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Coexpression cluster:C2216: Difference between revisions

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|full_id=C2216_keratoacanthoma_cervical_synovial_Wilms_gastric_oral_mesothelioma
|full_id=C2216_keratoacanthoma_cervical_synovial_Wilms_gastric_oral_mesothelioma
|id=C2216
|id=C2216
|ontology_enrichment_celltype=CL:0000066!5.90e-19!254;CL:0000076!1.03e-10!62;CL:0000077!4.78e-07!19
|ontology_enrichment_celltype=CL:0000066!1.64e-19!253;CL:0000076!1.63e-13!63;CL:0002327!7.78e-08!4;CL:0000077!4.99e-07!19;CL:0002251!9.20e-07!20
|ontology_enrichment_disease=DOID:0050687!7.83e-42!143;DOID:162!2.25e-35!235;DOID:14566!8.26e-34!239;DOID:305!1.82e-30!106;DOID:1749!2.89e-14!14;DOID:0050686!1.03e-07!137
|ontology_enrichment_disease=DOID:0050687!3.54e-39!143;DOID:162!4.74e-35!235;DOID:14566!8.57e-34!239;DOID:305!8.05e-30!106;DOID:1749!2.20e-18!14;DOID:5093!2.08e-07!4;DOID:1612!2.08e-07!4
|ontology_enrichment_uberon=UBERON:0001737!4.84e-11!9;UBERON:0000310!9.41e-08!10;UBERON:0001557!1.14e-07!19;UBERON:0000072!2.38e-07!46;UBERON:0008947!6.76e-07!38;UBERON:0003258!6.76e-07!38;UBERON:0001443!7.90e-07!11;UBERON:0004921!9.05e-07!129;UBERON:0004185!9.05e-07!129
|ontology_enrichment_uberon=UBERON:0001737!7.82e-16!9;UBERON:0000310!3.16e-09!10;UBERON:0001443!3.04e-08!11;UBERON:0001557!5.87e-08!19;UBERON:0001911!7.78e-08!4;UBERON:0005333!7.78e-08!4;UBERON:0008425!7.78e-08!4;UBERON:0005311!7.78e-08!4;UBERON:0003343!1.28e-07!4;UBERON:0004785!1.28e-07!4
|tf_chipseq_enrich=ATF3#467;4:22.4631745260087:3.92475754624726e-06:0.000127139501666414!CCNT2#905;4:6.33620157696263:0.000620310058721564:0.0051148399039019!CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.0026762340161674!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106308774269651!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00995451998316797!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101309499703552!FOS#2353;4:8.9979553088944:0.000152514771116863:0.0019458209358263!GATA3#2625;4:27.236516357206:1.81561517799785e-06:6.75288581107254e-05!IRF1#3659;4:7.6371637535639:0.000293885399618549:0.00306930972507616!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00484682776424219!MXI1#4601;4:9.9615716287593:0.000101522475495045:0.00142149159649108!NFE2#4778;4:77.204260651629:2.80776035215453e-08:1.91534737699978e-06!NFYB#4801;4:16.7597932535365:1.26678572070404e-05:0.000311078847600774!NRF1#4899;4:12.2102794477109:4.49717228915276e-05:0.000792441668140417!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129117196451743!SMARCB1#6598;4:18.2527157811574:9.00423392720929e-06:0.000240817717573319!SMARCC2#6601;4:94.1553744268976:1.26854362961227e-08:9.39612965482805e-07!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00683191152633427!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0243613319210016!TFAP2A#7020;4:16.518634373045:1.34240829060362e-05:0.000326045998749654!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.00114387671503244!THAP1#55145;4:31.3691446028513:1.03171810326891e-06:4.31006427949207e-05!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00507119450819112!USF2#7392;4:12.9921973850696:3.50833029870167e-05:0.000680168012003162
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91994,0.268299,0.198844,0.104946,0.127738,0.207615,0.161213,0.118999,0.0737069,0.0734014,0.00325259,0.178782,0.019419,0.0866228,0.271849,0.282657,0.105411,0.0997542,0.209692,0.0339332,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.00213676,0.226143,0.460406,0.0438521,0.00283228,0.281453,0.0522771,0.0787278,0.515487,0.159873,0.142462,0.143935,0.332403,0.0379537,0.6545,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.0303627,0.302909,0.0757292,0.100188,0.223102,0.107653,0.000176103,0.419621,0.191914,0.184022,0.216557,0.182956,0.116818,0.00167639,0.36316,0.0625685,0.124464,0.186295,0.173134,0.101893,0.142875,0.167635,0.171311,0.458838,0.548036,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.0187576,0.0451012,0.0976