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Coexpression cluster:C2876: Difference between revisions

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|full_id=C2876_squamous_gastric_pharyngeal_renal_signet_papillotubular_gall
|full_id=C2876_squamous_gastric_pharyngeal_renal_signet_papillotubular_gall
|id=C2876
|id=C2876
|ontology_enrichment_celltype=CL:0000066!5.07e-43!254;CL:0000220!1.63e-19!246;CL:0002321!7.18e-19!248;CL:0002076!5.90e-13!43;CL:0000223!1.08e-12!59;CL:0000076!1.40e-11!62;CL:0000075!4.33e-07!27
|ontology_enrichment_celltype=CL:0000066!5.46e-43!253;CL:0002321!2.74e-16!250;CL:0002076!1.68e-13!42;CL:0000223!6.83e-13!58;CL:0000076!3.42e-11!63;CL:0000075!1.16e-07!27
|ontology_enrichment_disease=DOID:305!9.45e-14!106;DOID:0050687!3.33e-12!143
|ontology_enrichment_disease=DOID:305!5.56e-15!106;DOID:0050687!2.29e-12!143
|ontology_enrichment_uberon=UBERON:0000467!5.56e-17!625;UBERON:0000480!1.02e-16!626;UBERON:0000468!4.36e-14!659;UBERON:0004119!4.68e-13!169;UBERON:0000925!4.68e-13!169;UBERON:0006595!4.68e-13!169;UBERON:0000062!4.84e-11!511;UBERON:0003104!5.78e-11!238;UBERON:0009142!5.78e-11!238;UBERON:0000481!2.45e-10!347;UBERON:0002050!3.80e-10!605;UBERON:0005423!3.80e-10!605;UBERON:0000923!4.06e-10!604;UBERON:0005291!4.06e-10!604;UBERON:0006598!4.06e-10!604;UBERON:0002532!4.06e-10!604;UBERON:0001007!7.87e-10!155;UBERON:0001555!7.87e-10!155;UBERON:0007026!7.87e-10!155;UBERON:0000483!9.20e-10!309;UBERON:0000922!1.42e-09!612;UBERON:0000077!2.76e-09!130;UBERON:0000475!3.14e-09!365;UBERON:0000119!3.67e-09!312;UBERON:0008947!3.02e-08!38;UBERON:0003258!3.02e-08!38;UBERON:0005911!3.76e-08!82;UBERON:0004921!7.59e-08!129;UBERON:0004185!7.59e-08!129;UBERON:0001004!1.67e-07!72;UBERON:0002100!4.10e-07!216;UBERON:0000490!4.67e-07!138;UBERON:0000065!5.85e-07!53;UBERON:0000064!7.82e-07!219
|ontology_enrichment_uberon=UBERON:0000467!2.24e-12!624;UBERON:0000480!4.00e-12!625;UBERON:0004119!8.84e-11!160;UBERON:0000925!8.84e-11!160;UBERON:0006595!8.84e-11!160;UBERON:0000468!1.66e-09!656;UBERON:0000483!8.47e-09!306;UBERON:0008947!1.71e-08!38;UBERON:0003258!1.71e-08!38;UBERON:0000062!2.27e-08!503;UBERON:0000119!3.01e-08!309;UBERON:0000481!6.38e-08!342;UBERON:0005911!6.98e-08!82;UBERON:0001007!8.91e-08!145;UBERON:0001555!8.91e-08!145;UBERON:0007026!8.91e-08!145;UBERON:0000065!2.41e-07!54;UBERON:0000477!2.81e-07!373;UBERON:0001004!6.32e-07!74;UBERON:0005631!7.73e-07!14;UBERON:0000158!7.73e-07!14
|tf_chipseq_enrich=BHLHE40#8553;4:44.8718135469774:2.46312701995675e-07:1.28816486147853e-05!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00819825085964601!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106800623394334!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00999315018441238!FOS#2353;4:8.9979553088944:0.000152514771116863:0.00195417619686837!JUND#3727;4:6.99466394187103:0.00041768421781858:0.0039257129251939!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00486444120600839!MXI1#4601;4:9.9615716287593:0.000101522475495045:0.00142742404661106!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00889836030757316!NR3C1#2908;4:14.973023331173:1.98868032687801e-05:0.00044455433360191!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323294268175509!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115744310672683!TFAP2A#7020;4:16.518634373045:1.34240829060362e-05:0.000327416579781297!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.00114885980422216!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00509022262106713!USF2#7392;4:12.9921973850696:3.50833029870167e-05:0.000682957144578012
|tf_chipseq_enrich=BHLHE40#8553;4:44.8718135469774:2.46312701995675e-07:1.28816486147853e-05!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00819825085964601!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106800623394334!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00999315018441238!FOS#2353;4:8.9979553088944:0.000152514771116863:0.00195417619686837!JUND#3727;4:6.99466394187103:0.00041768421781858:0.0039257129251939!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00486444120600839!MXI1#4601;4:9.9615716287593:0.000101522475495045:0.00142742404661106!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00889836030757316!NR3C1#2908;4:14.973023331173:1.98868032687801e-05:0.00044455433360191!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323294268175509!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115744310672683!TFAP2A#7020;4:16.518634373045:1.34240829060362e-05:0.000327416579781297!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.00114885980422216!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00509022262106713!USF2#7392;4:12.9921973850696:3.50833029870167e-05:0.000682957144578012
