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Difference between revisions of "Coexpression cluster:C2016"

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|ontology_enrichment_disease=
 
|ontology_enrichment_disease=
 
|ontology_enrichment_uberon=UBERON:0000475!1.39e-30!365;UBERON:0000468!1.46e-21!659;UBERON:0000914!7.01e-20!83;UBERON:0002329!7.01e-20!83;UBERON:0003077!7.01e-20!83;UBERON:0003059!7.01e-20!83;UBERON:0007282!7.01e-20!83;UBERON:0009618!7.01e-20!83;UBERON:0007285!7.01e-20!83;UBERON:0000481!7.39e-20!347;UBERON:0000467!3.49e-17!625;UBERON:0000480!7.94e-17!626;UBERON:0002050!1.00e-15!605;UBERON:0005423!1.00e-15!605;UBERON:0000923!1.38e-15!604;UBERON:0005291!1.38e-15!604;UBERON:0006598!1.38e-15!604;UBERON:0002532!1.38e-15!604;UBERON:0000922!1.43e-15!612;UBERON:0000033!2.26e-15!123;UBERON:0000486!3.46e-15!82;UBERON:0004290!3.63e-15!70;UBERON:0000119!3.28e-14!312;UBERON:0000153!3.46e-14!129;UBERON:0007811!3.46e-14!129;UBERON:0002616!3.49e-14!59;UBERON:0001049!4.02e-14!57;UBERON:0005068!4.02e-14!57;UBERON:0006241!4.02e-14!57;UBERON:0007135!4.02e-14!57;UBERON:0007023!7.64e-14!115;UBERON:0000062!8.10e-14!511;UBERON:0000955!9.90e-14!69;UBERON:0006238!9.90e-14!69;UBERON:0000483!1.16e-13!309;UBERON:0005256!1.26e-13!143;UBERON:0003102!2.33e-13!95;UBERON:0000479!3.85e-13!787;UBERON:0002385!6.49e-13!63;UBERON:0001015!6.49e-13!63;UBERON:0000383!6.49e-13!63;UBERON:0001134!9.57e-13!61;UBERON:0002036!9.57e-13!61;UBERON:0003082!9.57e-13!61;UBERON:0001017!1.29e-12!82;UBERON:0004121!2.47e-12!169;UBERON:0000924!5.15e-12!173;UBERON:0006601!5.15e-12!173;UBERON:0000073!9.54e-12!94;UBERON:0001016!9.54e-12!94;UBERON:0002100!1.17e-11!216;UBERON:0005743!1.60e-11!86;UBERON:0000477!2.32e-11!286;UBERON:0003075!1.15e-10!86;UBERON:0007284!1.15e-10!86;UBERON:0003080!1.47e-10!42;UBERON:0002780!2.32e-10!41;UBERON:0001890!2.32e-10!41;UBERON:0006240!2.32e-10!41;UBERON:0002346!3.74e-10!90;UBERON:0001893!4.73e-10!34;UBERON:0002020!6.03e-10!34;UBERON:0003528!6.03e-10!34;UBERON:0002791!1.37e-09!33;UBERON:0004111!5.06e-09!241;UBERON:0001869!5.81e-09!32;UBERON:0002619!1.80e-07!22;UBERON:0003056!3.71e-07!61;UBERON:0000064!3.87e-07!219;UBERON:0003104!4.29e-07!238;UBERON:0009142!4.29e-07!238;UBERON:0001950!7.90e-07!20
 