639,0.351199,0.0360207,0.00342886,0.278645,0.365775,0.0128057,0.248017,0.22995,0.091341,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.379174,0.0939463,0.286748,0.367925,0.0471607,0.163865,0.226359,1.64154e-06,0.000439133,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.00776177,0.22302,0.137423,0.00484807,0.0754883,0.299492,0.100006,0.0756617,0.197817,0.251078,0.279874,0.133127,0.00213292,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.240896,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,1.3012e-05,0.201169,0.220353,0.24948,0.178639,0.291976,0.320355,0.0763252,0.15547,0.110256,0.415419,0.14794,0.147307,0.240761,0.225961,0.124417,0.0639386,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.00134589,2.47544e-10,0.243266,0.107021,0.238657,0.0220967,0.000169487,0.61565,0.0780061,0.0559668,0.00246552,0.279823,0.0487563,0.502112,0.0103352,0.0478217,0.507599,0.170854,0.0575231,0.174063,0.514243,0.003653,0.00888122,0.502211,0.296013,0.282366,0.537932,0.459994,0.523209,0.548059,0.25423,0.490559,0.45013,0.153911,0.135135,0.685908,0.0510811,0.529642,0.0301009,0.483077,0.590496,0.603763,0.541914,0.0181844,0.000629457,0.757308,0.290703,0.622694,1.20073e-07,0.478691,0.360199,0.608176,0.0937029,4.35335e-08,0.0768516,0.212703,0.56318,0.364079,0.680099,0.579886,0.421038,0.569409,0.328518,0.0458249,0.310552,6.33411e-12,0.142433,0.0342735,0.00104728,0.209437,0.000136886,0.748403,0.598945,9.40572e-09,0.464001,6.80207e-10,3.39195e-05,0.00125006,0.000125145,0.0155453,0.261575,3.21722e-08,0.264245,0.0126705,0.326516,0.522925,0.00284816,0.475063,0.202522,0.183837,8.35813e-07,0.126097,0.3955,0.442469,0.212239,0.294954,0.156999,0.35974,0.667777,0.39549,0.234254,0.0011219,5.47898e-10,0.137737,0.00575146,0.0171443,0.0958848,0.759068,0.106633,0.0388817,0.139684,0.62689,0.36666,9.8413e-05,0.284496,0.00629645,0.512178,0.0515768,0.829402,0.321001,0.263302,0.00919591,0.180735,0.0646927,0.000120607,0.254659,0.109605,0.0924199,0.217863,0.226491,0.102502,0.129731,0.0782409,0.0342559,0.454761,0.639483,0.483658,0.452129,0.301581,0.00371213,0.346776,0.466529,0.545655,1.81732e-07,0.349112,0.000509621,8.41045e-07,0.307816,0.128211,0.0866806,0.382854,0.0141241,0.478745,6.88674e-06,0.00716065,0.136743,0.00154102,0.0153563,0.282281,0.612712,0.00335455,0.000214659,0.202347,0.00849832,0.387134,0.050476,0.358813,0.668972,0.574252,0.493455,0.346636,0.457747,0.348802,0.476541,0.00199432,0.447581,0.42505,0.254628,0.00183295,0.479347,0.416962,0.264955,0.378333,0.152547,0.00382285,0.22798,0.102495,0.350933,0.263896,0.00101415,0.002982,0.0613938,0.242783,0.0947248,0.336551,0.00184947,0.246234,0.00186673,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.546295,0.231754,0.00317894,0.00479755,0.285648,0.0191181,0.391071,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.000336791,0.16188,0.23235,0.290415,0.00106183,0.112422,0.170886,0.267687,0.315656,0.000403294,0.0887542,0.267811,0.338547,0.0115158,0.189388,3.16476e-05,0.210125,0.292967,0.218414,0.0509944,0.000118011,0.0689852,0.00185385,0.341188,0.259328,0.437467,0.201057,0.0130187,0.129351,0.141936,0.00317461,0.276997,0.205513,0.282389,0.251421,0.162089,0.00796989,0.0136966,0.233244,0.00175674,0.00774558,0.195748,2.35297e-05,0.161712,0.0308468,0.00277578,0.095257,0.0078603,0.332769,0.262022,0.274403,0.00394881,0.184534,0.248707,0.31749,0.15156,0.287598,0.313858,0.223773,0.25788,0.181895,0.253768,0.30702,0.00164332,0.0155028,0.327002,0.28543,0.0268645,0.228479,0.127111,0.259989,0.390754,9.51843e-05,0.279739,0.108118,0.259901,0.000507733,0.0708274,0.0710478,0.0206568,0.102645,0.0539258,0.0709978,0.401939,4.3119e-06,0.00417718,0.242121,0.298673,0.244395,0.106889,0.00865251,0.0845989,0.159153,0.0842401,0.00984212,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.000297685,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.081972,0.322827,0.229571,0.0739466,0.00844265,0.171704,0.208256,0.265058,0.256405,0.362898,0.00593844,0.40806,0.151361,0.27960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}}
}}

