Coexpression cluster:C3034: Difference between revisions

Revision as of 15:53, 26 November 2012

Full id: C3034_extraskeletal_Basophils_Natural_CD8_pineal_Neutrophils_CD14

Phase1 CAGE Peaks

Hg19::chr10:65028561..65028577,-	p11@JMJD1C
Hg19::chr10:65028616..65028646,-	p5@JMJD1C
Hg19::chr10:65028677..65028708,-	p3@JMJD1C

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
leukocyte	6.84e-35	136
hematopoietic lineage restricted progenitor cell	2.17e-29	120
hematopoietic stem cell	4.30e-29	168
angioblastic mesenchymal cell	4.30e-29	168
hematopoietic oligopotent progenitor cell	5.59e-27	161
hematopoietic multipotent progenitor cell	5.59e-27	161
nongranular leukocyte	1.32e-26	115
myeloid leukocyte	7.12e-26	72
hematopoietic cell	8.40e-26	177
classical monocyte	2.86e-23	42
CD14-positive, CD16-negative classical monocyte	2.86e-23	42
granulocyte monocyte progenitor cell	3.27e-22	67
myeloid lineage restricted progenitor cell	8.89e-22	66
defensive cell	4.96e-20	48
phagocyte	4.96e-20	48
macrophage dendritic cell progenitor	5.29e-20	61
myeloid cell	3.16e-19	108
common myeloid progenitor	3.16e-19	108
monopoietic cell	7.47e-19	59
monocyte	7.47e-19	59
monoblast	7.47e-19	59
promonocyte	7.47e-19	59
nucleate cell	3.16e-08	55
lymphoid lineage restricted progenitor cell	1.05e-07	52
lymphocyte	1.52e-07	53
common lymphoid progenitor	1.52e-07	53
stuff accumulating cell	2.66e-07	87

Uber Anatomy
Ontology term	p-value	n
hematopoietic system	9.28e-24	98
blood island	9.28e-24	98
hemolymphoid system	1.81e-19	108
bone element	2.95e-18	82
bone marrow	8.19e-18	76
skeletal element	2.22e-16	90
immune system	5.49e-15	93
skeletal system	1.34e-12	100
adult organism	9.71e-08	114

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
BCL3#602	3	34.5471028037383	2.42397750207122e-05	0.000526096812840433
BCLAF1#9774	2	14.4350984067479	0.00620114743554613	0.0273705365996535
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189068117250149
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00435168724011573
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320274398161824
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0166783053291471
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.007595716907533
GTF2B#2959	3	31.9438299343242	3.06634405746243e-05	0.000625602475126624
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00432600137424567
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00389776457719411
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293088936368113
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0268458990161145
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00879232554889242
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275310195661197
STAT1#6772	3	20.7065874971992	0.000112599244104667	0.00154367976569274
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00540341749294286
TRIM28#10155	3	18.5905250452625	0.000155596929725528	0.00196521801228738
WRNIP1#56897	3	109.819964349376	7.53682839543883e-07	3.3212608472204e-05