|ontology_enrichment_uberon=UBERON:0000475!1.39e-30!365;UBERON:0000468!1.46e-21!659;UBERON:0000914!7.01e-20!83;UBERON:0002329!7.01e-20!83;UBERON:0003077!7.01e-20!83;UBERON:0003059!7.01e-20!83;UBERON:0007282!7.01e-20!83;UBERON:0009618!7.01e-20!83;UBERON:0007285!7.01e-20!83;UBERON:0000481!7.39e-20!347;UBERON:0000467!3.49e-17!625;UBERON:0000480!7.94e-17!626;UBERON:0002050!1.00e-15!605;UBERON:0005423!1.00e-15!605;UBERON:0000923!1.38e-15!604;UBERON:0005291!1.38e-15!604;UBERON:0006598!1.38e-15!604;UBERON:0002532!1.38e-15!604;UBERON:0000922!1.43e-15!612;UBERON:0000033!2.26e-15!123;UBERON:0000486!3.46e-15!82;UBERON:0004290!3.63e-15!70;UBERON:0000119!3.28e-14!312;UBERON:0000153!3.46e-14!129;UBERON:0007811!3.46e-14!129;UBERON:0002616!3.49e-14!59;UBERON:0001049!4.02e-14!57;UBERON:0005068!4.02e-14!57;UBERON:0006241!4.02e-14!57;UBERON:0007135!4.02e-14!57;UBERON:0007023!7.64e-14!115;UBERON:0000062!8.10e-14!511;UBERON:0000955!9.90e-14!69;UBERON:0006238!9.90e-14!69;UBERON:0000483!1.16e-13!309;UBERON:0005256!1.26e-13!143;UBERON:0003102!2.33e-13!95;UBERON:0000479!3.85e-13!787;UBERON:0002385!6.49e-13!63;UBERON:0001015!6.49e-13!63;UBERON:0000383!6.49e-13!63;UBERON:0001134!9.57e-13!61;UBERON:0002036!9.57e-13!61;UBERON:0003082!9.57e-13!61;UBERON:0001017!1.29e-12!82;UBERON:0004121!2.47e-12!169;UBERON:0000924!5.15e-12!173;UBERON:0006601!5.15e-12!173;UBERON:0000073!9.54e-12!94;UBERON:0001016!9.54e-12!94;UBERON:0002100!1.17e-11!216;UBERON:0005743!1.60e-11!86;UBERON:0000477!2.32e-11!286;UBERON:0003075!1.15e-10!86;UBERON:0007284!1.15e-10!86;UBERON:0003080!1.47e-10!42;UBERON:0002780!2.32e-10!41;UBERON:0001890!2.32e-10!41;UBERON:0006240!2.32e-10!41;UBERON:0002346!3.74e-10!90;UBERON:0001893!4.73e-10!34;UBERON:0002020!6.03e-10!34;UBERON:0003528!6.03e-10!34;UBERON:0002791!1.37e-09!33;UBERON:0004111!5.06e-09!241;UBERON:0001869!5.81e-09!32;UBERON:0002619!1.80e-07!22;UBERON:0003056!3.71e-07!61;UBERON:0000064!3.87e-07!219;UBERON:0003104!4.29e-07!238;UBERON:0009142!4.29e-07!238;UBERON:0001950!7.90e-07!20
 +
|tfbs_overrepresentation=0.23317,0.0958562,0.0624685,0.078254,0.310241,0.43203,0.0706464,0.5903,0.0539364,0.0424746,0.221396,0.346629,0.294377,0.201017,0.235304,0.101024,0.223746,0.158251,0.0865245,0.173528,0.29418,0.211047,0.13286,0.153106,0.0683222,0.332688,0.324018,0.146582,0.227906,0.150721,0.31768,0.182756,0.0298713,0.322378,0.108398,0.136785,0.00387794,0.070583,0.192426,0.108683,0.155571,0.0406818,0.222325,0.287476,0.193292,0.0596699,0.0625547,0.28382,0.178503,0.193726,0.243359,0.0886583,0.114185,0.150136,0.308837,0.0632035,0.172598,0.328738,0.127101,0.169687,0.0485674,0.236408,0.174369,0.123348,0.0892839,0.0827236,0.515105,0.0980005,0.139298,0.262613,0.188991,0.110232,0.143944,0.190944,0.012429,0.0283664,0.155593,0.0717582,0.0613084,0.0120583,0.154245,0.348799,0.0698251,0.183986,0.436695,0.0131713,0.104918,0.323505,0.790836,0.102375,0.138802,0.0812726,0.153861,0.0777027,0.138224,0.184264,0.430512,0.242703,0.149747,0.413729,0.0939617,0.416542,0.225088,0.0610111,0.337778,0.0672793,0.109136,0.497282,0.228612,0.407248,0.285407,0.0560173,0.23661,0.0293017,0.162943,0.0556189,0.0336673,0.0926302,0.220791,0.13579,0.262107,0.331577,0.222452,0.138843,0.164723,0.277102,0.146529,0.0245339,0.136609,0.214614,0.0973103,0.121587,0.0935301,0.0376876,0.200735,0.173595,0.105753,0.0905147,0.0544577,0.0065834,0.037671,0.203496,0.316207,0.246229,0.446477,0.112838,0.159217,0.1364,0.0640569,0.193163,0.311509,0.227801,0.282656,0.0439093,0.070163,0.188135,0.121467,0.350865,0.0846706,0.0555742,0.349932,0.153706,0.186743,0