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Coexpression cluster:C2510: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005743!2.26e-22!86;UBERON:0000073!2.74e-21!94;UBERON:0001016!2.74e-21!94;UBERON:0001017!1.33e-20!82;UBERON:0004121!5.01e-20!169;UBERON:0000924!3.27e-19!173;UBERON:0006601!3.27e-19!173;UBERON:0000475!7.68e-19!365;UBERON:0003075!3.41e-17!86;UBERON:0007284!3.41e-17!86;UBERON:0000033!1.09e-16!123;UBERON:0002616!2.20e-16!59;UBERON:0000153!4.22e-16!129;UBERON:0007811!4.22e-16!129;UBERON:0002346!5.41e-16!90;UBERON:0000955!5.49e-16!69;UBERON:0006238!5.49e-16!69;UBERON:0001049!1.83e-14!57;UBERON:0005068!1.83e-14!57;UBERON:0006241!1.83e-14!57;UBERON:0007135!1.83e-14!57;UBERON:0003056!4.25e-14!61;UBERON:0002780!1.07e-10!41;UBERON:0001890!1.07e-10!41;UBERON:0006240!1.07e-10!41;UBERON:0003080!1.15e-10!42;UBERON:0002020!3.82e-10!34;UBERON:0003528!3.82e-10!34;UBERON:0001893!6.79e-10!34;UBERON:0000481!9.22e-10!347;UBERON:0002791!1.09e-09!33;UBERON:0001869!1.34e-09!32;UBERON:0007625!4.08e-08!11;UBERON:0000956!4.13e-08!25;UBERON:0000203!4.13e-08!25;UBERON:0000468!5.46e-07!659
|ontology_enrichment_uberon=UBERON:0005743!2.26e-22!86;UBERON:0000073!2.74e-21!94;UBERON:0001016!2.74e-21!94;UBERON:0001017!1.33e-20!82;UBERON:0004121!5.01e-20!169;UBERON:0000924!3.27e-19!173;UBERON:0006601!3.27e-19!173;UBERON:0000475!7.68e-19!365;UBERON:0003075!3.41e-17!86;UBERON:0007284!3.41e-17!86;UBERON:0000033!1.09e-16!123;UBERON:0002616!2.20e-16!59;UBERON:0000153!4.22e-16!129;UBERON:0007811!4.22e-16!129;UBERON:0002346!5.41e-16!90;UBERON:0000955!5.49e-16!69;UBERON:0006238!5.49e-16!69;UBERON:0001049!1.83e-14!57;UBERON:0005068!1.83e-14!57;UBERON:0006241!1.83e-14!57;UBERON:0007135!1.83e-14!57;UBERON:0003056!4.25e-14!61;UBERON:0002780!1.07e-10!41;UBERON:0001890!1.07e-10!41;UBERON:0006240!1.07e-10!41;UBERON:0003080!1.15e-10!42;UBERON:0002020!3.82e-10!34;UBERON:0003528!3.82e-10!34;UBERON:0001893!6.79e-10!34;UBERON:0000481!9.22e-10!347;UBERON:0002791!1.09e-09!33;UBERON:0001869!1.34e-09!32;UBERON:0007625!4.08e-08!11;UBERON:0000956!4.13e-08!25;UBERON:0000203!4.13e-08!25;UBERON:0000468!5.46e-07!659
|tf_chipseq_enrich=EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101455751011394!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322309716801782
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8498,0.140114,0.348988,0.00641248,0.224626,0.183585,0.00419343,0.03989,0.171436,0.05892,0.0691994,0.268299,0.198844,0.00571021,0.127738,0.207615,0.161213,0.118999,0.0737069,0.357807,8.9567e-07,0.178782,0.019419,0.0866228,0.271849,0.044355,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.00282365,0.0552936,0.0457886,0.0514927,0.324236,0.0262915,0.258624,0.064656,0.226143,0.460406,0.0438521,0.112715,0.281453,0.0522771,0.0787278,0.515487,0.159873,0.142462,0.0108948,0.332403,0.0379537,0.00471564,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.144756,0.051371,0.00120516,0.100188,0.223102,0.107653,0.235857,2.26512e-05,0.191914,0.184022,0.0253522,0.182956,0.116818,0.389792,0.000107259,0.0625685,0.124464,0.186295,0.173134,0.101893,0.142875,0.167635,0.171311,0.00111708,1.98082e-05,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,1.0777e-11,0.0560157,0.278645,0.365775,0.155708,0.248017,0.22995,0.652972,0.0760151,4.36248e-05,3.88771e-08,0.0803251,0.226641,0.379174,0.0939463,0.00500232,0.367925,0.0471607,0.163865,0.226359,1.64154e-06,0.0792764,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.000625037,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.0756617,0.197817,0.251078,0.279874,0.133127,0.410303,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.0153391,0.0219712,0.00463136,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.00318161,0.178639,0.0475113,0.320355,0.364334,0.15547,0.110256,0.415419,0.14794,0.147307,0.240761,0.00231398,0.124417,0.335582,0.317428,0.182843,0.130771,0.000756078,0.135777,0.147842,0.0339286,0.217363,0.119015,0.32805,0.21618,0.243266,0.107021,0.238657,0.20272,0.392453,7.44388e-06,0.0780061,0.315336,0.230477,0.279823,0.295555,0.000772604,1.35123e-08,0.0478217,0.507599,0.170854,0.0575231,0.0161134,0.514243,0.459091,0.54832,0.502211,0.0489167,0.000760863,0.0434876,0.459994,0.00100779,0.548059,0.25423,0.031106,0.45013,0.153911,0.472542,0.685908,0.747471,0.529642,1.90238e-06,0.483077,4.12862e-05,0.0147688,0.00835925,7.66752e-05,1.44819e-06,5.70475e-09,0.0470729,0.00328655,5.85899e-05,0.00448166,0.360199,5.5711e-05,0.0937029,0.099511,6.92122e-11,0.212703,1.07589e-15,0.364079,0.0287777,0.215551,0.421038,0.0537414,0.328518,0.00132729,0.310552,5.7293e-11,0.00472069,1.68304e-05,0.0201581,0.209437,8.88741e-08,0.000572229,0.598945,1.24727e-09,0.0255132,6.80207e-10,0.579004,5.09521e-09,2.24964e-05,2.45601e-08,0.261575,0.257956,0.264245,0.379063,0.00074309,0.522925,0.436016,0.475063,0.202522,0.183837,8.35813e-07,0.126097,0.3955,0.442469,0.212239,0.294954,0.156999,0.35974,2.46176e-06,0.39549,0.234254,0.0103854,5.02151e-05,0.000364106,0.034133,0.620526,0.404625,1.85051e-05,0.0187136,0.715362,0.479581,0.003448,0.36666,0.0207342,0.284496,0.512545,0.512178,0.563206,2.64616e-06,0.00123784,0.263302,0.552023,0.180735,0.000163899,0.216102,0.254659,0.109605,0.0924199,0.000293714,0.226491,0.417131,0.000469228,7.76449e-05,0.0342559,0.124057,0.0840572,0.483658,0.452129,0.301581,8.35017e-07,0.346776,0.466529,0.0458396,0.438176,0.349112,0.741477,0.00159055,0.00631453,0.461541,0.386339,0.382854,0.000370843,0.478745,6.70696e-08,0.0576521,0.475047,0.00972177,0.608127,0.282281,0.0159965,0.2536,0.0333324,0.0103145,7.43989e-10,0.00162371,0.559969,0.358813,0.000153433,0.574252,0.0317703,0.346636,0.457747,0.348802,0.476541,0.00199432,0.447581,0.106831,0.0355841,0.000319058,0.139532,0.416962,0.0191073,0.378333,0.00260167,0.264038,0.22798,0.102495,0.350933,0.0383658,0.0446972,1.14442e-05,0.329284,0.242783,0.0947248,0.336551,0.210656,0.000212417,0.211271,0.0439036,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.000301162,0.187728,0.231754,0.249415,0.283107,0.285648,0.427316,0.0890097,0.0433305,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.0469743,0.353147,0.112422,0.170886,0.267687,0.00686166,0.284866,0.0887542,0.267811,0.0651578,0.147872,0.189388,0.000460864,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.000533222,0.0786166,5.6445e-08,0.205513,0.0442657,0.0346487,0.162089,0.330223,0.387837,0.000167787,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.0612213,0.332769,0.262022,0.274403,0.0392261,0.184534,0.248707,0.31749,0.15156,0.287598,0.313858,0.223773,0.25788,0.0176484,0.253768,0.30702,0.202977,0.170837,0.327002,0.0452813,0.222656,0.228479,0.127111,0.259989,0.390754,0.0725176,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.032013,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.000106401,0.433518,0.184359,0.334474,0.325785,0.257476,0.000444529,0.3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}}
}}

