Coexpression cluster:C3634: Difference between revisions

Revision as of 16:15, 26 November 2012

Full id: C3634_testicular_Trabecular_osteosarcoma_gastric_Fibroblast_teratocarcinoma_lung

Phase1 CAGE Peaks

Hg19::chr17:41622982..41623001,-	p11@ETV4
Hg19::chr17:41623009..41623053,-	p4@ETV4
Hg19::chr17:41623075..41623101,-	p9@ETV4

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 disease_data

Cell Type
Ontology term	p-value	n
epithelial cell	5.68e-31	253
embryonic cell	6.89e-23	250
animal cell	3.45e-22	679
eukaryotic cell	3.45e-22	679
native cell	7.09e-11	722
mesodermal cell	5.57e-09	121
squamous epithelial cell	9.48e-09	63
somatic cell	7.10e-08	588
endodermal cell	8.23e-08	58
endo-epithelial cell	6.56e-07	42

Uber Anatomy
Ontology term	p-value	n
organism subdivision	1.94e-15	264
unilaminar epithelium	5.15e-13	148
epithelial tube	8.42e-12	117
trunk	1.70e-11	199
cell layer	8.88e-11	309
epithelium	4.91e-10	306
mesenchyme	3.64e-09	160
entire embryonic mesenchyme	3.64e-09	160
trunk region element	4.06e-09	101
trunk mesenchyme	9.65e-09	122
primordium	1.36e-07	160
artery	1.84e-07	42
arterial blood vessel	1.84e-07	42
arterial system	1.84e-07	42
anatomical cluster	1.86e-07	373
vasculature	2.80e-07	78
vascular system	2.80e-07	78
multi-tissue structure	3.42e-07	342
epithelial tube open at both ends	4.53e-07	59
blood vessel	4.53e-07	59
blood vasculature	4.53e-07	59
vascular cord	4.53e-07	59
immaterial anatomical entity	4.88e-07	117
endoderm-derived structure	7.75e-07	160
endoderm	7.75e-07	160
presumptive endoderm	7.75e-07	160
multilaminar epithelium	9.04e-07	83
epithelial vesicle	9.48e-07	78

Disease
Ontology term	p-value	n
cancer	7.61e-12	235
carcinoma	7.77e-12	106
cell type cancer	8.63e-12	143
disease of cellular proliferation	2.35e-11	239

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
BHLHE40#8553	3	44.8718135469774	1.10603738662898e-05	0.000284375772087996
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.018982872606365
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00659954329511599
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0279145022374432
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324897730965635
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321694794247817
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0320220568039347
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167322965561203
FOSL2#2355	3	16.9302006045617	0.000206016205317162	0.00242763471365441
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00580769743727339
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0153946848794509
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00390868564569493
HNF4A#3172	3	23.1322903629537	8.07584663437677e-05	0.00122734771048847
HNF4G#3174	3	28.7534225264468	4.20470658818262e-05	0.000756347487707897
RXRA#6256	3	20.0746171391333	0.000123573034843222	0.0016516309426659
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276324611656599
SP1#6667	3	5.6983813781409	0.00540396270171217	0.024620881237365
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00612923848077604
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328937077249128
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.013999320572769

