e-07!24;UBERON:0007005!2.48e-07!24;UBERON:0004139!2.48e-07!24;UBERON:0004291!2.48e-07!24;UBERON:0002780!3.27e-07!41;UBERON:0001890!3.27e-07!41;UBERON:0006240!3.27e-07!41;UBERON:0003102!3.28e-07!95;UBERON:0004872!3.92e-07!84;UBERON:0003104!4.18e-07!238;UBERON:0009142!4.18e-07!238;UBERON:0002385!4.23e-07!63;UBERON:0001015!4.23e-07!63;UBERON:0000383!4.23e-07!63;UBERON:0004290!6.08e-07!70;UBERON:0002346!7.07e-07!90
|ontology_enrichment_uberon=UBERON:0000475!4.25e-23!365;UBERON:0007023!6.35e-23!115;UBERON:0000481!2.27e-18!347;UBERON:0000468!1.33e-17!659;UBERON:0004111!2.38e-16!241;UBERON:0000477!2.60e-16!286;UBERON:0000483!1.51e-12!309;UBERON:0000119!1.91e-12!312;UBERON:0000025!3.61e-12!194;UBERON:0000467!4.90e-12!625;UBERON:0000480!4.94e-12!626;UBERON:0001049!8.60e-11!57;UBERON:0005068!8.60e-11!57;UBERON:0006241!8.60e-11!57;UBERON:0007135!8.60e-11!57;UBERON:0002616!2.64e-10!59;UBERON:0000062!1.26e-09!511;UBERON:0002100!3.19e-09!216;UBERON:0000955!3.93e-09!69;UBERON:0006238!3.93e-09!69;UBERON:0001017!1.18e-08!82;UBERON:0000033!1.35e-08!123;UBERON:0007100!1.71e-08!27;UBERON:0000153!1.81e-08!129;UBERON:0007811!1.81e-08!129;UBERON:0005743!2.36e-08!86;UBERON:0003075!3.00e-08!86;UBERON:0007284!3.00e-08!86;UBERON:0000914!5.83e-08!83;UBERON:0002329!5.83e-08!83;UBERON:0003077!5.83e-08!83;UBERON:0003059!5.83e-08!83;UBERON:0007282!5.83e-08!83;UBERON:0009618!5.83e-08!83;UBERON:0007285!5.83e-08!83;UBERON:0005256!1.03e-07!143;UBERON:0003080!1.10e-07!42;UBERON:0000922!1.15e-07!612;UBERON:0000948!2.48e-07!24;UBERON:0005498!2.48e-07!24;UBERON:0004140!2.48e-07!24;UBERON:0009881!2.48e-07!24;UBERON:0004141!2.48e-07!24;UBERON:0003084!2.48e-07!24;UBERON:0007005!2.48e-07!24;UBERON:0004139!2.48e-07!24;UBERON:0004291!2.48e-07!24;UBERON:0002780!3.27e-07!41;UBERON:0001890!3.27e-07!41;UBERON:0006240!3.27e-07!41;UBERON:0003102!3.28e-07!95;UBERON:0004872!3.92e-07!84;UBERON:0003104!4.18e-07!238;UBERON:0009142!4.18e-07!238;UBERON:0002385!4.23e-07!63;UBERON:0001015!4.23e-07!63;UBERON:0000383!4.23e-07!63;UBERON:0004290!6.08e-07!70;UBERON:0002346!7.07e-07!90
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2998,0.123097,0.254847,0.300809,0.0898207,0.126545,0.0918749,0.0686325,0.0569043,0.0639461,0.387306,0.267408,0.312064,0.080156,0.274185,0.53753,0.0545112,0.510703,0.33844,0.0649137,0.0974216,0.595767,0.0205318,0.174786,0.176557,0.396547,0.0472148,0.735114,0.229138,0.0639045,0.141461,0.0900204,0.0283292,0.385962,0.334921,0.296227,0.208788,0.566117,0.36304,0.430936,0.123626,0.0404561,0.132705,0.285556,0.493429,0.233835,0.224471,0.262929,0.223204,0.143824,0.460679,0.11021,0.0775891,0.153079,0.62577,0.211515,0.125701,0.175283,0.204954,0.0236242,0.576888,0.629422,0.084895,0.160115,0.0819954,0.10091,0.00785048,0.151161,0.228398,0.056055,0.120552,0.41771,0.893893,0.830533,0.335207,0.434016,0.190688,0.299739,0.278645,0.0114247,0.0940982,0.0780533,0.564811,0.0993772,0.274769,0.448923,0.11602,0.067657,0.436413,0.0585992,0.20045,0.274438,0.76735,0.180484,0.319826,0.336512,0.00100702,0.109708,0.174594,0.0809806,0.154589,0.318794,0.122767,0.0749261,0.0166527,0.114361,0.347759,0.0321076,0.0620267,0.211111,0.0738743,0.0882327,0.0178827,0.150073,0.270522,0.16872,0.341388,0.0934526,0.359135,0.123404,0.110025,0.240825,0.0515122,0.336623,0.0141682,0.483244,0.27134,0.154031,0.239667,0.10226,0.049649,0.235147,0.689826,0.245965,0.116923,0.148426,0.0983658,0.228743,0.238223,0.156976,0.244789,0.267391,0.301441,0.21807,0.350528,0.0850129,0.432408,0.190404,0.135865,0.488841,0.18137,0.180609,0.291283,0.0415219,0.153023