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Coexpression cluster:C2065: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!2.73e-66!57;UBERON:0005068!2.73e-66!57;UBERON:0006241!2.73e-66!57;UBERON:0007135!2.73e-66!57;UBERON:0005743!5.19e-65!86;UBERON:0000073!6.32e-65!94;UBERON:0001016!6.32e-65!94;UBERON:0001017!1.27e-64!82;UBERON:0002616!3.65e-57!59;UBERON:0000955!9.01e-56!69;UBERON:0006238!9.01e-56!69;UBERON:0002780!7.09e-53!41;UBERON:0001890!7.09e-53!41;UBERON:0006240!7.09e-53!41;UBERON:0007023!1.92e-52!115;UBERON:0003075!4.46e-52!86;UBERON:0007284!4.46e-52!86;UBERON:0003080!2.78e-51!42;UBERON:0002346!1.99e-50!90;UBERON:0002020!1.04e-43!34;UBERON:0003528!1.04e-43!34;UBERON:0001893!1.67e-43!34;UBERON:0002791!3.79e-42!33;UBERON:0001869!9.96e-41!32;UBERON:0003056!5.05e-40!61;UBERON:0004121!1.18e-34!169;UBERON:0000924!2.78e-34!173;UBERON:0006601!2.78e-34!173;UBERON:0000033!5.86e-34!123;UBERON:0000153!1.11e-33!129;UBERON:0007811!1.11e-33!129;UBERON:0000956!1.89e-31!25;UBERON:0000203!1.89e-31!25;UBERON:0002619!1.15e-28!22;UBERON:0001950!1.14e-25!20;UBERON:0000025!5.91e-18!194;UBERON:0003076!1.63e-15!15;UBERON:0003057!1.63e-15!15;UBERON:0004111!1.90e-14!241;UBERON:0000477!1.31e-13!286;UBERON:0002308!1.45e-13!9;UBERON:0000125!1.45e-13!9;UBERON:0002420!2.12e-13!9;UBERON:0007245!2.12e-13!9;UBERON:0010009!2.12e-13!9;UBERON:0010011!2.12e-13!9;UBERON:0000454!2.12e-13!9;UBERON:0000483!1.34e-12!309;UBERON:0004732!1.78e-12!13;UBERON:0000119!2.95e-12!312;UBERON:0000475!3.29e-12!365;UBERON:0004733!2.30e-11!12;UBERON:0002028!2.30e-11!12;UBERON:0007277!2.30e-11!12;UBERON:0009663!1.03e-10!7;UBERON:0001894!1.42e-10!7;UBERON:0006222!1.42e-10!7;UBERON:0000481!3.95e-10!347;UBERON:0000064!4.54e-10!219;UBERON:0002298!1.26e-09!8;UBERON:0000200!1.70e-09!6;UBERON:0001871!2.56e-09!7;UBERON:0000922!3.14e-09!612;UBERON:0000349!8.66e-09!5;UBERON:0002050!2.71e-08!605;UBERON:0005423!2.71e-08!605;UBERON:0000062!5.60e-08!511;UBERON:0000923!6.52e-08!604;UBERON:0005291!6.52e-08!604;UBERON:0006598!6.52e-08!604;UBERON:0002532!6.52e-08!604;UBERON:0001872!7.10e-08!5;UBERON:0000468!7.49e-08!659;UBERON:0002021!8.67e-08!5;UBERON:0002680!1.21e-07!9;UBERON:0001895!1.21e-07!9;UBERON:0010092!1.21e-07!9;UBERON:0000467!3.62e-07!625;UBERON:0000480!4.18e-07!626;UBERON:0000369!6.35e-07!4;UBERON:0002435!6.35e-07!4;UBERON:0000204!6.35e-07!4;UBERON:0010082!6.35e-07!4
|ontology_enrichment_uberon=UBERON:0001049!2.73e-66!57;UBERON:0005068!2.73e-66!57;UBERON:0006241!2.73e-66!57;UBERON:0007135!2.73e-66!57;UBERON:0005743!5.19e-65!86;UBERON:0000073!6.32e-65!94;UBERON:0001016!6.32e-65!94;UBERON:0001017!1.27e-64!82;UBERON:0002616!3.65e-57!59;UBERON:0000955!9.01e-56!69;UBERON:0006238!9.01e-56!69;UBERON:0002780!7.09e-53!41;UBERON:0001890!7.09e-53!41;UBERON:0006240!7.09e-53!41;UBERON:0007023!1.92e-52!115;UBERON:0003075!4.46e-52!86;UBERON:0007284!4.46e-52!86;UBERON:0003080!2.78e-51!42;UBERON:0002346!1.99e-50!90;UBERON:0002020!1.04e-43!34;UBERON:0003528!1.04e-43!34;UBERON:0001893!1.67e-43!34;UBERON:0002791!3.79e-42!33;UBERON:0001869!9.96e-41!32