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Coexpression cluster:C1784: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.06e-48!115;UBERON:0001049!2.95e-25!57;UBERON:0005068!2.95e-25!57;UBERON:0006241!2.95e-25!57;UBERON:0007135!2.95e-25!57;UBERON:0002616!3.00e-23!59;UBERON:0005743!2.38e-22!86;UBERON:0003075!2.39e-22!86;UBERON:0007284!2.39e-22!86;UBERON:0000955!3.77e-22!69;UBERON:0006238!3.77e-22!69;UBERON:0000475!4.45e-22!365;UBERON:0001017!1.63e-21!82;UBERON:0002346!8.07e-21!90;UBERON:0000073!3.01e-20!94;UBERON:0001016!3.01e-20!94;UBERON:0003080!1.61e-18!42;UBERON:0000481!4.17e-18!347;UBERON:0002780!4.33e-18!41;UBERON:0001890!4.33e-18!41;UBERON:0006240!4.33e-18!41;UBERON:0000153!3.31e-17!129;UBERON:0007811!3.31e-17!129;UBERON:0000033!1.76e-16!123;UBERON:0001893!2.14e-15!34;UBERON:0003056!2.39e-15!61;UBERON:0002020!2.49e-15!34;UBERON:0003528!2.49e-15!34;UBERON:0000477!7.22e-15!286;UBERON:0004121!7.56e-15!169;UBERON:0002791!7.60e-15!33;UBERON:0001869!2.24e-14!32;UBERON:0000924!3.56e-14!173;UBERON:0006601!3.56e-14!173;UBERON:0004111!1.04e-12!241;UBERON:0002619!2.17e-12!22;UBERON:0000119!3.68e-12!312;UBERON:0000468!4.47e-12!659;UBERON:0000483!6.46e-12!309;UBERON:0000025!1.53e-11!194;UBERON:0001950!2.44e-11!20;UBERON:0000956!2.11e-10!25;UBERON:0000203!2.11e-10!25;UBERON:0000064!2.50e-10!219;UBERON:0000062!7.16e-10!511;UBERON:0000467!1.09e-08!625;UBERON:0000480!1.57e-08!626;UBERON:0003076!6.32e-08!15;UBERON:0003057!6.32e-08!15;UBERON:0000922!1.82e-07!612;UBERON:0002050!9.36e-07!605;UBERON:0005423!9.36e-07!605;UBERON:0002420!9.72e-07!9;UBERON:0007245!9.72e-07!9;UBERON:0010009!9.72e-07!9;UBERON:0010011!9.72e-07!9;UBERON:0000454!9.72e-07!9
|ontology_enrichment_uberon=UBERON:0007023!1.06e-48!115;UBERON:0001049!2.95e-25!57;UBERON:0005068!2.95e-25!57;UBERON:0006241!2.95e-25!57;UBERON:0007135!2.95e-25!57;UBERON:0002616!3.00e-23!59;UBERON:0005743!2.38e-22!86;UBERON:0003075!2.39e-22!86;UBERON:0007284!2.39e-22!86;UBERON:0000955!3.77e-22!69;UBERON:0006238!3.77e-22!69;UBERON:0000475!4.45e-22!365;UBERON:0001017!1.63e-21!82;UBERON:0002346!8.07e-21!90;UBERON:0000073!3.01e-20!94;UBERON:0001016!3.01e-20!94;UBERON:0003080!1.61e-18!42;UBERON:0000481!4.17e-18!347;UBERON:0002780!4.33e-18!41;UBERON:0001890!4.33e-18!41;UBERON:0006240!4.33e-18!41;UBERON:0000153!3.31e-17!129;UBERON:0007811!3.31e-17!129;UBERON:0000033!1.76e-16!123;UBERON:0001893!2.14e-15!34;UBERON:0003056!2.39e-15!61;UBERON:0002020!2.49e-15!34;UBERON:0003528!2.49e-15!34;UBERON:0000477!7.22e-15!286;UBERON:0004121!7.56e-15!169;UBERON:0002791!7.60e-15!33;UBERON:0001869!2.24e-14!32;UBERON:0000924!3.56e-14!173;UBERON:0006601!3.56e-14!173;UBERON:0004111!1.04e-12!241;UBERON:0002619!2.17e-12!22;UBERON:0000119!3.68e-12!312;UBERON:0000468!4.47e-12!659;UBERON:0000483!6.46e-12!309;UBERON:0000025!1.53e-11!194;UBERON:0001950!2.44e-11!