.23397,0.0169705,0.183121,0.065826,0.203135,0.0663482,0.463935,0.281162,0.218835,0.646289,0.0885874,0.129639,0.145577,0.22277,0.284267,0.27935,0.0586816,0.250461,0.195671,0.0452583,0.185103,0.11983,0.190123,0.286036,0.0660586,0.134265,0.272191,0.172119,0.292239,0.196376,0.351465,0.18064,0.0772176,0.126988,0.0984435,0.110187,0.176022,0.144361,0.0986228,0.0508565,0.0989516,0.21691,0.393782,0.412989,0.240045,0.319604,0.279218,0.0752697,0.167805,0.193654,0.180992,0.464566,0.265567,0.258402,0.162511,0.102771,0.165687,0.225173,0.540012,0.246322,0.253699,0.120044,0.201982,0.220536,0.139142,0.0987108,0.09782,0.410084,0.554981,0.0687568,0.124225,0.0126357,0.150448,0.0774663,0.398789,0.257365,0.331711,0.285222,0.511,0.158559,0.134615,0.186192,0.217494,0.132125,0.179065,0.540443,0.187334,0.250769,0.289141,0.289982,0.157983,0.158078,0.251693,0.172268,0.313249,0.113261,0.427135,0.101058,0.274448,0.25718,0.204241,0.0568578,0.131428,0.131579,0.148683,0.188945,0.122666,0.419402,0.103245,0.387442,0.627158,0.14011,0.0626022,0.2074,0.769028,0.345431,0.72202,0.814323,0.748392,0.328801,0.000137949,0.493893,0.492619,0.396701,0.626645,0.541514,0.460217,0.675971,0.487888,0.568246,0.486439,0.720623,0.796904,0.410803,0.43779,0.579996,0.569955,0.766049,0.447317,0.292173,0.528152,0.284119,0.601223,0.176507,0.488132,0.336705,0.604733,0.545464,0.645432,0.518524,0.132079,0.346724,0.537972,0.591562,0.668584,0.385794,0.417358,0.450485,0.665656,0.470142,0.344006,0.688397,0.201404,0.426591,0.467379,0.762263,0.437202,0.628658,0.419367,0.592924,0.438692,0.0954848,0.619033,0.541742,0.420673,0.790857,0.285074,0.605239,0.000792741,0.199887,0.415372,0.362164,0.289863,0.507647,0.721501,0.409489,0.487549,0.688223,0.699429,0.707862,0.379008,0.423719,0.655494,0.256985,0.109234,0.11883,0.288602,0.779806,0.429909,0.766165,0.588284,0.553251,0.0112976,0.737273,0.0785559,0.337121,0.464864,0.588557,0.0740433,0.121457,0.351733,0.256178,0.773103,0.112469,0.441154,0.503865,0.0958387,0.43388,0.483295,0.300529,0.418989,0.144008,0.606622,0.350461,0.495024,0.307173,0.246694,0.752605,0.598317,0.666615,0.597346,0.702113,3.71426e-07,0.493489,0.229501,0.230597,0.555864,0.544572,0.627794,0.641833,0.383956,0.241286,0.0764074,0.217887,0.393543,0.214395,0.158849,0.732038,0.439833,0.427746,0.504398,0.456725,0.455709,0.453202,0.688249,0.708682,0.427794,0.398041,0.524026,0.347879,0.58021,0.593219,0.529253,0.64728,0.00283093,0.319495,0.711229,0.524241,0.248788,0.407113,0.498776,0.152069,0.423517,0.224914,0.636791,0.125979,0.251608,0.365107,0.539805,0.356278,0.295455,0.144104,0.0972855,0.352039,0.226009,0.508875,0.725283,0.512109,0.658411,0.214417,0.508758,0.493686,0.469232,0.113555,0.0910724,0.299839,0.126587,0.0940929,0.22877,0.343849,0.315824,0.622796,0.000511762,0.29873,0.179502,0.43406,0.0715061,0.452515,0.201779,0.214491,0.171725,0.412647,0.102448,0.191372,0.029672,0.0234987,0.421335,0.561724,0.0762646,0.266371,0.183582,0.168118,0.145381,0.140277,0.251925,0.172066,0.0720324,0.00647589,0.19738,0.205854,0.32541,0.301472,0.507714,0.0818982,0.134306,0.108669,0.284804,0.178494,0.338195,0.490571,0.304235,0.210475,0.0483057,0.0790025,0.310539,0.580279,0.203728,0.275452,0.288155,0.265827,0.141761,0.153627,0.0186891,0.342497,0.171961,0.415228,0.00800917,0.272406,0.223952,0.327153,0.0496113,0.20949,0.0730994,0.0857377,0.323267,0.24204,0.129414,0.157037,0.252398,0.197279,0.146467,0.0912686,0.425114,0.342921,0.218241,0.0242146,0.10708,0.327369,0.339826,0.12998,0.123097,0.254847,0.30080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}}
 
