Coexpression cluster:C4365: Difference between revisions

Revision as of 16:42, 26 November 2012

Full id: C4365_Fibroblast_basal_mesenchymal_Adipocyte_melanoma_Mesothelial_hepatic

Phase1 CAGE Peaks

Hg19::chr4:120133777..120133790,+	p4@USP53
Hg19::chr4:120133791..120133802,+	p3@USP53
Hg19::chr4:120133857..120133881,+	p1@USP53

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 uberon_data

Uber Anatomy
Ontology term	p-value	n
adult organism	9.14e-10	114
multi-cellular organism	1.74e-07	656
body cavity	3.69e-07	46

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
BRCA1#672	3	20.1842306432238	0.000121570486027164	0.00164379854870416
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00662084708399847
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0280635367043181
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.032680825795345
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323621034992961
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00917875564293935
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0464054653575863
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0168017494774125
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00764126766588961
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00583020105141265
GATA2#2624	3	12.744931733554	0.000482952770428379	0.00438143714304808
GATA3#2625	3	27.236516357206	4.94721007899563e-05	0.000853173172787689
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00435172253709125
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00392678634195666
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128505983574509
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157296172380515
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295522288008119
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00472640897651721
REST#5978	3	9.65002871612802	0.00111263624711459	0.00769910667278875
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277696642128953
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.00644522088785777
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00544637864223588
TAL1#6886	3	29.8686166774402	3.75103522793067e-05	0.000721197290445234
ZBTB33#10009	3	31.6647250299812	3.14815888737575e-05	0.000634485847237816
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00243388477609224

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=BRCA1#672;3:20.1842306432238:0.000121570486027164:0.00164379854870416!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00662084708399847!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280635367043181!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.032680825795345!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323621034992961!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00917875564293935!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464054653575863!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168017494774125!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00764126766588961!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00583020105141265!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00438143714304808!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.000853173172787689!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00435172253709125!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00392678634195666!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128505983574509!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157296172380515!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295522288008119!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00472640897651721!REST#5978;3:9.65002871612802:0.00111263624711459:0.00769910667278875!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277696642128953!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00644522088785777!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00544637864223588!TAL1#6886;3:29.8686166774402:3.75103522793067e-05:0.000721197290445234!ZBTB33#10009;3:31.6647250299812:3.14815888737575e-05:0.000634485847237816!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00243388477609224
 |tfbs_overrepresentation=0.147255,0.0586687,0.716932,0.0477154,0.199763,0.0460856,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.688181,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.0102981,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.0244227,8.50717e-05,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.608896,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.58489,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.0177901,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.230347,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.46397,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.0142864,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.569726,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.0695582,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.21774,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.119261,0.0865903,0.0380459,0.130174,0.584917,0.713218,0.782949,0.635872,0.563047,0.823736,0.807281,0.335423,0.629514,0.261553,0.118991,0.373681,0.309233,0.49143,0.330703,0.0146881,0.061507,0.53472,0.615744,0.271958,0.292154,0.405773,0.39729,0.217139,0.597171,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.376924,0.129235,0.647576,0.528324,0.520763,0.370782,0.415647,0.484505,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.503224,0.603208,0.283727,0.314747,0.577664,0.291709,0.448095,0.576651,0.416816,0.0478086,0.476744,0.439556,0.373868,0.57762,0.608919,0.18237,0.706298,0.248484,0.161148,0.275351,0.236471,0.185661,0.346319,0.535598,0.270984,0.625945,0.503058,0.513852,0.522083,0.248634,0.281576,0.0271848,0.163244,0.0670502,0.0730934,0.184794,0.596648,0.762864,0.581837,0.1002,0.671377,0.546839,0.551561,0.448039,0.218623,0.312808,0.695172,0.0451077,0.0747529,0.0284893,0.650179,0.589326,0.50215,0.294698,0.34331,0.0282052,0.289204,0.327108,0.683186,0.278044,0.490301,0.428671,0.228096,0.336314,0.19763,0.15631,0.20495,0.421464,0.48267,0.420626,0.516462,0.582303,0.335105,0.144809,0.145539,0.385517,0.376191,0.447325,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.305777,0.601433,0.503082,0.522888,0.284629,0.262537,0.359455,0.226257,0.405955,0.41707,0.0760312,0.464871,0.753577,0.206222,0.525396,0.651524,0.437176,0.269226,0.339277,0.192529,0.281425,0.141758,0.455379,0.520495,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.625309,0.347298,0.539392,0.34988,0.475069,0.404569,0.6408,0.630264,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.441735,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.0129363,0.0179103,0.303939,0.0434097,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.166024,0.137332,0.0145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+|tfbs_overrepresentation_for_novel_motifs=2.80639,0.442617,1.65103,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,1.84557,0.820209,0.985163,1.11328,0.925331,0.639839,1.60265,1.17594,0.575162,0.452865,0.824321,0.69094,0.680949,4.68287,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,1.00813,0.795576,1.21459,0.534793,1.11965,2.48753,0.137917,1.45286,0.855276,0.567465,0.469078,0.598234,1.82956,0.718382,0.63803,0.461452,0.726632,0.939121,0.808003,0.69206,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,2.0644,1.25741,3.5644,0.492369,1.14672,2.20718,1.11026,1.54311,1.91674,1.2037,1.75271,4.33203,0.502203,1.5923,1.45054,0.430728,0.414196,1.02656,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.507157,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,1.68795,0.569121,1.22626,1.27082,1.1798,1.09802,1.90788,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,1.94007,1.58942,0.594137,0.188952,0.794219,2.50498,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,3.36921,0.853445,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,1.51317,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.0768232
 }}

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Coexpression cluster:C4365: Difference between revisions

From FANTOM5_SSTAR

Revision as of 16:42, 26 November 2012

Phase1 CAGE Peaks

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