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Coexpression cluster:C2976: Difference between revisions

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|full_id=C2976_Small_Gingival_Urothelial_keratoacanthoma_Keratinocyte_neuroectodermal_Bronchial
|full_id=C2976_Small_Gingival_Urothelial_keratoacanthoma_Keratinocyte_neuroectodermal_Bronchial
|id=C2976
|id=C2976
|ontology_enrichment_celltype=CL:0002076!6.73e-08!43;CL:0000223!1.93e-07!59
|ontology_enrichment_celltype=CL:0002076!1.32e-07!42;CL:0000223!6.14e-07!58
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000924!3.17e-15!173;UBERON:0006601!3.17e-15!173;UBERON:0004121!5.53e-14!169;UBERON:0000467!1.04e-13!625;UBERON:0000468!1.18e-13!659;UBERON:0000480!2.18e-13!626;UBERON:0000475!6.06e-13!365;UBERON:0003102!8.13e-12!95;UBERON:0007023!1.96e-11!115;UBERON:0000922!1.79e-10!612;UBERON:0000033!6.63e-10!123;UBERON:0002050!7.28e-10!605;UBERON:0005423!7.28e-10!605;UBERON:0000153!7.56e-10!129;UBERON:0007811!7.56e-10!129;UBERON:0000923!1.37e-09!604;UBERON:0005291!1.37e-09!604;UBERON:0006598!1.37e-09!604;UBERON:0002532!1.37e-09!604;UBERON:0004111!1.54e-09!241;UBERON:0000481!1.05e-08!347;UBERON:0000483!1.09e-08!309;UBERON:0000064!1.15e-08!219;UBERON:0000119!2.67e-08!312;UBERON:0004119!4.43e-08!169;UBERON:0000925!4.43e-08!169;UBERON:0006595!4.43e-08!169;UBERON:0000165!6.00e-08!28;UBERON:0000930!6.00e-08!28;UBERON:0000062!6.07e-08!511;UBERON:0000166!9.99e-08!21;UBERON:0001049!1.43e-07!57;UBERON:0005068!1.43e-07!57;UBERON:0006241!1.43e-07!57;UBERON:0007135!1.43e-07!57;UBERON:0000161!3.36e-07!35;UBERON:0000073!9.07e-07!94;UBERON:0001016!9.07e-07!94
|ontology_enrichment_uberon=UBERON:0004121!4.24e-16!171;UBERON:0000924!4.24e-16!171;UBERON:0006601!4.24e-16!171;UBERON:0000467!1.68e-13!624;UBERON:0000468!1.82e-13!656;UBERON:0000480!3.38e-13!625;UBERON:0003102!3.70e-13!99;UBERON:0002050!1.14e-11!564;UBERON:0011216!1.87e-11!223;UBERON:0007023!8.48e-11!114;UBERON:0000923!2.34e-10!560;UBERON:0010316!2.34e-10!560;UBERON:0005291!2.34e-10!560;UBERON:0006598!2.34e-10!560;UBERON:0010317!2.34e-10!560;UBERON:0002532!2.34e-10!560;UBERON:0000481!3.06e-10!342;UBERON:0005423!4.67e-10!581;UBERON:0000922!5.38e-10!592;UBERON:0000483!1.62e-09!306;UBERON:0000477!1.74e-09!373;UBERON:0004119!1.84e-09!160;UBERON:0000925!1.84e-09!160;UBERON:0006595!1.84e-09!160;UBERON:0000064!2.57e-09!218;UBERON:0004111!2.80e-09!240;UBERON:0010371!3.49e-09!104;UBERON:0000119!5.24e-09!309;UBERON:0000062!8.20e-08!503;UBERON:0001049!1.12e-07!56;UBERON:0005068!1.12e-07!56;UBERON:0006241!1.12e-07!56;UBERON:0007135!1.12e-07!56;UBERON:0001016!2.90e-07!89;UBERON:0000165!3.06e-07!29;UBERON:0000930!3.06e-07!29;UBERON:0000073!4.86e-07!53;UBERON:0002616!4.86e-07!53;UBERON:0000166!5.45e-07!22;UBERON:0000161!5.95e-07!36;UBERON:0010314!6.91e-07!132
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278103180153282!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00661506655448476
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278103180153282!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00661506655448476
|tfbs_overrepresentation=0.147255,0.0586687,0.00192761,0.0477154,0.199763,2.83221e-05,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.0275521,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,3.01505e-05,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.00104991,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.00327964,0.064341,0.209032,5.63916e-05,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,4.06954e-06,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.00862108,0.144217,0.0400492,0.182599,0.0339971,0.0117862,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.0249033,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.00166778,0.155998,4.57719e-05,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.0174119,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.0255071,0.0541353,0.0799324,0.090079,0.0103428,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.00186183,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.0142864,0.100942,0.062995,0.10299,0.14193,0.37245,0.0128655,0.161026,0.0738599,0.00837667,0.138852,0.085973,0.060453,0.059896,0.0108418,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.0695582,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.0802194,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,3.22083e-08,0.0619218,0.1751,0.0141386,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.00453939,0.063292,0.0356268,0.446759,0.0865903,0.0380459,0.130174,0.584917,8.22817e-07,6.57717e-07,0.0821962,0.20128,0.00879988,2.60602e-13,0.335423,0.000572844,0.261553,0.118991,0.373681,0.309233,0.147559,0.330703,0.395854,0.00791734,0.042539,0.615744,0.271958,0.292154,0.405773,0.0148713,0.0582602,0.597171,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.00257817,0.376924,0.025356,0.000737505,0.0407001,0.168255,0.370782,0.415647,0.484505,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.503224,0.0669244,0.283727,0.314747,0.577664,0.291709,0.448095,0.0563639,0.416816,0.0478086,0.00439271,0.115044,0.0807167,0.213592,0.608919,0.18237,4.27123e-05,4.6495e-09,0.0512465,0.275351,0.236471,0.185661,0.346319,0.535598,0.270984,0.000544819,0.503058,5.45881e-09,0.000993751,0.248634,0.281576,0.135034,0.163244,0.0670502,0.0730934,0.184794,3.77697e-09,2.01623e-05,0.581837,0.1002,0.00102656,0.0462094,0.191921,3.09479e-06,0.218623,0.0550136,0.117923,0.0451077,0.0747529,0.229003,8.57818e-12,0.000323853,0.0338328,0.294698,0.00907354,0.477304,0.289204,0.327108,2.73928e-05,0.278044,2.63372e-13,0.0193295,0.228096,0.336314,0.19763,0.15631,0.0530502,0.421464,0.48267,0.420626,0.516462,1.09487e-06,0.335105,0.144809,0.145539,0.0134194,0.0818086,0.000374104,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.048108,0.284593,0.343734,0.306556,0.305777,0.2348,0.503082,0.0391885,0.284629,0.262537,0.359455,0.226257,0.0965765,0.00230458,0.363685,0.464871,2.30954e-13,0.206222,0.03988,0.0224921,0.00288466,0.269226,0.339277,0.0014397,0.281425,0.141758,0.455379,0.0385377,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.0178839,0.347298,0.539392,0.34988,0.475069,0.404569,0.6408,0.0793778,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.00307017,0.00034627,0.191777,0.111931,0.046606,0.0435386,0.303336,0.126478,0.134852,0.10689,0.0413156,0.0627924,0.381386,0.0179103,0.00605613,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.0205132,0.132201,0.00130383,0.0481795,0.199971,0.0966069,0.127758,0.175785,0.184486,4.24693e-05,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.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23831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435
}}
}}