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8844,0.000209068,0.127738,0.207615,0.0137555,0.118999,0.0737069,2.14681e-12,8.9567e-07,0.178782,0.019419,0.0866228,0.271849,0.282657,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.000719925,0.220368,0.258624,0.064656,0.226143,0.460406,0.0438521,0.435508,0.281453,0.0522771,0.0787278,0.000108486,0.159873,0.142462,0.143935,0.0626466,0.0379537,1.85381e-08,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.0303627,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.103852,0.191914,0.184022,0.216557,0.182956,0.116818,0.389792,0.36316,0.0625685,0.124464,0.186295,0.173134,0.101893,2.08152e-05,0.167635,0.171311,0.0721023,0.0465855,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.00252788,0.171375,0.278645,0.000111859,0.155708,0.248017,0.22995,0.652972,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.012683,0.0939463,0.286748,0.0114526,0.0471607,0.163865,0.226359,0.000536417,1.13442e-11,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.0385301,0.0994829,0.0604041,0.144185,0.0925862,0.00516485,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.000106752,0.197817,0.251078,0.279874,0.133127,0.00213292,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,2.87418e-11,0.202165,0.0946865,0.120618,0.00324728,0.18762,0.0205193,0.127688,0.201169,0.0262879,0.24948,0.178639,3.07057e-05,0.320355,0.0763252,0.15547,0.110256,0.101581,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.32805,0.0252604,0.243266,0.107021,0.238657,0.20272,0.392453,0.0724243,0.0780061,0.315336,0.028874,0.279823,0.000475092,0.00567943,0.00214569,0.0478217,0.507599,0.170854,0.0575231,0.174063,0.0368787,0.459091,0.54832,0.00568499,0.296013,0.0895871,0.0434876,0.459994,0.170061,0.548059,0.25423,0.490559,0.121268,0.153911,0.472542,0.00125523,0.000563368,0.0074346,1.24344e-05,0.483077,0.0131065,0.603763,0.541914,0.627201,0.0635843,6.14083e-06,0.290703,0.254935,0.0413786,0.478691,0.360199,6.43357e-06,0.0236144,0.824761,0.365494,0.212703,0.56318,0.364079,0.107716,0.579886,0.421038,0.569409,0.328518,0.187186,0.310552,0.0166677,0.483764,0.00234287,0.0201581,0.209437,0.00302432,0.00298496,0.598945,0.000386547,0.464001,0.0572812,0.0118057,5.52018e-05,0.278028,0.000213717,0.261575,0.257956,0.264245,0.379063,0.0602936,0.0069676,0.113006,0.136753,0.202522,0.183837,0.00598078,0.126097,0.3955,0.442469,0.212239,0.294954,0.156999,0.35974,0.0999766,0.39549,0.234254,0.357409,0.017253,0.137737,0.50338,0.0746831,0.404625,0.172147,0.424691,0.0388817,0.479581,0.003448,0.00176979,0.00410246,0.044968,0.512545,0.512178,0.563206,0.00957951,0.0299859,0.263302,0.552023,0.180735,0.00434967,0.216102,0.254659,0.109605,0.397869,0.000293714,0.226491,0.417131,0.463987,0.260097,0.503881,0.454761,0.639483,0.00471559,0.452129,0.301581,0.261657,0.346776,0.000485493,0.545655,0.438176,0.349112,1.6645e-06,0.385425,0.00631453,0.0250382,0.386339,0.382854,0.0650585,0.478745,0.000445343,5.14014e-05,0.475047,0.557967,0.241014,0.282281,0.245336,0.2536,0.246827,0.202347,0.70712,0.387134,0.559969,0.358813,0.100705,0.0554837,0.493455,0.346636,0.457747,0.348802,0.476541,0.579645,0.447581,0.106831,0.254628,0.713293,0.00451196,0.416962,0.632833,0.0125878,0.387805,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.0613938,0.242783,0.0947248,0.0643357,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,1.87566e-06,0.231754,0.249415,0.283107,0.285648,0.427316,0.391071,0.279553,0.25563,0.00284468,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.290415,0.353147,0.112422,0.170886,0.267687,0.315656,0.284866,0.0887542,0.00400315,0.00865954,0.147872,0.189388,0.00540153,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.0015944,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.0606443,0.195748,0.0429696,0.161712,0.237871,0.239139,0.095257,0.0078603,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,0.0567862,0.15156,0.287598,0.313858,0.223773,0.25788,0.181895,0.253768,0.30702,0.202977,0.170837,0.327002,0.28543,0.222656,0.00239762,0.127111,0.259989,0.390754,0.355805,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,1.20241e-06,0.332746,0.271338,0.242121,3.48958e-05,0.000205581,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.00137371,0.0755696,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,6.90596e-07,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.00113802,0.318525,0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}}
}}