Revision as of 12:12, 19 October 2012


Full id: C2216_keratoacanthoma_cervical_synovial_Wilms_gastric_oral_mesothelioma



Phase1 CAGE Peaks

Hg19::chr12:54332608..54332636,+p1@HOXC13
Hg19::chr12:54332652..54332671,+p2@HOXC13
Hg19::chr12:54332675..54332686,+p4@HOXC13
Hg19::chr12:54332687..54332701,+p3@HOXC13


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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell1.64e-19253
squamous epithelial cell1.63e-1363
mammary gland epithelial cell7.78e-084
mesothelial cell4.99e-0719
epithelial cell of alimentary canal9.20e-0720
Uber Anatomy
Ontology termp-valuen
larynx7.82e-169
breast3.16e-0910
chest3.04e-0811
upper respiratory tract5.87e-0819
mammary gland7.78e-084
mammary bud7.78e-084
mammary ridge7.78e-084
mammary placode7.78e-084
mucosa of oral region1.28e-074
respiratory system mucosa1.28e-074
Disease
Ontology termp-valuen
cell type cancer3.54e-39143
cancer4.74e-35235
disease of cellular proliferation8.57e-34239
carcinoma8.05e-30106
squamous cell carcinoma2.20e-1814
thoracic cancer2.08e-074
breast cancer2.08e-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
ATF3#467422.46317452600873.92475754624726e-060.000127139501666414
CCNT2#90546.336201576962630.0006203100587215640.0051148399039019
CEBPB#105147.971147625824820.0002476385788090830.0026762340161674
E2F1#186944.907389214879320.001724022357361790.0106308774269651
E2F6#187645.017155731697390.00157802193473060.00995451998316797
EGR1#195844.988179094810140.001615011500076050.0101309499703552
FOS#235348.99795530889440.0001525147711168630.0019458209358263
GATA3#2625427.2365163572061.81561517799785e-066.75288581107254e-05
IRF1#365947.63716375356390.0002938853996185490.00306930972507616
MAX#414946.452555509007120.0005767613195645490.00484682776424219
MXI1#460149.96157162875930.0001015224754950450.00142149159649108
NFE2#4778477.2042606516292.80776035215453e-081.91534737699978e-06
NFYB#4801416.75979325353651.26678572070404e-050.000311078847600774
NRF1#4899412.21027944771094.49717228915276e-050.000792441668140417
RAD21#5885410.35503389545638.6948481184721e-050.00129117196451743
SMARCB1#6598418.25271578115749.00423392720929e-060.000240817717573319
SMARCC2#6601494.15537442689761.26854362961227e-089.39612965482805e-07
SP1#666745.69838137814090.0009482606065333980.00683191152633427
TBP#690843.706770687096390.005296377814784350.0243613319210016
TFAP2A#7020416.5186343730451.34240829060362e-050.000326045998749654
TFAP2C#7022410.80922860986027.32289634782688e-050.00114387671503244
THAP1#55145431.36914460285131.03171810326891e-064.31006427949207e-05
USF1#739146.361499277207960.0006105011399140830.00507119450819112
USF2#7392412.99219738506963.50833029870167e-050.000680168012003162



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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