20;UBERON:0000956!2.11e-10!25;UBERON:0000203!2.11e-10!25;UBERON:0000064!2.50e-10!219;UBERON:0000062!7.16e-10!511;UBERON:0000467!1.09e-08!625;UBERON:0000480!1.57e-08!626;UBERON:0003076!6.32e-08!15;UBERON:0003057!6.32e-08!15;UBERON:0000922!1.82e-07!612;UBERON:0002050!9.36e-07!605;UBERON:0005423!9.36e-07!605;UBERON:0002420!9.72e-07!9;UBERON:0007245!9.72e-07!9;UBERON:0010009!9.72e-07!9;UBERON:0010011!9.72e-07!9;UBERON:0000454!9.72e-07!9
|tf_chipseq_enrich=HNF4A#3172;3:13.8793742177722:0.000756140884743427:0.0059452381135074
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0.252398,0.197279,0.146467,0.0912686,0.425114,0.123863,0.218241,0.0242146,0.10708,3.84967e-06,4.99513e-06,0.12998,0.123097,0.254847,0.300809,0.0898207,0.126545,0.0918749,0.0686325,0.0569043,0.0639461,0.00162707,0.267408,0.312064,0.080156,0.274185,0.53753,0.0545112,0.00618348,4.85428e-06,0.0649137,0.0974216,0.229627,0.195675,0.174786,0.176557,0.0147764,0.0472148,0.735114,0.229138,0.0639045,0.141461,0.0900204,0.228387,0.385962,0.334921,0.296227,0.208788,0.203834,0.0109471,0.0196869,0.123626,0.270619,0.132705,0.285556,0.0317643,0.0025827,0.0273238,0.262929,0.00222481,0.143824,0.460679,0.431098,0.0775891,0.153079,0.257945,0.211515,0.125701,0.175283,0.204954,0.209341,0.000898851,0.000572102,0.084895,0.160115,0.0819954,0.10091,0.122658,0.151161,0.228398,0.056055,0.120552,0.41771,0.0022265,0.529713,0.335207,0.00278609,0.190688,0.299739,0.278645,0.381281,0.0940982,0.0780533,0.000227,0.0993772,0.274769,3.7413e-05,0.11602,0.067657,0.436413,0.0585992,0.20045,0.274438,8.40657e-05,0.0445114,0.319826,0.336512,0.173868,0.109708,0.174594,0.0809806,0.154589,0.318794,0.122767,0.0749261,0.176858,0.114361,0.347759,0.242462,0.0620267,0.211111,0.0738743,0.0882327,0.183058,0.150073,0.270522,0.16872,0.341388,0.0934526,0.359135,0.123404,0.110025,0.240825,0.3033,0.336623,0.163542,0.483244,0.27134,0.500871,0.239667,0.10226,0.29809,0.0301117,0.689826,0.245965,0.116923,0.148426,0.0983658,0.228743,0.238223,0.156976,0.244789,0.267391,0.301441,0.00206528,0.350528,0.382904,2.82789e-05,0.190404,0.135865,0.488841,0.18137,0.180609,0.291283,0.273972,0.153023,0.400137,0.37958,0.22307,0.160699,0.0891264,0.166736,0.181253,0.0422294,0.263877,0.146486,0.769574,0.0379349,0.00544137,0.131936,0.288826,0.246621,0.463617,3.5974e-05,0.0965376,0.0822869,0.279263,0.336564,0.35463,0.0121078,0.0243626,0.0594155,0.000315574,0.208795,0.0713793,0.212621,0.063279,0.53612,0.629713,0.581874,0.355154,0.145569,0.251388,0.537088,0.603804,0.629445,0.306963,0.206759,0.526495,0.0119447,0.191067,0.0592373,7.83315e-05,0.0156811,0.0219218,0.561689,0.306829,0.000202015,9.22796e-07,0.708698,0.000969861,0.00854007,0.349068,4.10924e-05,0.0792617,0.557035,0.427789,0.114323,0.737642,0.0238314,0.0201302,0.0367004,0.00423004,0.11079,3.94e-08,0.09639,0.494975,0.28382,0.392155