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Coexpression cluster:C2076: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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615,0.161213,0.118999,0.0737069,0.357807,0.0173365,0.178782,0.019419,0.0866228,0.271849,0.282657,0.105411,0.0997542,0.209692,0.0339332,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.0593965,0.220368,0.258624,0.064656,0.226143,0.460406,0.0438521,0.435508,0.281453,0.0522771,0.0787278,0.164404,0.159873,0.142462,0.143935,0.332403,0.0379537,0.0230803,0.187953,0.051459,0.114868,0.0726892,0.18732,0.0589328,0.278397,0.245002,0.170848,0.000638111,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.103852,0.191914,0.0180783,0.216557,0.182956,0.116818,0.0883765,0.0757944,0.0625685,0.124464,0.0454742,0.173134,0.101893,0.142875,0.167635,0.171311,0.20386,0.0465855,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.00979133,0.267945,0.415079,0.278645,0.365775,0.155708,0.0336707,0.22995,0.0227764,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.012683,0.0939463,0.0457255,0.367925,0.0471607,0.163865,0.226359,0.0464703,0.0339072,0.265324,0.043404,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.0385301,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.000482136,0.284016,0.0754883,0.299492,0.100006,0.0756617,0.197817,0.251078,0.00462092,0.133127,0.410303,0.223717,0.00256165,0.196838,0.0826805,0.246601,0.193021,0.0153391,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.0217469,0.220353,0.24948,0.178639,0.291976,0.00720587,0.0763252,0.15547,0.110256,0.0173373,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.32805,0.21618,0.0323312,0.107021,0.238657,0.20272,0.392453,0.0164195,0.0780061,0.0559668,0.028874,0.043419,0.0487563,0.00567943,0.0420826,0.0478217,0.00599702,0.170854,0.0575231,0.174063,0.00640224,0.459091,0.000178027,0.154964,0.296013,0.282366,0.537932,0.459994,0.0392766,0.189126,0.25423,0.000666016,0.121268,0.153911,0.0272171,0.322168,0.0133357,0.529642,0.244786,0.483077,0.00226518,0.0671621,0.541914,0.627201,0.0237007,0.0594404,0.290703,0.00328655,0.138899,0.139104,0.360199,0.0690757,0.290133,0.099511,0.365494,0.212703,0.201391,0.364079,0.00628541,0.00199999,0.0181617,0.569409,0.328518,0.187186,0.310552,0.324103,0.00472069,0.0342735,0.784052,0.209437,0.284058,0.0514874,0.00249952,0.169076,0.0255132,0.152018,0.214786,0.150592,0.113944,0.137711,0.261575,0.257956,0.264245,0.379063,0.326516,0.0391986,0.113006,0.475063,0.202522,0.183837,0.507324,0.126097,0.0912229,0.0215868,0.212239,0.294954,0.156999,0.35974,0.0999766,0.39549,0.234254,0.357409,0.328421,0.000364106,0.15578,0.0171443,0.404625,0.0563812,0.424691,0.132999,0.139684,0.0181348,0.172925,0.642173,0.284496,0.16228,0.512178,0.201413,0.527709,2.83089e-05,0.263302,0.192292,0.180735,0.189249,0.216102,0.254659,0.109605,0.397869,0.0585759,0.226491,0.417131,0.463987,0.260097,0.156131,0.0237654,0.271678,0.483658,0.0232851,0.301581,0.261657,0.000976975,0.466529,0.0458396,0.114247,0.349112,0.0485429,0.385425,0.307816,0.128211,0.0135171,0.382854,0.598787,0.478745,0.611661,0.319747,0.475047,0.197104,0.241014,0.282281,0.0159965,0.2536,0.246827,0.00166308,0.12664,0.0870695,0.050476,0.358813,0.00554889,0.210703,0.0317703,0.0685505,0.457747,0.348802,0.137708,0.0574793,0.0032303,0.106831,0.254628,0.713293,0.139532,0.416962,0.0191073,0.378333,0.152547,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.00817168,0.215123,0.321224,0.469461,0.0597961,0.266651,0.546295,0.231754,0.249415,0.283107,0.0453548,0.10809,0.0890097,0.0433305,0.25563,0.0316941,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.0469743,0.0713545,0.112422,0.170886,0.267687,0.0560879,0.284866,0.0887542,0.0395756,0.00865954,0.147872,0.189388,0.293546,0.210125,0.0478543,0.0258076,0.0509944,0.0871471,0.0689852,0.0602698,0.0662546,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.04166,0.0392261,0.184534,0.248707,0.00699456,0.15156,0.287598,0.0554083,0.0271466,0.25788,0.181895,0.253768,0.0528669,0.202977,0.170837,0.327002,0.28543,0.222656,0.228479,0.127111,0.259989,0.390754,0.0725176,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.0627853,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.0149493,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.038024,0.373453,0.362662,0.433518,0.184359,0.334474,0.0600054,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.000968095,0.208256,0.265058,0.256405,0.362898,0.302133,0.00207843,0.151361,0.279606,0.0457079,0.150674,0.251128,0.246177,0.0729297,0.35852,0.0571822,0.213257,0.00502917,0.122782,0.410951,0.289049,0.0393151,0.125746,0.112897,0.398354,0.222091,0.205977,0.000944652,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113
}}
}}