;UBERON:0003056!5.05e-40!61;UBERON:0004121!1.18e-34!169;UBERON:0000924!2.78e-34!173;UBERON:0006601!2.78e-34!173;UBERON:0000033!5.86e-34!123;UBERON:0000153!1.11e-33!129;UBERON:0007811!1.11e-33!129;UBERON:0000956!1.89e-31!25;UBERON:0000203!1.89e-31!25;UBERON:0002619!1.15e-28!22;UBERON:0001950!1.14e-25!20;UBERON:0000025!5.91e-18!194;UBERON:0003076!1.63e-15!15;UBERON:0003057!1.63e-15!15;UBERON:0004111!1.90e-14!241;UBERON:0000477!1.31e-13!286;UBERON:0002308!1.45e-13!9;UBERON:0000125!1.45e-13!9;UBERON:0002420!2.12e-13!9;UBERON:0007245!2.12e-13!9;UBERON:0010009!2.12e-13!9;UBERON:0010011!2.12e-13!9;UBERON:0000454!2.12e-13!9;UBERON:0000483!1.34e-12!309;UBERON:0004732!1.78e-12!13;UBERON:0000119!2.95e-12!312;UBERON:0000475!3.29e-12!365;UBERON:0004733!2.30e-11!12;UBERON:0002028!2.30e-11!12;UBERON:0007277!2.30e-11!12;UBERON:0009663!1.03e-10!7;UBERON:0001894!1.42e-10!7;UBERON:0006222!1.42e-10!7;UBERON:0000481!3.95e-10!347;UBERON:0000064!4.54e-10!219;UBERON:0002298!1.26e-09!8;UBERON:0000200!1.70e-09!6;UBERON:0001871!2.56e-09!7;UBERON:0000922!3.14e-09!612;UBERON:0000349!8.66e-09!5;UBERON:0002050!2.71e-08!605;UBERON:0005423!2.71e-08!605;UBERON:0000062!5.60e-08!511;UBERON:0000923!6.52e-08!604;UBERON:0005291!6.52e-08!604;UBERON:0006598!6.52e-08!604;UBERON:0002532!6.52e-08!604;UBERON:0001872!7.10e-08!5;UBERON:0000468!7.49e-08!659;UBERON:0002021!8.67e-08!5;UBERON:0002680!1.21e-07!9;UBERON:0001895!1.21e-07!9;UBERON:0010092!1.21e-07!9;UBERON:0000467!3.62e-07!625;UBERON:0000480!4.18e-07!626;UBERON:0000369!6.35e-07!4;UBERON:0002435!6.35e-07!4;UBERON:0000204!6.35e-07!4;UBERON:0010082!6.35e-07!4
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621787,0.178782,0.019419,0.0866228,0.271849,0.282657,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.226143,0.460406,0.0438521,0.435508,0.281453,0.0522771,0.0787278,0.515487,0.159873,0.142462,0.143935,0.332403,0.000729529,0.6545,0.187953,0.051459,0.00686557,0.0726892,6.53673e-05,0.32305,0.278397,0.245002,0.170848,0.487259,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.184022,0.216557,0.182956,0.116818,0.389792,0.36316,0.0625685,0.124464,0.544477,0.173134,0.101893,0.142875,0.167635,0.171311,0.787798,0.189107,0.0685131,0.130287,0.002238,0.0815772,0.0993937,0.122878,0.187329,0.0451012,1.49831e-09,0.351199,0.535567,0.758305,0.278645,0.365775,0.155708,0.248017,0.22995,0.091341,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.379174,0.0939463,0.00500232,0.367925,0.0471607,0.163865,0.226359,0.960445,0.974549,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.0269564,0.137423,0.284016,0.0754883,0.299492,0.100006,0.0109294,0.197817,0.251078,0.279874,0.133127,0.410303,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.608002,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.291976,0.320355,0.364334,0.15547,0.110256,0.415419,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.690952,0.21618,0.243266,0.107021,0.238657,0.20272,0.392453,0.248134,0.0780061,0.315336,0.028874,0.279823,0.295555,0.502112,0.724669,0.0478217,0.158752,0.170854,0.0575231,0.174063