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Coexpression cluster:C2771: Difference between revisions

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|id=C2771
|id=C2771
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=DOID:1749!3.05e-07!14
|ontology_enrichment_disease=DOID:1749!2.52e-07!14
|ontology_enrichment_uberon=UBERON:0007023!1.39e-20!115;UBERON:0004111!2.47e-17!241;UBERON:0000922!7.95e-16!612;UBERON:0000025!1.21e-15!194;UBERON:0002050!5.76e-15!605;UBERON:0005423!5.76e-15!605;UBERON:0000923!1.24e-14!604;UBERON:0005291!1.24e-14!604;UBERON:0006598!1.24e-14!604;UBERON:0002532!1.24e-14!604;UBERON:0000467!4.58e-14!625;UBERON:0000480!8.04e-14!626;UBERON:0001049!9.54e-14!57;UBERON:0005068!9.54e-14!57;UBERON:0006241!9.54e-14!57;UBERON:0007135!9.54e-14!57;UBERON:0001017!2.74e-13!82;UBERON:0000062!3.17e-13!511;UBERON:0005743!4.69e-13!86;UBERON:0000477!8.94e-13!286;UBERON:0003075!1.33e-12!86;UBERON:0007284!1.33e-12!86;UBERON:0000468!8.22e-12!659;UBERON:0000119!1.01e-11!312;UBERON:0000483!1.90e-11!309;UBERON:0002616!3.24e-11!59;UBERON:0002346!6.19e-11!90;UBERON:0000153!1.16e-10!129;UBERON:0007811!1.16e-10!129;UBERON:0004121!1.90e-10!169;UBERON:0000033!1.96e-10!123;UBERON:0003080!4.99e-10!42;UBERON:0002780!7.38e-10!41;UBERON:0001890!7.38e-10!41;UBERON:0006240!7.38e-10!41;UBERON:0000073!8.78e-10!94;UBERON:0001016!8.78e-10!94;UBERON:0000955!1.17e-09!69;UBERON:0006238!1.17e-09!69;UBERON:0000924!1.97e-09!173;UBERON:0006601!1.97e-09!173;UBERON:0003056!8.32e-09!61;UBERON:0002020!1.07e-08!34;UBERON:0003528!1.07e-08!34;UBERON:0001893!1.17e-08!34;UBERON:0001869!2.18e-08!32;UBERON:0000064!2.29e-08!219;UBERON:0002791!2.88e-08!33;UBERON:0003103!8.04e-08!69;UBERON:0000956!2.36e-07!25;UBERON:0000203!2.36e-07!25;UBERON:0002619!6.14e-07!22;UBERON:0001950!8.54e-07!20
|ontology_enrichment_uberon=UBERON:0007023!1.05e-18!114;UBERON:0000477!6.94e-13!373;UBERON:0001017!7.99e-13!81;UBERON:0004111!9.27e-13!240;UBERON:0001049!1.86e-12!56;UBERON:0005068!1.86e-12!56;UBERON:0006241!1.86e-12!56;UBERON:0007135!1.86e-12!56;UBERON:0005423!3.50e-12!581;UBERON:0000062!6.78e-12!503;UBERON:0000922!6.85e-12!592;UBERON:0010371!2.38e-11!104;UBERON:0000073!2.49e-11!53;UBERON:0002616!2.49e-11!53;UBERON:0003075!2.70e-11!82;UBERON:0007284!2.70e-11!82;UBERON:0000025!8.27e-11!192;UBERON:0011216!2.22e-10!223;UBERON:0001016!5.95e-10!89;UBERON:0002346!6.75e-10!86;UBERON:0002780!1.07e-09!41;UBERON:0001890!1.07e-09!41;UBERON:0003080!1.07e-09!41;UBERON:0006240!1.07e-09!41;UBERON:0002050!1.30e-09!564;UBERON:0000467!1.53e-09!624;UBERON:0000955!1.63e-09!68;UBERON:0006238!1.63e-09!68;UBERON:0000480!2.10e-09!625;UBERON:0004121!3.20e-09!171;UBERON:0000924!3.20e-09!171;UBERON:0006601!3.20e-09!171;UBERON:0000923!7.24e-09!560;UBERON:0010316!7.24e-09!560;UBERON:0005291!7.24e-09!560;UBERON:0006598!7.24e-09!560;UBERON:0010317!7.24e-09!560;UBERON:0002532!7.24e-09!560;UBERON:0010314!1.33e-08!132;UBERON:0003528!1.64e-08!34;UBERON:0002020!1.64e-08!34;UBERON:0001893!1.97e-08!34;UBERON:0000119!2.77e-08!309;UBERON:0000483!3.15e-08!306;UBERON:0001869!3.65e-08!32;UBERON:0000468!5.11e-08!656;UBERON:0002791!6.89e-08!32;UBERON:0000064!7.49e-08!218;UBERON:0003056!8.10e-08!61;UBERON:0003103!5.38e-07!68;UBERON:0000956!7.18e-07!25;UBERON:0000203!7.18e-07!25;UBERON:0001950!7.19e-07!20;UBERON:0000481!7.49e-07!342
|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00819028830053602!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129744426724547!REST#5978;3:7.23752153709602:0.00410469730419261:0.0195883245032018!SMC3#9126;4:15.0449328449328:1.95092670935632e-05:0.000439027870283268!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106998825075537!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249616646567736
|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00819028830053602!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129744426724547!REST#5978;3:7.23752153709602:0.00410469730419261:0.0195883245032018!SMC3#9126;4:15.0449328449328:1.95092670935632e-05:0.000439027870283268!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106998825075537!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249616646567736