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=BCL3#602;3:34.5471028037383:2.42397750207122e-05:0.000526096812840433!BCLAF1#9774;2:14.4350984067479:0.00620114743554613:0.0273705365996535!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189068117250149!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00435168724011573!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320274398161824!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0166783053291471!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.007595716907533!GTF2B#2959;3:31.9438299343242:3.06634405746243e-05:0.000625602475126624!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00432600137424567!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00389776457719411!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293088936368113!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0268458990161145!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00879232554889242!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0275310195661197!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00154367976569274!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00540341749294286!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00196521801228738!WRNIP1#56897;3:109.819964349376:7.53682839543883e-07:3.3212608472204e-05
 |tfbs_overrepresentation=0.147255,0.0586687,0.716932,0.0477154,0.199763,0.287811,0.0430074,0.101122,0.03272,0.0257057,0.139423,0.225367,0.188771,0.00829112,0.148679,0.0619003,0.000522123,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.00181435,0.0907212,0.0108656,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.688181,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.0117644,0.108602,0.0759481,0.054569,0.0504887,0.0709764,0.0600088,0.00381532,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.000916199,0.00686288,0.291327,0.251834,0.064341,0.0235519,0.608896,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.58489,0.153631,0.00444039,0.00431873,0.0574857,0.0422457,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.005305,0.0337525,0.0203386,0.0566549,0.0101452,0.0838393,0.16671,0.214708,0.140123,0.00378931,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,1.29771e-05,0.203923,0.155998,0.596561,0.0693171,0.00505227,0.0842275,0.0389418,2.65174e-07,0.200647,0.143677,7.34359e-08,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.0281563,0.0952829,0.116642,0.0115024,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.0172085,0.00995227,0.46397,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.00109304,0.0356339,0.0133424,0.00782633,0.0274061,8.59467e-06,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.00976435,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.0549274,0.169057,0.164202,0.100942,0.062995,0.10299,0.0105855,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.569726,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.00982118,0.0815104,0.000253111,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.582402,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.00292601,0.278352,0.00204659,0.254773,0.119261,0.0865903,0.0380459,0.130174,0.584917,0.713218,0.782949,0.635872,0.563047,0.823736,0.807281,0.0638737,0.0185583,0.261553,0.118991,0.0806291,0.309233,0.0313047,0.330703,0.395854,0.000775053,0.178727,0.248224,0.271958,0.292154,0.0964816,0.39729,0.217139,0.597171,0.187251,0.0756284,0.181715,0.423979,0.109988,0.0620388,0.218329,0.0190732,0.376924,0.463191,0.280025,0.528324,0.520763,0.0792797,0.415647,0.142924,0.253571,0.276829,0.301787,0.0291592,0.316882,0.223503,0.503224,0.0669244,0.283727,0.314747,0.577664,0.291709,0.120054,0.576651,0.416816,0.292835,0.476744,0.0210941,0.373868,0.00194724,0.608919,0.18237,0.346458,0.821217,0.400457,0.0419647,0.236471,0.185661,0.00934251,0.179399,0.270984,0.625945,0.155555,0.513852,0.169228,0.248634,0.0439966,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.596648,0.0582356,0.0583074,0.412837,0.102184,0.546839,0.551561,0.448039,0.00208206,0.312808,0.695172,0.0451077,0.0747529,0.229003,0.650179,0.589326,0.50215,0.294698,0.0671437,0.138202,0.289204,0.327108,0.109738,0.00452305,0.807485,0.428671,0.228096,0.336314,0.19763,0.15631,0.20495,0.00242214,0.141711,0.0181002,0.165111,0.311758,0.0637439,0.144809,0.145539,0.385517,0.376191,0.119597,0.0247309,0.00329638,0.152681,0.0465712,0.00985947,0.259235,0.134788,0.0985856,0.546222,0.293698,0.000401581,0.343734,0.306556,0.305777,0.601433,0.00573447,0.169823,0.284629,0.262537,0.359455,0.226257,0.405955,0.41707,8.05867e-06,0.130283,0.753577,0.206222,0.171685,0.651524,0.437176,0.269226,0.0654598,0.552319,0.00470507,0.141758,0.00351186,0.168058,0.159617,0.00275523,0.0799758,0.0293409,0.189515,0.0891382,0.0595618,0.524997,0.257493,0.347298,0.0081614,0.34988,0.0277379,0.404569,0.00403911,0.630264,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.0270501,0.203656,0.442884,0.441735,0.191777,0.000255104,0.28934,0.0435386,0.303336,0.000372475,0.0095312,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.000346732,0.000397518,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.00915124,0.188694,0.00117973,0.199971,0.0966069,0.00853267,0.175785,0.184486,0.169234,0.0876426,0.0046858,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.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115817,0.218052,0.223831,0.00691586,0.0203812,0.00135479,0.0440463,0.00480369,0.249955,0.164638,0.00225856,0.0935776,0.327622,0.0276507,0.207791,0.0958756,0.0859274,3.07111e-06,0.171683,0.158847,0.271275,0.071111,0.270604,0.00528373,0.222548,0.0164735,0.157274,0.00199458,0.035048,0.0228361,0.00118119
+|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,2.25583,1.11328,0.925331,1.54465,0.667627,1.17594,2.40732,0.452865,0.824321,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,1.05396,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.461452,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,1.0078,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.886337,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.946807,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,1.44883,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,2.04753,1.08214,2.31409,0.773313,0.539692,0.318511,0.698641,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.0768232
 }}

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Coexpression cluster:C3034: Difference between revisions

From FANTOM5_SSTAR

Revision as of 15:53, 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