,0.514243,0.459091,0.54832,0.502211,0.296013,0.000760863,0.537932,0.459994,0.523209,0.00885937,0.25423,0.490559,0.121268,0.00559995,0.0272171,0.685908,0.747471,0.529642,0.244786,0.483077,0.590496,0.603763,0.541914,0.000554528,0.938109,0.934991,0.290703,0.622694,0.366999,0.478691,0.360199,0.608176,0.000842547,0.824761,0.365494,0.212703,0.56318,0.364079,0.680099,0.215551,0.104625,0.569409,0.328518,0.545608,0.310552,0.865054,0.483764,0.829658,0.784052,0.209437,0.843495,0.748403,0.598945,0.882403,0.464001,0.871271,0.579004,0.870272,0.839946,0.860705,0.261575,0.257956,0.264245,0.379063,0.326516,0.522925,0.436016,0.00431716,0.202522,0.183837,0.507324,0.126097,0.3955,0.442469,0.212239,0.294954,0.156999,0.35974,0.667777,0.39549,0.0298727,0.357409,0.86719,0.721266,0.50338,0.0746831,0.404625,0.172147,0.424691,0.715362,0.139684,0.62689,0.884725,0.0207342,0.284496,0.00629645,0.512178,0.563206,0.527709,0.684899,0.263302,0.047857,0.180735,0.439629,0.216102,0.254659,0.109605,0.397869,0.217863,0.226491,0.417131,0.0255104,0.0782409,0.503881,0.454761,0.639483,6.5959e-05,0.452129,0.301581,0.261657,0.346776,0.466529,0.545655,0.00291646,0.349112,0.741477,0.0134085,0.307816,0.461541,0.386339,0.382854,0.598787,0.478745,0.611661,0.000676019,0.475047,0.557967,0.241014,0.282281,0.612712,0.2536,0.246827,0.564333,0.70712,0.387134,0.050476,0.0105234,0.668972,0.574252,0.493455,0.346636,0.00360135,0.348802,0.00438353,0.0574793,0.447581,0.42505,0.254628,0.713293,0.00451196,0.416962,0.632833,0.378333,0.738545,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,6.08224e-05,0.242783,0.0947248,6.89591e-05,0.210656,0.246234,0.211271,0.000381355,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,1.87566e-06,0.231754,0.249415,0.283107,0.285648,0.427316,0.0890097,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.0138731,0.23235,0.290415,0.353147,0.112422,0.170886,0.267687,0.315656,0.284866,0.0887542,0.267811,0.338547,0.147872,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.113839,0.201057,0.15696,0.129351,0.141936,0.0786166,0.042497,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.000187008,3.8626e-06,0.000767461,0.00817635,0.262022,0.274403,0.266687,0.184534,2.41686e-08,0.31749,0.15156,0.287598,0.00673322,0.223773,0.25788,0.181895,0.000242325,0.30702,0.202977,0.170837,0.0604859,0.28543,0.222656,0.228479,0.127111,0.259989,0.0888526,0.355805,0.279739,0.108118,0.259901,3.04244e-10,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.00984212,0.0874421,0.100355,1.49818e-06,0.142846,0.0583767,0.088258,0.000297685,0.0486914,0.0164443,0.038024,0.373453,0.0755696,0.433518,0.184359,0.00831677,0.325785,0.257476,0.0472356,0.376537,0.322827,0.229571,0.0105454,1.36264e-08,1.69054e-06,0.208256,0.0387226,0.256405,0.0109327,0.302133,0.40806,0.151361,0.279606,0.286696,0.0119686,0.251128,0.000212201,0.0103202,0.0737175,0.00707033,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,1.86078e-07,0.0150081,0.222091,0.205977,0.34423,0.0936726,0.0671916,0.132374,0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}}
}}