Revision as of 14:31, 19 October 2012


Full id: C2876_squamous_gastric_pharyngeal_renal_signet_papillotubular_gall



Phase1 CAGE Peaks

Hg19::chr7:116312352..116312368,+p6@MET
Hg19::chr7:116312411..116312502,+p1@MET
Hg19::chr7:116312521..116312532,+p4@MET
Hg19::chr7:116312540..116312549,+p14@MET


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 cell5.46e-43253
embryonic cell2.74e-16250
endo-epithelial cell1.68e-1342
endodermal cell6.83e-1358
squamous epithelial cell3.42e-1163
columnar/cuboidal epithelial cell1.16e-0727
Uber Anatomy
Ontology termp-valuen
anatomical system2.24e-12624
anatomical group4.00e-12625
endoderm-derived structure8.84e-11160
endoderm8.84e-11160
presumptive endoderm8.84e-11160
multi-cellular organism1.66e-09656
epithelium8.47e-09306
respiratory primordium1.71e-0838
endoderm of foregut1.71e-0838
organ2.27e-08503
cell layer3.01e-08309
multi-tissue structure6.38e-08342
endo-epithelium6.98e-0882
digestive system8.91e-08145
digestive tract8.91e-08145
primitive gut8.91e-08145
respiratory tract2.41e-0754
anatomical cluster2.81e-07373
respiratory system6.32e-0774
extraembryonic membrane7.73e-0714
membranous layer7.73e-0714
Disease
Ontology termp-valuen
carcinoma5.56e-15106
cell type cancer2.29e-12143


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
BHLHE40#8553444.87181354697742.46312701995675e-071.28816486147853e-05
CTCF#1066445.360256373075030.001211145381643620.00819825085964601
E2F1#186944.907389214879320.001724022357361790.0106800623394334
E2F6#187645.017155731697390.00157802193473060.00999315018441238
FOS#235348.99795530889440.0001525147711168630.00195417619686837
JUND#372746.994663941871030.000417684217818580.0039257129251939
MAX#414946.452555509007120.0005767613195645490.00486444120600839
MXI1#460149.96157162875930.0001015224754950450.00142742404661106
MYC#460945.22228187160940.001344309395272740.00889836030757316
NR3C1#2908414.9730233311731.98868032687801e-050.00044455433360191
TAF1#687243.343046285745290.008005664898701650.0323294268175509
TCF7L2#6934410.77017656313737.42969445082454e-050.00115744310672683
TFAP2A#7020416.5186343730451.34240829060362e-050.000327416579781297
TFAP2C#7022410.80922860986027.32289634782688e-050.00114885980422216
USF1#739146.361499277207960.0006105011399140830.00509022262106713
USF2#7392412.99219738506963.50833029870167e-050.000682957144578012



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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