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=BHLHE40#8553;3:44.8718135469774:1.10603738662898e-05:0.000284375772087996!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.018982872606365!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00659954329511599!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279145022374432!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324897730965635!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321694794247817!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320220568039347!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167322965561203!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00242763471365441!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00580769743727339!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0153946848794509!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00390868564569493!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00122734771048847!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.000756347487707897!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.0016516309426659!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276324611656599!SP1#6667;3:5.6983813781409:0.00540396270171217:0.024620881237365!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00612923848077604!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328937077249128!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.013999320572769
 |tfbs_overrepresentation=0.147255,0.0586687,5.24277e-05,0.0477154,0.199763,0.0460856,0.0430074,0.101122,0.03272,0.0257057,0.139423,0.00229455,0.188771,0.125978,0.148679,0.0619003,5.95171e-07,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,5.73559e-06,0.00181435,0.000133517,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.688181,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.00190755,0.0783235,0.105572,0.000437377,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.0126543,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.0472875,0.251834,0.064341,0.209032,2.96037e-11,0.062747,0.0857568,0.0495878,0.0953825,0.00114029,0.0853887,0.115028,3.75188e-05,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.0649715,0.144217,0.269326,0.0177901,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.00954291,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.00156008,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,4.57719e-05,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,2.1277e-05,0.114283,0.0400322,0.127369,0.0403542,0.0547453,0.179689,0.137725,4.22512e-06,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.000379027,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.000260351,0.0470731,0.0782523,0.0602859,0.0676496,0.00624688,0.0893019,0.060398,0.0308319,0.00187466,0.136451,0.037005,0.0413967,0.15185,0.206299,0.0169462,0.0458667,0.104357,0.121154,0.1129,4.51675e-05,0.169057,0.164202,0.100942,0.00202722,0.10299,0.14193,0.37245,0.0128655,3.44213e-05,0.0738599,1.25606e-05,0.138852,0.085973,0.060453,0.059896,0.00177343,0.0859236,0.0418404,0.0765029,0.00475494,0.0931946,0.0472272,0.0381183,0.163502,0.214803,0.182472,0.0695582,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.0119747,0.117027,0.159052,0.00122826,0.01843,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,3.87374e-06,0.0619218,0.0163125,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.00292601,0.000364005,0.063292,0.000246553,0.119261,0.0865903,0.0380459,0.130174,0.584917,0.00183105,0.00102762,0.268011,0.051522,2.22013e-06,0.0263372,0.00083951,0.00355277,0.261553,0.446302,0.000126821,0.309233,0.49143,0.330703,0.395854,0.329568,0.53472,0.615744,0.0408801,0.292154,0.405773,0.39729,0.0121013,0.0139202,0.187251,0.0109219,0.181715,2.44439e-05,0.109988,0.0620388,0.218329,0.427027,0.0821552,0.000464237,0.000737505,0.173877,0.03861,0.370782,0.0173702,0.484505,0.00335333,0.276829,0.0509673,0.0291592,0.316882,0.00223433,0.155672,0.000394966,0.283727,0.0557438,3.31481e-05,0.291709,0.0225637,0.00192508,0.416816,0.292835,0.0280875,0.439556,0.0807167,0.00194724,0.241757,0.18237,6.93298e-07,2.05465e-06,9.55652e-05,0.275351,0.236471,0.0184133,0.346319,0.179399,0.270984,0.00341096,0.00573308,0.000896465,0.00691094,0.248634,0.281576,0.000524881,0.163244,0.0670502,0.0730934,0.184794,0.000359684,2.85971e-06,0.00204647,9.99552e-08,0.00570056,0.00875805,0.191921,0.448039,0.0258593,0.312808,3.44841e-05,0.0451077,0.0747529,0.00241532,1.67378e-06,4.04707e-05,8.8271e-05,0.0054714,0.34331,0.0282052,0.289204,0.000749204,0.000194033,2.33387e-05,3.0019e-11,0.428671,0.228096,0.336314,0.19763,0.15631,0.000235935,0.000260039,0.141711,0.0181002,0.0374607,3.89235e-05,0.0637439,0.144809,0.145539,0.385517,0.376191,0.000374104,0.0247309,0.252232,0.152681,0.0465712,0.137098,0.00360191,0.134788,0.0985856,0.0460163,0.293698,0.00488039,0.000938454,0.0526965,0.00617767,0.601433,8.95617e-05,0.0391885,0.0450125,0.0379506,0.359455,0.0277799,0.405955,0.41707,0.363685,0.464871,2.2584e-06,0.0228979,0.171685,0.00455998,0.000324942,0.269226,0.339277,0.000188895,0.281425,0.141758,0.455379,0.168058,0.159617,0.238587,0.0119179,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.0178839,8.26983e-05,0.539392,0.34988,0.475069,0.404569,0.273024,0.0186811,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.000351837,0.00034627,0.0196924,0.111931,0.28934,0.0435386,0.00601662,0.126478,0.134852,0.10689,0.0413156,0.0627924,0.381386,0.0179103,3.8523e-05,0.00461664,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.0684384,0.0499762,0.0828956,0.0666953,0.182185,0.111277,6.32154e-06,0.062811,0.19559,0.132201,0.188694,0.0481795,0.199971,0.00202975,0.127758,0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+|tfbs_overrepresentation_for_novel_motifs=1.66899,0.869629,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,1.23181,0.221898,0.820209,0.985163,1.11328,0.925331,0.639839,1.60265,1.17594,0.575162,0.452865,0.824321,0.69094,1.26332,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,1.55576,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,0.596053,0.855276,1.39264,0.469078,0.598234,0.777097,0.718382,1.54087,0.901413,0.726632,0.939121,0.808003,0.247669,2.63353,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,1.23315,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,1.7986,1.25415,1.5923,1.45054,1.92922,0.414196,1.81344,1.12884,1.20029,0.73687,2.02451,1.14559,0.960908,0.498519,1.39759,0.977977,9.66649,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,3.50198,0.743661,0.622396,1.67826,1.26794,0.684398,0.830777,1.58942,0.594137,1.05469,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,2.2314,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,1.99724,3.03644,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,1.69223,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,1.3017,0.936473,0.951408
 }}

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Coexpression cluster:C3634: Difference between revisions

From FANTOM5_SSTAR

Revision as of 16:15, 26 November 2012

Phase1 CAGE Peaks

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