Revision as of 14:39, 19 October 2012


Full id: C2976_Small_Gingival_Urothelial_keratoacanthoma_Keratinocyte_neuroectodermal_Bronchial



Phase1 CAGE Peaks

Hg19::chr10:105615282..105615323,-p6@SH3PXD2A
Hg19::chr10:105615327..105615342,-p8@SH3PXD2A
Hg19::chr10:105615456..105615531,-p3@SH3PXD2A


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><br>


Cell Type
Ontology termp-valuen
endo-epithelial cell1.32e-0742
endodermal cell6.14e-0758
Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure4.24e-16171
ectoderm4.24e-16171
presumptive ectoderm4.24e-16171
anatomical system1.68e-13624
multi-cellular organism1.82e-13656
anatomical group3.38e-13625
surface structure3.70e-1399
embryonic structure1.14e-11564
organ system subdivision1.87e-11223
adult organism8.48e-11114
germ layer2.34e-10560
germ layer / neural crest2.34e-10560
embryonic tissue2.34e-10560
presumptive structure2.34e-10560
germ layer / neural crest derived structure2.34e-10560
epiblast (generic)2.34e-10560
multi-tissue structure3.06e-10342
developing anatomical structure4.67e-10581
embryo5.38e-10592
epithelium1.62e-09306
anatomical cluster1.74e-09373
endoderm-derived structure1.84e-09160
endoderm1.84e-09160
presumptive endoderm1.84e-09160
organ part2.57e-09218
anatomical conduit2.80e-09240
ecto-epithelium3.49e-09104
cell layer5.24e-09309
organ8.20e-08503
neural tube1.12e-0756
neural rod1.12e-0756
future spinal cord1.12e-0756
neural keel1.12e-0756
nervous system2.90e-0789
mouth3.06e-0729
stomodeum3.06e-0729
regional part of nervous system4.86e-0753
regional part of brain4.86e-0753
oral opening5.45e-0722
orifice5.95e-0736
structure with developmental contribution from neural crest6.91e-07132


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#1066435.360256373075030.0064925092527670.0278103180153282
RAD21#5885310.35503389545630.0009004912073565420.00661506655448476



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.