Coexpression cluster:C4400: Difference between revisions

Revision as of 16:43, 26 November 2012

Full id: C4400_Fibroblast_Preadipocyte_mesodermal_Small_Keratinocyte_Gingival_basal

Phase1 CAGE Peaks

Hg19::chr4:187647702..187647734,-	p4@FAT1
Hg19::chr4:187647737..187647763,-	p3@FAT1
Hg19::chr4:187647773..187647864,-	p1@FAT1

Enriched pathways on this co-expression clusterSummary: 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. Analyst: Emmanuel Dimont link to source dataset data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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. Analyst: Erik Arner link to source dataset data

No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji links to source dataset cell_data uberon_data

Cell Type
Ontology term	p-value	n
endo-epithelial cell	2.11e-12	42
endodermal cell	1.10e-09	58
embryonic cell	4.96e-07	250

Uber Anatomy
Ontology term	p-value	n
surface structure	6.42e-14	99
organism subdivision	5.77e-12	264
multi-tissue structure	1.41e-10	342
endoderm-derived structure	5.13e-10	160
endoderm	5.13e-10	160
presumptive endoderm	5.13e-10	160
digestive system	1.32e-08	145
digestive tract	1.32e-08	145
primitive gut	1.32e-08	145
multi-cellular organism	1.87e-08	656
orifice	1.62e-07	36
anatomical system	3.88e-07	624
anatomical group	5.72e-07	625
skin of body	7.46e-07	41
mouth	8.72e-07	29
stomodeum	8.72e-07	29

Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon link to source data Novel motifs data Jaspar motifs data

Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}

ENCODE TF ChIP-seq peak enrichment analysisSummary: 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. Analyst: Erik Arner link to source dataset data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
ATF3#467	3	22.4631745260087	8.81932387510763e-05	0.001299677389858
BCL3#602	3	34.5471028037383	2.42397750207122e-05	0.000527741893556006
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190737166280374
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00662177645613266
CTBP2#1488	3	62.7170003393281	4.049570681927e-06	0.000130173318697991
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0280670215592422
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326892885720751
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321861970996936
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0168067925237789
FOSL2#2355	3	16.9302006045617	0.000206016205317162	0.00243781174565138
JUN#3725	3	12.5128291923363	0.000510331399272625	0.004456023828161
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157312390152696
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00666806588238158
RXRA#6256	3	20.0746171391333	0.000123573034843222	0.00165778345356343
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277790154488974
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247493624190544
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00631045956837498
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00616267972884634
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00617857641327964
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330639496865854
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140682679760182

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. Analyst:NA link to data source data

This analysis result is provided for C0 - C305 clusters.