Revision as of 13:37, 5 September 2012


Full id: C2076_Melanocyte_corpus_brain_occipital_temporal_postcentral_pons



Phase1 CAGE Peaks

Hg19::chr10:83635613..83635633,+p3@NRG3
Hg19::chr8:22005612..22005623,-p@chr8:22005612..22005623
-
Hg19::chr8:22014298..22014326,-p1@LGI3
Hg19::chr8:22014339..22014342,-p4@LGI3


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:0030297transmembrane receptor protein tyrosine kinase activator activity0.00565129725365418
GO:0030971receptor tyrosine kinase binding0.00565129725365418
GO:0030296protein tyrosine kinase activator activity0.00565129725365418
GO:0030295protein kinase activator activity0.00791088449005495
GO:0030879mammary gland development0.00791088449005495
GO:0019209kinase activator activity0.00847544856163342
GO:0048732gland development0.0185576153148636
GO:0019887protein kinase regulator activity0.0370325943749413
GO:0019207kinase regulator activity0.0382378355329935
GO:0001558regulation of cell growth0.0446438476068774
GO:0016049cell growth0.0446438476068774
GO:0040008regulation of growth0.0446438476068774
GO:0008361regulation of cell size0.0446438476068774
GO:0009790embryonic development0.0472706531134139
GO:0008083growth factor activity0.0474859976685569



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
melanocyte4.93e-0710
melanoblast4.93e-0710
Uber Anatomy
Ontology termp-valuen
adult organism1.57e-55115
neural tube2.96e-4957
neural rod2.96e-4957
future spinal cord2.96e-4957
neural keel2.96e-4957
brain2.17e-4369
future brain2.17e-4369
central nervous system5.32e-4382
regional part of nervous system3.26e-4194
nervous system3.26e-4194
regional part of brain2.63e-4059
anterior neural tube1.02e-3942
regional part of forebrain5.99e-3941
forebrain5.99e-3941
future forebrain5.99e-3941
neural plate9.37e-3986
presumptive neural plate9.37e-3986
neurectoderm2.17e-3790
telencephalon4.66e-3234
gray matter7.00e-3234
brain grey matter7.00e-3234
anterior region of body1.73e-31129
craniocervical region1.73e-31129
regional part of telencephalon7.72e-3133
pre-chordal neural plate2.42e-3061
head4.69e-30123
cerebral hemisphere1.25e-2932
ectoderm-derived structure6.28e-27169
ectoderm1.52e-26173
presumptive ectoderm1.52e-26173
regional part of cerebral cortex3.37e-2422
neocortex3.92e-2220
cerebral cortex4.03e-2225
pallium4.03e-2225
anatomical conduit4.28e-16241
tube8.61e-15194
anatomical cluster5.95e-14286
organism subdivision2.48e-12365
organ part9.16e-12219
nucleus of brain2.77e-119
neural nucleus2.77e-119
basal ganglion3.76e-119
nuclear complex of neuraxis3.76e-119
aggregate regional part of brain3.76e-119
collection of basal ganglia3.76e-119
cerebral subcortex3.76e-119
posterior neural tube1.36e-1015
chordal neural plate1.36e-1015
epithelium2.90e-10309
brainstem3.81e-108
cell layer6.49e-10312
organ1.35e-09511
telencephalic nucleus4.73e-097
segmental subdivision of nervous system1.46e-0813
gyrus1.64e-086
diencephalon3.22e-087
future diencephalon3.22e-087
multi-tissue structure4.88e-08347
embryo7.30e-08612
temporal lobe8.73e-087
segmental subdivision of hindbrain1.34e-0712
hindbrain1.34e-0712
presumptive hindbrain1.34e-0712
parietal lobe3.12e-075
occipital lobe4.28e-075
embryonic structure6.24e-07605
developing anatomical structure6.24e-07605
limbic system7.50e-075


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
SUZ12#23512225.05789045553150.002325256716520610.0131831869180118



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.