,0.400137,0.37958,0.22307,0.160699,0.391307,0.166736,0.0175198,0.0422294,0.263877,0.146486,0.769574,0.262486,0.294204,0.131936,0.288826,0.246621,0.463617,0.697373,0.0965376,0.377203,0.279263,0.336564,0.35463,0.21719,0.800557,0.0594155,0.222245,0.208795,0.0713793,0.212621,0.228454,0.53612,0.0791056,0.581874,0.355154,0.145569,0.251388,0.180545,0.0147743,0.261576,0.306963,0.206759,0.526495,0.580285,0.550495,0.000754989,0.248142,0.0156811,0.167927,0.561689,0.672416,0.321844,0.255366,0.708698,0.0636035,0.663441,0.349068,0.344004,0.217481,0.196345,0.108354,0.689998,0.737642,0.176145,0.433702,0.258394,0.644878,0.432123,0.416657,0.295122,0.494975,0.651196,0.392155,0.259088,0.371758,0.457109,0.562417,0.025506,0.85279,0.254547,0.0309722,0.51445,0.1082,0.0547927,0.541378,0.725301,0.660884,0.469682,0.666904,0.705225,0.315485,0.311289,0.318577,0.4488,0.088424,0.603509,0.511254,0.553178,0.246387,0.224252,0.587237,0.155054,0.466978,0.518234,0.257848,0.353942,0.192234,0.427276,0.400353,0.466967,0.283682,0.424668,0.111989,0.797471,0.583101,0.341421,0.138015,0.831202,0.152704,0.465544,0.0498097,0.349033,0.00662882,0.139363,0.34194,0.226858,0.592314,0.644904,0.647996,0.177129,0.317485,0.633504,0.220564,0.556368,0.262394,0.307462,0.135076,0.469588,0.664443,0.274593,0.147074,0.183857,0.350314,0.583627,0.531474,0.137231,0.562305,0.528646,0.361524,0.31558,0.412744,0.54408,0.259136,0.513592,0.415367,0.815658,0.45585,0.36864,0.538745,0.0241542,0.0234438,0.316163,0.196391,0.693441,0.382214,0.553161,0.0841037,0.68995,0.339393,0.694478,0.306231,0.298354,0.278436,0.0701109,0.457741,0.641611,0.426239,0.401917,0.0931042,0.572661,0.100067,0.534679,0.41502,0.55475,0.0962475,0.170461,0.0331565,0.307426,0.206772,0.557732,0.490527,0.356232,0.119992,0.499536,0.318338,0.276338,0.126433,0.102654,0.318174,0.0555558,0.295666,0.393022,0.293641,0.116969,0.401231,0.255983,0.297663,0.256708,0.338258,0.322052,0.145568,0.153833,0.261242,0.0132275,0.54721,0.388459,0.00728123,0.627637,0.0437263,0.301366,0.0659025,0.343265,0.00566245,0.128553,0.336254,0.053444,0.291523,0.19697,0.309816,0.0537285,0.15063,0.198077,0.281455,0.348739,0.419895,0.138495,0.208834,0.32256,0.377566,0.342366,0.109684,0.0587975,0.403482,0.181288,0.230841,0.352328,0.255358,0.0707105,0.265112,0.0633313,0.10772,0.0854747,0.0747609,0.0968383,0.312881,0.512825,0.244656,0.192188,0.0133669,0.174153,0.00489362,0.333309,0.249919,0.339517,0.303699,0.198326,0.394084,0.126349,0.0443031,0.0348179,0.390891,0.238377,0.334983,0.197875,0.287909,0.289389,0.000297378,0.392533,0.0919602,0.316002,0.330317,0.321404,0.225079,0.300542,0.379651,0.185715,0.345505,0.0814929,0.0407047,0.311201,0.221943,0.306427,0.367733,0.246925,0.208775,0.390438,0.343014,0.270094,0.276922,0.156279,0.055329,0.461742,0.422872,0.0643015,0.13327,0.313545,0.17149,0.0877361,0.0880065,0.238969,0.126615,0.0669467,0.0879453,0.474066,0.396935,0.326779,0.292869,0.358198,0.29552,0.131776,0.158116,0.104606,0.194814,0.104167,0.0150105,0.108081,0.123829,0.205215,0.175247,0.0724304,0.109077,0.144842,0.0604892,0.0248943,0.316879,0.442567,0.430541,0.00605341,0.00227842,0.398887,0.389061,0.310732,0.349611,0.445995,0.385709,0.278202,0.426488,0.400591,0.209809,0.253154,0.319519,0.309489,0.430805,0.362154,0.480785,0.185476,0.336314,0.344469,0.184651,0.303359,0.0494743,0.42392,0.425912,0.0840133,0.259046,0.00922992,0.151046,0.483953,0.00941969,0.321735,0.15463,0.13907,0.133591,0.0400826,0.250466,0.0986342,0.115686,0.408975,0.162633,0.0668707,0.27567,0.248127,0.33299,0.384731,0.319112,0.526476
}}
}}

