Coexpression cluster:C3434: Difference between revisions

Revision as of 16:08, 26 November 2012

Full id: C3434_prostate_Reticulocytes_mucinous_epidermoid_testis_teratocarcinoma_chronic

Phase1 CAGE Peaks

Hg19::chr14:54863667..54863678,+	p3@CDKN3
Hg19::chr14:54863682..54863738,+	p1@CDKN3
Hg19::chr14:54863739..54863769,+	p2@CDKN3

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
animal cell	3.10e-19	679
eukaryotic cell	3.10e-19	679
epithelial cell	6.20e-16	253
native cell	6.88e-11	722

Uber Anatomy
Ontology term	p-value	n
larynx	5.37e-07	9

Disease
Ontology term	p-value	n
cancer	1.20e-49	235
disease of cellular proliferation	3.75e-48	239
organ system cancer	3.44e-25	137
cell type cancer	5.13e-25	143
carcinoma	5.92e-22	106
hematologic cancer	3.63e-16	51
immune system cancer	3.63e-16	51
leukemia	8.11e-12	39
myeloid leukemia	1.76e-08	31
disease of anatomical entity	1.38e-07	39

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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.018961829237194
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00659400831331969
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0278869493666351
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.032436106474336
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00436314683104706
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321257369313914
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319758138093862
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.04610494255797
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00896114350537463
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108515804486776
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127819347819081
IRF3#3661	3	46.9819522114896	9.63568551583244e-06	0.000253358851860026
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293840627156266
NANOG#79923	3	29.2447784810127	3.99627955670032e-05	0.000736357516976403
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.00199197606278319
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.0024526360095005
PBX3#5090	3	21.9145126867441	9.49854535978121e-05	0.00136359942107243
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00880856615022477
REST#5978	3	9.65002871612802	0.00111263624711459	0.00766255305060341
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00483797974597793
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275943330832688
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0245951305444771
SP2#6668	3	26.1535304938446	5.58768218891694e-05	0.000938822297503693
SRF#6722	3	13.7971782621678	0.000380661502580019	0.00374419915878269
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00612564493677852
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328618292248066

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=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.018961829237194!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00659400831331969!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278869493666351!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.032436106474336!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00436314683104706!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321257369313914!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319758138093862!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.04610494255797!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00896114350537463!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108515804486776!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127819347819081!IRF3#3661;3:46.9819522114896:9.63568551583244e-06:0.000253358851860026!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293840627156266!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000736357516976403!NFYA#4800;3:18.4255806998305:0.000159813550781416:0.00199197606278319!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.0024526360095005!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00136359942107243!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00880856615022477!REST#5978;3:9.65002871612802:0.00111263624711459:0.00766255305060341!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00483797974597793!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0275943330832688!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245951305444771!SP2#6668;3:26.1535304938446:5.58768218891694e-05:0.000938822297503693!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00374419915878269!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00612564493677852!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328618292248066
 |tfbs_overrepresentation=0.147255,0.0586687,0.134243,0.0477154,0.199763,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.324808,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.00612307,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.608896,0.062747,0.0857568,0.0495878,0.00470085,0.0473737,0.0853887,0.115028,0.21992,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.00862108,0.144217,0.0400492,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.596561,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.00847953,0.0403542,0.312091,0.179689,0.137725,0.0255071,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.0549274,0.169057,0.164202,0.00527533,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.569726,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.582402,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.584917,0.713218,0.198118,0.635872,0.563047,0.823736,0.489965,0.335423,0.629514,0.261553,0.446302,0.0120704,0.309233,0.49143,0.330703,0.395854,0.329568,0.53472,0.615744,0.271958,0.292154,0.405773,0.39729,0.581713,0.0139202,0.00127255,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.376924,0.463191,0.0883629,0.528324,0.520763,0.370782,0.101703,0.000615629,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.503224,0.603208,0.283727,0.314747,0.577664,0.0474194,0.448095,0.576651,0.416816,0.292835,0.476744,0.439556,0.373868,0.57762,0.241757,0.00117064,0.0359955,0.821217,0.747852,0.275351,0.236471,0.185661,0.346319,0.535598,0.270984,0.625945,0.503058,0.163222,0.522083,0.00314692,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.230427,0.762864,0.581837,0.412837,0.671377,0.546839,0.551561,0.448039,0.218623,0.0550136,0.333034,0.0451077,0.0747529,0.229003,0.28275,0.589326,0.154921,0.294698,0.34331,0.477304,0.289204,0.327108,0.683186,0.278044,0.807485,0.428671,0.0282539,0.336314,0.19763,0.15631,0.0530502,0.421464,0.48267,0.420626,0.516462,0.582303,0.335105,0.144809,0.145539,0.385517,0.376191,0.447325,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.0526965,0.305777,0.601433,0.503082,0.522888,0.284629,0.262537,0.359455,0.226257,0.405955,0.41707,0.363685,0.464871,0.40841,0.206222,0.525396,0.651524,0.437176,0.269226,0.339277,0.552319,0.281425,0.141758,0.455379,0.520495,0.159617,0.238587,0.0799758,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.625309,0.347298,0.539392,0.34988,0.475069,0.404569,0.6408,0.630264,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.441735,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.0238665,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.00915124,0.188694,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0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+|tfbs_overrepresentation_for_novel_motifs=0.699513,1.40091,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,1.60265,1.17594,0.575162,1.14835,0.824321,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,1.05396,0.842925,0.645155,0.388328,0.795576,1.21459,1.3235,0.439574,0.599922,0.427404,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.718382,0.63803,0.151453,0.726632,0.939121,0.808003,0.69206,1.55608,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,2.58389,0.961293,4.08293,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.886337,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,1.24629,1.39759,2.22068,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,4.59048,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,1.50815,0.703975,1.26794,1.63757,0.830777,1.58942,0.594137,1.05469,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,1.37952,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,1.8537,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,1.33389,0.318511,0.698641,1.37083,0.481626,0.941179,1.78371,1.03563,1.51317,0.744018,0.710709,1.56892,1.35169,4.35547,1.69998,1.11698,0.960047,1.3017,0.936473,0.56135
 }}

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Coexpression cluster:C3434: Difference between revisions

From FANTOM5_SSTAR

Revision as of 16:08, 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