,0.626931,0.371758,6.24073e-05,0.562417,0.00204667,0.128028,0.254547,0.000678098,7.9918e-05,0.0011703,2.426e-05,0.00831689,7.64553e-05,0.0243913,1.54374e-05,0.000139187,1.09358e-05,0.315485,0.0544455,0.318577,0.4488,0.389888,0.0670531,0.0361061,0.553178,0.246387,0.224252,0.587237,0.155054,0.466978,0.0379309,0.257848,0.353942,0.192234,0.108067,2.5718e-11,4.47656e-06,0.283682,0.424668,6.68885e-05,0.078383,0.583101,0.702164,0.477016,0.263776,0.498956,0.465544,0.55798,0.349033,0.0205893,0.0415773,7.55811e-05,0.592696,0.592314,0.644904,0.000485662,2.06495e-05,0.317485,0.633504,0.0263405,0.000706094,0.262394,0.307462,0.135076,0.133253,0.000932465,0.274593,0.490712,0.541363,4.53691e-05,0.583627,8.69803e-09,0.720644,0.200667,0.174119,0.361524,0.31558,3.10482e-10,0.0453518,0.018149,0.513592,0.415367,0.0290437,0.45585,0.36864,0.538745,0.456862,0.453004,0.680686,0.557093,0.693441,0.382214,0.553161,0.639572,0.0313098,0.339393,5.17822e-07,0.0525779,0.298354,0.278436,0.00497056,0.0243185,0.641611,0.426239,0.401917,0.656093,0.572661,0.412586,0.534679,0.41502,0.55475,0.66153,0.523749,0.499347,0.307426,0.000221754,0.196912,0.490527,0.132075,0.44799,0.813041,0.318338,0.276338,0.126433,0.0176264,0.318174,0.0555558,0.295666,0.393022,0.293641,0.116969,0.401231,0.255983,0.297663,0.256708,0.0086349,0.322052,0.145568,0.153833,0.261242,0.38389,0.54721,0.388459,0.321362,0.259785,0.280757,0.301366,0.340343,0.343265,0.501812,0.462092,0.336254,0.308589,0.291523,0.19697,0.309816,0.0537285,0.15063,0.198077,0.281455,0.348739,0.419895,0.138495,0.0235054,0.32256,0.377566,0.342366,0.109684,0.322704,0.403482,0.181288,0.230841,0.352328,0.255358,0.351665,0.265112,0.0633313,0.10772,0.0854747,0.0747609,0.406458,0.00666418,0.000104137,0.244656,0.192188,0.158985,0.174153,0.0972854,0.333309,0.249919,0.339517,0.00604041,0.198326,0.394084,0.126349,0.282501,0.252005,0.390891,0.238377,0.334983,0.197875,0.287909,0.289389,0.117618,0.014271,0.396962,0.316002,0.330317,0.321404,0.225079,0.300542,0.379651,0.185715,0.345505,0.375521,0.271405,0.311201,0.221943,0.306427,0.367733,0.246925,0.208775,0.390438,0.00904736,0.270094,0.276922,0.156279,0.055329,0.461742,0.422872,0.336468,0.13327,0.00671106,0.17149,0.0877361,0.0880065,0.238969,0.126615,0.0669467,0.0879453,0.474066,0.396935,0.326779,0.292869,0.358198,0.29552,0.131776,0.158116,0.104606,0.194814,0.104167,0.168186,0.108081,0.123829,0.205215,0.175247,0.0724304,0.109077,0.144842,0.0604892,0.214671,0.316879,0.442567,0.430541,0.0354176,0.0274256,0.398887,0.389061,0.0542381,0.349611,0.445995,0.385709,0.278202,0.426488,0.400591,0.209809,0.253154,0.0071437,0.309489,0.430805,0.362154,0.480785,0.185476,0.336314,0.344469,0.184651,0.303359,0.297596,0.018596,0.425912,0.380826,0.259046,0.345068,0.151046,0.483953,0.0687784,0.32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}}
}}

