Coexpression cluster:C3281: Difference between revisions

Revision as of 16:02, 26 November 2012

Full id: C3281_bronchogenic_CD4_CD8_acute_Dendritic_somatostatinoma_small

Phase1 CAGE Peaks

Hg19::chr12:46662772..46662835,-	p1@SLC38A1
Hg19::chr12:46662836..46662861,-	p4@SLC38A1
Hg19::chr12:46662888..46662910,-	p9@SLC38A1

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
lymphocyte	7.50e-15	53
common lymphoid progenitor	7.50e-15	53
lymphoid lineage restricted progenitor cell	1.25e-14	52
nucleate cell	6.19e-13	55
mature alpha-beta T cell	2.10e-12	18
alpha-beta T cell	2.10e-12	18
immature T cell	2.10e-12	18
mature T cell	2.10e-12	18
immature alpha-beta T cell	2.10e-12	18
T cell	5.84e-10	25
pro-T cell	5.84e-10	25
CD8-positive, alpha-beta T cell	2.40e-08	11
endo-epithelial cell	2.79e-08	42
epithelial cell	6.24e-07	253
epithelial cell of alimentary canal	8.42e-07	20

Uber Anatomy
Ontology term	p-value	n
organ system subdivision	1.31e-07	223
respiratory system	9.06e-07	74

Disease
Ontology term	p-value	n
carcinoma	6.56e-17	106
cell type cancer	2.90e-14	143
cancer	1.47e-10	235
disease of cellular proliferation	1.24e-09	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
ATF3#467	3	22.4631745260087	8.81932387510763e-05	0.00129347193679591
BRCA1#672	3	20.1842306432238	0.000121570486027164	0.00164018860485608
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115005645842973
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0278640301561427
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.032407556705187
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00436129442940358
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320920739167933
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00913112387213519
ELK4#2005	2	10.823787772312	0.0109128471951648	0.0401779126525827
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186004861200524
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00718814451949857
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293499540089559
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0268870281490015
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00308218323068483
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172476392451633
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.008803519546663
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00662345244067257
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00308310378158087
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00541178774697886
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189695713334123
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00420762856901915
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328312350367971
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00388069588010299
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.010901673834765

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-05:0.00129347193679591!BRCA1#672;3:20.1842306432238:0.000121570486027164:0.00164018860485608!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115005645842973!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278640301561427!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.032407556705187!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00436129442940358!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320920739167933!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00913112387213519!ELK4#2005;2:10.823787772312:0.0109128471951648:0.0401779126525827!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186004861200524!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00718814451949857!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293499540089559!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0268870281490015!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00308218323068483!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172476392451633!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.008803519546663!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00662345244067257!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00308310378158087!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00541178774697886!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0189695713334123!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00420762856901915!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328312350367971!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00388069588010299!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.010901673834765
 |tfbs_overrepresentation=0.147255,0.0586687,0.35968,0.0477154,0.199763,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.113083,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.0212153,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.00989266,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.0693924,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.00212123,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.0400492,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.0128549,0.230347,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.46397,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.0169462,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.569726,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.582402,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.119261,0.0865903,0.0380459,0.130174,0.584917,0.0381789,0.198118,0.635872,0.563047,0.0986134,0.228731,0.335423,0.629514,0.261553,0.118991,0.373681,0.309233,0.49143,0.330703,0.0914012,0.329568,0.53472,0.0724671,0.271958,0.292154,0.0159894,0.39729,0.217139,0.597171,0.187251,0.362792,0.181715,0.10624,0.109988,0.330894,0.218329,0.427027,0.376924,0.000464237,0.280025,0.173877,0.168255,0.370782,0.101703,0.484505,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.155672,0.236436,0.283727,0.314747,0.577664,0.291709,0.448095,0.212757,0.416816,0.292835,0.137839,0.439556,0.0120909,0.57762,0.608919,0.18237,0.346458,0.0310069,0.400457,0.275351,0.236471,0.185661,0.346319,0.535598,0.270984,0.625945,0.155555,0.163222,0.0389686,0.248634,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.230427,0.762864,0.581837,0.1002,0.671377,0.188159,0.551561,0.448039,0.218623,0.312808,0.117923,0.0451077,0.0747529,0.229003,0.28275,0.223844,0.50215,0.294698,0.34331,0.477304,0.289204,0.327108,0.683186,0.278044,0.807485,0.428671,0.228096,0.336314,0.19763,0.15631,0.0530502,0.421464,0.48267,0.420626,0.516462,0.00404127,0.335105,0.144809,0.145539,0.385517,0.376191,0.447325,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.305777,0.601433,0.503082,0.522888,0.284629,0.262537,0.359455,0.226257,0.405955,0.41707,0.363685,0.464871,0.166672,0.206222,0.525396,0.651524,0.437176,0.269226,0.339277,0.0479524,0.281425,0.141758,0.455379,0.0385377,0.159617,0.238587,0.0119179,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.625309,0.347298,0.539392,0.34988,0.475069,0.404569,0.6408,0.630264,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.441735,0.191777,0.111931,0.046606,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.0966069,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.517717,0.1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+|tfbs_overrepresentation_for_novel_motifs=0.699513,1.40091,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,2.1336,0.221898,0.820209,0.985163,1.11328,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,2.2774,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,2.27558,0.439574,0.599922,0.427404,1.45286,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,1.54087,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,1.23315,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,2.54768,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,2.22068,3.14048,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,2.29164,0.853445,0.698641,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,1.69223,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.951408
 }}

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Coexpression cluster:C3281: Difference between revisions

From FANTOM5_SSTAR

Revision as of 16:02, 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