Revision as of 12:41, 5 September 2012


Full id: C1962_Adipocyte_Synoviocyte_Mast_mature_tenocyte_Chondrocyte_leiomyoblastoma



Phase1 CAGE Peaks

Hg19::chr5:54721817..54721840,-p@chr5:54721817..54721840
-
Hg19::chr5:54771166..54771206,+p@chr5:54771166..54771206
+
Hg19::chr5:54830488..54830506,-p2@RNF138P1
Hg19::chr5:54830511..54830588,-p1@RNF138P1
Hg19::chr5:54830784..54830799,-p1@PPAP2A


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:0008195phosphatidate phosphatase activity0.0139516400949588
GO:0008354germ cell migration0.0139516400949588
GO:0046839phospholipid dephosphorylation0.028399509486818
GO:0019216regulation of lipid metabolic process0.028399509486818
GO:0030521androgen receptor signaling pathway0.028399509486818
GO:0007205protein kinase C activation0.028399509486818
GO:0030518steroid hormone receptor signaling pathway0.028399509486818
GO:0030258lipid modification0.028399509486818
GO:0030522intracellular receptor-mediated signaling pathway0.028399509486818
GO:0032147activation of protein kinase activity0.0325231595799832
GO:0007200G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)0.0371594678851849
GO:0048015phosphoinositide-mediated signaling0.0454807681646362
GO:0045860positive regulation of protein kinase activity0.0454807681646362
GO:0033674positive regulation of kinase activity0.0454807681646362
GO:0051347positive regulation of transferase activity0.0454807681646362



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>


Cell Type
Ontology termp-valuen
non-terminally differentiated cell3.94e-13180
fibroblast3.48e-1275
fat cell7.22e-1115
Uber Anatomy
Ontology termp-valuen
organism subdivision4.25e-23365
adult organism6.35e-23115
multi-tissue structure2.27e-18347
multi-cellular organism1.33e-17659
anatomical conduit2.38e-16241
anatomical cluster2.60e-16286
epithelium1.51e-12309
cell layer1.91e-12312
tube3.61e-12194
anatomical system4.90e-12625
anatomical group4.94e-12626
neural tube8.60e-1157
neural rod8.60e-1157
future spinal cord8.60e-1157
neural keel8.60e-1157
regional part of brain2.64e-1059
organ1.26e-09511
trunk3.19e-09216
brain3.93e-0969
future brain3.93e-0969
central nervous system1.18e-0882
head1.35e-08123
primary circulatory organ1.71e-0827
anterior region of body1.81e-08129
craniocervical region1.81e-08129
neural plate3.00e-0886
presumptive neural plate3.00e-0886
somite5.83e-0883
paraxial mesoderm5.83e-0883
presomitic mesoderm5.83e-0883
presumptive segmental plate5.83e-0883
trunk paraxial mesoderm5.83e-0883
presumptive paraxial mesoderm5.83e-0883
trunk mesenchyme1.03e-07143
anterior neural tube1.10e-0742
embryo1.15e-07612
heart2.48e-0724
primitive heart tube2.48e-0724
primary heart field2.48e-0724
anterior lateral plate mesoderm2.48e-0724
heart tube2.48e-0724
heart primordium2.48e-0724
cardiac mesoderm2.48e-0724
cardiogenic plate2.48e-0724
heart rudiment2.48e-0724
regional part of forebrain3.27e-0741
forebrain3.27e-0741
future forebrain3.27e-0741
surface structure3.28e-0795
splanchnic layer of lateral plate mesoderm3.92e-0784
mesenchyme4.18e-07238
entire embryonic mesenchyme4.18e-07238
muscle tissue4.23e-0763
musculature4.23e-0763
musculature of body4.23e-0763
dermomyotome6.08e-0770
neurectoderm7.07e-0790


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#290838.983813998703820.002687995788940450.0147987133474513
TFAP2C#702236.485537165916130.006858951517940.0290664247345156



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.