}}

Revision as of 08:55, 8 August 2012


Full id: C2016_Fibroblast_corpus_Nucleus_Anulus_globus_tridermal_Synoviocyte



Phase1 CAGE Peaks

  Short description
Hg19::chr9:113800341..113800373,- p4@LPAR1
Hg19::chr9:113800377..113800400,- p6@LPAR1
Hg19::chr9:113800467..113800520,- p2@LPAR1
Hg19::chr9:113800705..113800781,- p1@LPAR1
Hg19::chr9:113800994..113801032,- p3@LPAR1


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


No GOStat results

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


Uber Anatomy
Ontology termp-valuen
organism subdivision1.39e-30365
multi-cellular organism1.46e-21659
somite7.01e-2083
paraxial mesoderm7.01e-2083
presomitic mesoderm7.01e-2083
presumptive segmental plate7.01e-2083
trunk paraxial mesoderm7.01e-2083
presumptive paraxial mesoderm7.01e-2083
multi-tissue structure7.39e-20347
anatomical system3.49e-17625
anatomical group7.94e-17626
embryonic structure1.00e-15605
developing anatomical structure1.00e-15605
germ layer1.38e-15604
embryonic tissue1.38e-15604
presumptive structure1.38e-15604
epiblast (generic)1.38e-15604
embryo1.43e-15612
head2.26e-15123
multilaminar epithelium3.46e-1582
dermomyotome3.63e-1570
cell layer3.28e-14312
anterior region of body3.46e-14129
craniocervical region3.46e-14129
regional part of brain3.49e-1459
neural tube4.02e-1457
neural rod4.02e-1457
future spinal cord4.02e-1457
neural keel4.02e-1457
adult organism7.64e-14115
organ8.10e-14511
brain9.90e-1469
future brain9.90e-1469
epithelium1.16e-13309
trunk mesenchyme1.26e-13143
surface structure2.33e-1395
tissue3.85e-13787
muscle tissue6.49e-1363
musculature6.49e-1363
musculature of body6.49e-1363
skeletal muscle tissue9.57e-1361
striated muscle tissue9.57e-1361
myotome9.57e-1361
central nervous system1.29e-1282
ectoderm-derived structure2.47e-12169
ectoderm5.15e-12173
presumptive ectoderm5.15e-12173
regional part of nervous system9.54e-1294
nervous system9.54e-1294
trunk1.17e-11216
anatomical cluster2.32e-11286
neural plate1.15e-1086
presumptive neural plate1.15e-1086
anterior neural tube1.47e-1042
regional part of forebrain2.32e-1041
forebrain2.32e-1041
future forebrain2.32e-1041
neurectoderm3.74e-1090
telencephalon4.73e-1034
gray matter6.03e-1034
brain grey matter6.03e-1034
regional part of telencephalon1.37e-0933
anatomical conduit5.06e-09241
cerebral hemisphere5.81e-0932
regional part of cerebral cortex1.80e-0722
pre-chordal neural plate3.71e-0761
organ part3.87e-07219
mesenchyme4.29e-07238
entire embryonic mesenchyme4.29e-07238
neocortex7.90e-0720


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


No analysis results for this cluster

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.