@@ Line 8: / Line 8: @@
 |tf_chipseq_enrich=ATF3#467;3:22.4631745260087:8.81932387510763e-05:0.001299677389858!BCL3#602;3:34.5471028037383:2.42397750207122e-05:0.000527741893556006!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190737166280374!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00662177645613266!CTBP2#1488;3:62.7170003393281:4.049570681927e-06:0.000130173318697991!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280670215592422!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326892885720751!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321861970996936!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168067925237789!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00243781174565138!JUN#3725;3:12.5128291923363:0.000510331399272625:0.004456023828161!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157312390152696!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00666806588238158!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00165778345356343!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277790154488974!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247493624190544!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00631045956837498!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00616267972884634!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00617857641327964!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330639496865854!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140682679760182
 |tfbs_overrepresentation=0.147255,0.0586687,0.00192761,0.0477154,0.199763,0.287811,0.0430074,0.0022397,0.03272,0.0257057,0.139423,7.31979e-06,0.188771,0.125978,0.000616359,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.00920475,0.081977,0.0948982,0.0415721,0.215492,0.00181435,0.0907212,0.000554732,0.000145865,9.60364e-05,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.00687964,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.0102981,0.184019,0.120917,0.000664806,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.000113601,0.167053,0.378921,0.00234364,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.00472557,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.0154619,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,4.06954e-06,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.182599,0.000584565,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.230347,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.0174119,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,4.22512e-06,0.0541353,0.0799324,0.090079,0.140334,0.00115947,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.00127354,0.122935,0.00240885,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.000471598,0.259411,0.0413967,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.0800546,0.15606,0.161026,0.0738599,0.00837667,0.138852,0.085973,0.060453,0.059896,0.206862,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.014161,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.00136269,0.117027,0.0133783,0.185164,0.185743,0.0980288,0.00497632,0.159674,0.107242,0.201859,0.0695832,0.00029312,0.0619218,0.1751,0.163376,0.128096,7.03381e-06,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.0429376,0.063292,0.0356268,0.000371199,0.0865903,0.0380459,0.130174,0.584917,0.00183105,0.00485874,0.0821962,0.563047,0.00210428,0.00690237,0.0083957,0.629514,0.261553,0.446302,0.373681,0.309233,0.49143,0.330703,0.0914012,0.329568,0.178727,0.0164332,0.271958,0.0475727,0.0964816,0.39729,0.581713,0.0643874,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.376924,0.463191,0.280025,0.528324,0.520763,0.370782,0.0173702,0.142924,0.253571,0.276829,0.0509673,0.0291592,0.316882,0.223503,0.0340949,0.0669244,0.283727,0.314747,0.21363,0.291709,0.120054,0.0563639,0.416816,0.292835,0.0280875,0.439556,0.000127196,0.57762,0.241757,0.18237,0.00166394,0.00847576,9.55652e-05,0.275351,0.236471,0.185661,0.346319,0.0427964,0.270984,0.0179843,0.503058,0.000896465,0.00691094,0.248634,0.281576,0.0271848,0.163244,0.0670502,0.0730934,0.184794,4.58399e-05,0.0158541,0.217247,0.0021959,0.671377,0.546839,0.191921,0.448039,0.218623,0.312808,0.695172,0.0451077,0.0747529,0.0284893,0.00449125,0.000323853,8.6792e-06,0.294698,0.34331,4.3814e-07,0.289204,0.0605279,0.00650617,0.278044,0.0015747,0.428671,0.228096,0.336314,0.19763,0.15631,0.20495,0.421464,0.141711,0.420626,0.516462,0.0488795,0.335105,0.144809,0.145539,0.0134194,0.376191,0.119597,0.459928,0.252232,0.152681,0.0465712,0.137098,0.00360191,0.134788,0.0985856,0.18767,0.293698,0.284593,0.343734,0.306556,0.305777,0.0144637,0.503082,0.522888,0.284629,0.262537,0.359455,0.226257,0.405955,0.41707,0.363685,0.130283,0.000624133,0.206222,0.525396,0.000779217,0.020698,0.269226,0.339277,2.13553e-05,0.281425,0.141758,0.455379,0.000974263,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.625309,0.347298,0.539392,0.34988,0.475069,0.0958562,0.0204872,9.88726e-06,0.316179,0.0697683,0.0556835,7.3507e-05,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.116981,0.441735,0.0196924,0.111931,0.28934,0.0435386,0.303336,0.126478,0.000454603,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.0966069,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.0268081,0.107043,0.275244,0.00481323,0.0160457,0.141119,0.21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2,0.223831,0.11528,0.194982,0.190993,0.00472154,0.283218,0.249955,0.164638,0.0272695,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.000648999,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.035048,0.0228361,0.361435
+|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,1.91835,0.985163,1.94915,0.925331,0.639839,1.60265,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,2.48753,0.427404,0.596053,0.855276,1.39264,0.469078,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,1.0078,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.886337,1.45054,0.430728,1.87308,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.977977,0.82001,0.993996,3.90735,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,1.90788,2.61709,0.921547,0.743661,1.50815,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,1.05469,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,2.54931,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.853445,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,1.3017,0.936473,0.951408
 }}

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Coexpression cluster:C4400: Difference between revisions

From FANTOM5_SSTAR

Revision as of 16:43, 26 November 2012

Phase1 CAGE Peaks

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	Mozilla Cavendish skin modified by DaSch for the Web Community Wiki GitHub project page – Report a bug – Skin version: 2.6.0