Revision as of 12:09, 5 September 2012


Full id: C1784_heart_skeletal_left_tongue_diaphragm_cerebellum_temporal



Phase1 CAGE Peaks

Hg19::chr17:48172695..48172780,+p1@PDK2
Hg19::chr19:35629684..35629701,+p3@FXYD1
Hg19::chr19:35629702..35629742,+p1@FXYD1
Hg19::chr19:35629748..35629760,+p2@FXYD1
Hg19::chr19:35630028..35630083,+p7@FXYD1


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:0004740pyruvate dehydrogenase (acetyl-transferring) kinase activity0.0192090723048097
GO:0018106peptidyl-histidine phosphorylation0.0192090723048097
GO:0018202peptidyl-histidine modification0.0192090723048097
GO:0004673protein histidine kinase activity0.0335181977945929
GO:0016775phosphotransferase activity, nitrogenous group as acceptor0.0335181977945929
GO:0043168anion binding0.0448719349502542
GO:0031404chloride ion binding0.0448719349502542



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 organism1.06e-48115
neural tube2.95e-2557
neural rod2.95e-2557
future spinal cord2.95e-2557
neural keel2.95e-2557
regional part of brain3.00e-2359
neural plate2.39e-2286
presumptive neural plate2.39e-2286
brain3.77e-2269
future brain3.77e-2269
organism subdivision4.45e-22365
central nervous system1.63e-2182
neurectoderm8.07e-2190
regional part of nervous system3.01e-2094
nervous system3.01e-2094
anterior neural tube1.61e-1842
multi-tissue structure4.17e-18347
regional part of forebrain4.33e-1841
forebrain4.33e-1841
future forebrain4.33e-1841
anterior region of body3.31e-17129
craniocervical region3.31e-17129
head1.76e-16123
telencephalon2.14e-1534
pre-chordal neural plate2.39e-1561
gray matter2.49e-1534
brain grey matter2.49e-1534
anatomical cluster7.22e-15286
ectoderm-derived structure7.56e-15169
regional part of telencephalon7.60e-1533
cerebral hemisphere2.24e-1432
ectoderm3.56e-14173
presumptive ectoderm3.56e-14173
anatomical conduit1.04e-12241
regional part of cerebral cortex2.17e-1222
cell layer3.68e-12312
multi-cellular organism4.47e-12659
epithelium6.46e-12309
tube1.53e-11194
neocortex2.44e-1120
cerebral cortex2.11e-1025
pallium2.11e-1025
organ part2.50e-10219
organ7.16e-10511
anatomical system1.09e-08625
anatomical group1.57e-08626
posterior neural tube6.32e-0815
chordal neural plate6.32e-0815
embryo1.82e-07612
embryonic structure9.36e-07605
developing anatomical structure9.36e-07605
basal ganglion9.72e-079
nuclear complex of neuraxis9.72e-079
aggregate regional part of brain9.72e-079
collection of basal ganglia9.72e-079
cerebral subcortex9.72e-079


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
HNF4A#3172313.87937421777220.0007561408847434270.0059452381135074



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.