Revision as of 13:36, 5 September 2012


Full id: C2065_eye_retina_leiomyoblastoma_spinal_hippocampus_lung_rhabdomyosarcoma



Phase1 CAGE Peaks

Hg19::chr10:56560939..56560950,-p3@PCDH15
Hg19::chr10:56560953..56560969,-p2@PCDH15
Hg19::chr10:56560981..56560999,-p1@PCDH15
Hg19::chr10:56561022..56561033,-p4@PCDH15


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neural tube2.73e-6657
neural rod2.73e-6657
future spinal cord2.73e-6657
neural keel2.73e-6657
regional part of nervous system6.32e-6594
nervous system6.32e-6594
central nervous system1.27e-6482
regional part of brain3.65e-5759
brain9.01e-5669
future brain9.01e-5669
regional part of forebrain7.09e-5341
forebrain7.09e-5341
future forebrain7.09e-5341
adult organism1.92e-52115
neural plate4.46e-5286
presumptive neural plate4.46e-5286
anterior neural tube2.78e-5142
neurectoderm1.99e-5090
gray matter1.04e-4334
brain grey matter1.04e-4334
telencephalon1.67e-4334
regional part of telencephalon3.79e-4233
cerebral hemisphere9.96e-4132
pre-chordal neural plate5.05e-4061
ectoderm-derived structure1.18e-34169
ectoderm2.78e-34173
presumptive ectoderm2.78e-34173
head5.86e-34123
anterior region of body1.11e-33129
craniocervical region1.11e-33129
cerebral cortex1.89e-3125
pallium1.89e-3125
regional part of cerebral cortex1.15e-2822
neocortex1.14e-2520
tube5.91e-18194
posterior neural tube1.63e-1515
chordal neural plate1.63e-1515
anatomical conduit1.90e-14241
anatomical cluster1.31e-13286
nucleus of brain1.45e-139
neural nucleus1.45e-139
basal ganglion2.12e-139
nuclear complex of neuraxis2.12e-139
aggregate regional part of brain2.12e-139
collection of basal ganglia2.12e-139
cerebral subcortex2.12e-139
epithelium1.34e-12309
segmental subdivision of nervous system1.78e-1213
cell layer2.95e-12312
organism subdivision3.29e-12365
segmental subdivision of hindbrain2.30e-1112
hindbrain2.30e-1112
presumptive hindbrain2.30e-1112
telencephalic nucleus1.03e-107
diencephalon1.42e-107
future diencephalon1.42e-107
multi-tissue structure3.95e-10347
organ part4.54e-10219
brainstem1.26e-098
gyrus1.70e-096
temporal lobe2.56e-097
embryo3.14e-09612
limbic system8.66e-095
embryonic structure2.71e-08605
developing anatomical structure2.71e-08605
organ5.60e-08511
germ layer6.52e-08604
embryonic tissue6.52e-08604
presumptive structure6.52e-08604
epiblast (generic)6.52e-08604
parietal lobe7.10e-085
multi-cellular organism7.49e-08659
occipital lobe8.67e-085
regional part of metencephalon1.21e-079
metencephalon1.21e-079
future metencephalon1.21e-079
anatomical system3.62e-07625
anatomical group4.18e-07626
corpus striatum6.35e-074
striatum6.35e-074
ventral part of telencephalon6.35e-074
future corpus striatum6.35e-074


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
CTCF#1066445.360256373075030.001211145381643620.0081533332804872
RAD21#5885410.35503389545638.6948481184721e-050.0012902546783818
TRIM28#10155418.59052504526258.36730015875654e-060.000229543593716936



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.

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