Revision as of 11:55, 5 September 2012


Full id: C2510_Preadipocyte_Chondrocyte_Osteoblast_Wilms_rhabdomyosarcoma_adrenal_Lens



Phase1 CAGE Peaks

Hg19::chr1:103574001..103574014,-p3@COL11A1
Hg19::chr1:103574024..103574063,-p1@COL11A1
Hg19::chr1:103574068..103574099,-p2@COL11A1
Hg19::chr1:103574154..103574165,-p4@COL11A1


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>


Cell Type
Ontology termp-valuen
non-terminally differentiated cell4.59e-23180
stuff accumulating cell4.58e-1039
neurectodermal cell1.59e-0859
fibroblast3.69e-0875
columnar/cuboidal epithelial cell4.02e-0727
Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.74e-2194
nervous system2.74e-2194
central nervous system1.33e-2082
ectoderm-derived structure5.01e-20169
ectoderm3.27e-19173
presumptive ectoderm3.27e-19173
organism subdivision7.68e-19365
neural plate3.41e-1786
presumptive neural plate3.41e-1786
head1.09e-16123
regional part of brain2.20e-1659
anterior region of body4.22e-16129
craniocervical region4.22e-16129
neurectoderm5.41e-1690
brain5.49e-1669
future brain5.49e-1669
neural tube1.83e-1457
neural rod1.83e-1457
future spinal cord1.83e-1457
neural keel1.83e-1457
pre-chordal neural plate4.25e-1461
regional part of forebrain1.07e-1041
forebrain1.07e-1041
future forebrain1.07e-1041
anterior neural tube1.15e-1042
gray matter3.82e-1034
brain grey matter3.82e-1034
telencephalon6.79e-1034
multi-tissue structure9.22e-10347
regional part of telencephalon1.09e-0933
cerebral hemisphere1.34e-0932
pigment epithelium of eye4.08e-0811
cerebral cortex4.13e-0825
pallium4.13e-0825
multi-cellular organism5.46e-07659


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
EGR1#195844.988179094810140.001615011500076050.0101455751011394
TAF1#687243.343046285745290.008005664898701650.0322309716801782



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.