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198844,0.104946,0.127738,0.207615,0.161213,0.118999,0.0737069,0.357807,0.0173365,0.178782,0.019419,0.0866228,0.271849,0.282657,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.226143,0.460406,0.000975873,0.435508,0.000382303,0.0522771,0.0787278,0.0372041,0.159873,0.142462,0.143935,0.332403,0.0379537,0.0230803,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.487259,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.103852,0.191914,0.0180783,0.216557,0.182956,0.116818,0.00167639,0.36316,0.0625685,0.124464,0.0454742,0.173134,0.101893,0.142875,0.167635,0.171311,0.00520751,0.000177277,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.00103527,0.107849,0.0560157,0.278645,0.011228,0.155708,0.248017,0.22995,0.091341,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.379174,0.0939463,0.286748,0.367925,0.0471607,0.163865,0.226359,0.00188396,0.307186,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.362866,0.197817,0.251078,0.000372899,0.00928313,0.00022115,0.223717,0.0189842,0.196838,0.0826805,0.246601,0.193021,0.240896,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.0217469,0.220353,0.24948,0.178639,0.0475113,0.320355,0.364334,0.15547,0.110256,0.415419,0.14794,0.147307,0.240761,0.225961,0.124417,0.0639386,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.114979,0.21618,0.243266,0.107021,0.238657,0.20272,1.39025e-05,6.31811e-05,0.0780061,0.315336,0.230477,0.279823,0.295555,0.154895,0.140541,0.0478217,0.0351792,0.170854,0.00168712,0.174063,0.0368787,1.98361e-08,0.54832,0.502211,0.296013,0.649813,0.537932,0.459994,0.523209,0.00885937,0.25423,0.490559,0.45013,0.153911,0.472542,0.0302459,0.747471,0.529642,3.47626e-08,0.483077,0.224887,0.23695,0.184287,0.259354,0.0237007,0.142078,0.290703,0.622694,8.21916e-06,0.478691,0.360199,0.608176,0.000126158,4.35335e-08,0.365494,0.212703,0.56318,0.364079,0.680099,0.579886,0.421038,0.0537414,0.0610883,0.545608,0.310552,0.0166677,0.483764,2.66735e-06,0.784052,0.209437,2.49014e-05,0.748403,0.598945,8.0873e-05,0.464001,0.0184382,0.579004,0.870272,2.24964e-05,0.586133,0.261575,0.257956,0.264245,0.379063,0.326516,0.522925,0.436016,0.475063,0.202522,0.183837,0.0351103,0.126097,0.3955,0.116739,0.212239,0.294954,0.156999,0.00115593,0.667777,0.39549,0.234254,0.357409,0.599068,0.365184,0.15578,0.620526,0.404625,0.759068,0.424691,0.132999,0.479581,0.62689,0.00041289,0.0854676,0.284496,0.512545,0.512178,0.563206,2.64616e-06,0.684899,0.0381838,0.00919591,0.180735,0.439629,0.216102,0.254659,0.109605,0.397869,0.582542,0.226491,0.417131,0.463987,0.627953,0.503881,0.454761,0.271678,0.142363,0.0232851,0.301581,0.261657,0.346776,0.466529,0.545655,0.438176,0.349112,0.155207,0.385425,0.307816,0.461541,0.386339,0.382854,4.00803e-09,5.60558e-06,0.07062,0.319747,0.475047,0.0498053,0.00277992,0.282281,0.0710918,0.2536,0.246827,0.564333,0.12664,0.387134,0.00157847,0.358813,0.303004,0.574252,0.493455,0.346636,0.457747,0.348802,0.476541,0.0574793,0.447581,0.42505,0.254628,0.713293,0.479347,0.416962,0.0806585,0.378333,1.86504e-07,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.0029143,0.0947248,0.336551,0.210656,0.246234,0.211271,0.00469795,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.546295,0.231754,0.249415,0.283107,0.285648,0.427316,0.0140903,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.00521493,0.353147,0.112422,0.170886,0.267687,0.315656,0.284866,0.0887542,0.267811,0.338547,0.147872,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.328852,0.00817635,0.262022,0.274403,0.266687,0.184534,0.248707,0.0567862,0.15156,0.0460134,0.313858,0.223773,0.25788,0.181895,0.253768,0.30702,0.202977,0.170837,0.327002,0.28543,0.222656,0.228479,0.127111,0.259989,0.390754,0.355805,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.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}}
}}

Revision as of 14:24, 19 October 2012


Full id: C2771_tubular_Mast_mucinous_smallcell_bile_gall_cerebellum



Phase1 CAGE Peaks

Hg19::chr4:11430464..11430477,-p3@HS3ST1
Hg19::chr4:11430488..11430492,-p8@HS3ST1
Hg19::chr4:11430494..11430527,-p1@HS3ST1
Hg19::chr4:11430734..11430759,-p4@HS3ST1


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
adult organism1.05e-18114
anatomical cluster6.94e-13373
central nervous system7.99e-1381
anatomical conduit9.27e-13240
neural tube1.86e-1256
neural rod1.86e-1256
future spinal cord1.86e-1256
neural keel1.86e-1256
developing anatomical structure3.50e-12581
organ6.78e-12503
embryo6.85e-12592
ecto-epithelium2.38e-11104
regional part of nervous system2.49e-1153
regional part of brain2.49e-1153
neural plate2.70e-1182
presumptive neural plate2.70e-1182
tube8.27e-11192
organ system subdivision2.22e-10223
nervous system5.95e-1089
neurectoderm6.75e-1086
regional part of forebrain1.07e-0941
forebrain1.07e-0941
anterior neural tube1.07e-0941
future forebrain1.07e-0941
embryonic structure1.30e-09564
anatomical system1.53e-09624
brain1.63e-0968
future brain1.63e-0968
anatomical group2.10e-09625
ectoderm-derived structure3.20e-09171
ectoderm3.20e-09171
presumptive ectoderm3.20e-09171
germ layer7.24e-09560
germ layer / neural crest7.24e-09560
embryonic tissue7.24e-09560
presumptive structure7.24e-09560
germ layer / neural crest derived structure7.24e-09560
epiblast (generic)7.24e-09560
structure with developmental contribution from neural crest1.33e-08132
brain grey matter1.64e-0834
gray matter1.64e-0834
telencephalon1.97e-0834
cell layer2.77e-08309
epithelium3.15e-08306
cerebral hemisphere3.65e-0832
multi-cellular organism5.11e-08656
regional part of telencephalon6.89e-0832
organ part7.49e-08218
pre-chordal neural plate8.10e-0861
compound organ5.38e-0768
cerebral cortex7.18e-0725
pallium7.18e-0725
neocortex7.19e-0720
multi-tissue structure7.49e-07342
Disease
Ontology termp-valuen
squamous cell carcinoma2.52e-0714


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#1066445.360256373075030.001211145381643620.00819028830053602
RAD21#5885410.35503389545638.6948481184721e-050.00129744426724547
REST#597837.237521537096020.004104697304192610.0195883245032018
SMC3#9126415.04493284493281.95092670935632e-050.000439027870283268
YY1#752844.911170749853860.00171871838055440.0106998825075537
ZNF263#1012748.221841637010680.0002187871180958320.00249616646567736



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.