Coexpression cluster:C3605: Difference between revisions

Revision as of 16:14, 26 November 2012

Full id: C3605_CD14_adult_liver_Eosinophils_CD4_Dendritic_anaplastic

Phase1 CAGE Peaks

Hg19::chr17:14204341..14204353,+	p3@HS3ST3B1
Hg19::chr17:14204363..14204378,+	p2@HS3ST3B1
Hg19::chr17:14204389..14204416,+	p1@HS3ST3B1

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
stem cell	1.16e-15	441
multi fate stem cell	1.78e-15	427
connective tissue cell	4.60e-15	361
somatic stem cell	9.48e-15	433
mesenchymal cell	1.03e-14	354
motile cell	6.27e-13	386
fibroblast	5.47e-08	76
classical monocyte	4.77e-07	42
CD14-positive, CD16-negative classical monocyte	4.77e-07	42

Uber Anatomy
Ontology term	p-value	n
connective tissue	3.12e-14	371

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
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00659769726901945
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0279099063119874
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321594706418548
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0461552840518744
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00896618824744934
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127896053374237
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294111708718361
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.00199364159460826
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.0024550794148675
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00470740248986565
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172730308035771
PBX3#5090	3	21.9145126867441	9.49854535978121e-05	0.00136491273917197
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00881249528825138
REST#5978	3	9.65002871612802	0.00111263624711459	0.00766811515193353
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.027624364588508
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246133650503322
SP2#6668	3	26.1535304938446	5.58768218891694e-05	0.000939275615851112
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00542060446867681
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109276694510977

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=CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00659769726901945!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279099063119874!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321594706418548!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461552840518744!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00896618824744934!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127896053374237!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294111708718361!NFYA#4800;3:18.4255806998305:0.000159813550781416:0.00199364159460826!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.0024550794148675!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00470740248986565!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172730308035771!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00136491273917197!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00881249528825138!REST#5978;3:9.65002871612802:0.00111263624711459:0.00766811515193353!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.027624364588508!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246133650503322!SP2#6668;3:26.1535304938446:5.58768218891694e-05:0.000939275615851112!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00542060446867681!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109276694510977
 |tfbs_overrepresentation=0.147255,0.0586687,0.716932,0.0477154,0.199763,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.0275521,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.0108656,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.0308399,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.00766099,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.0126543,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.000234347,0.064341,0.209032,0.608896,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.58489,0.000682869,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.00056041,0.0400492,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.0249033,0.140123,0.0857827,0.102368,0.00106363,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.0641358,0.0693171,0.0988228,0.0842275,0.0389418,0.000323286,0.0015841,0.143677,0.180712,0.0265818,0.0427088,0.00719677,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.0413643,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.0255071,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.00278703,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,5.43543e-05,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.00976435,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.569726,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.582402,0.0619218,0.1751,0.0141386,0.128096,0.0345133,0.0810678,0.0811639,0.0043744,0.118078,0.0755168,0.0429376,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.584917,0.355018,0.198118,0.635872,0.051522,0.823736,0.228731,0.335423,0.000572844,0.261553,0.446302,0.373681,0.309233,0.147559,0.0619618,0.395854,0.329568,0.0078057,6.32807e-05,0.271958,0.0475727,0.0159894,0.0921263,0.0121013,0.00244849,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.376924,0.025356,0.647576,0.528324,8.98016e-08,0.370782,0.00226755,0.484505,0.253571,0.0424424,0.301787,0.481778,0.316882,0.223503,0.503224,0.603208,0.283727,0.0557438,0.21363,0.291709,0.120054,0.0563639,0.416816,0.292835,0.137839,0.439556,0.373868,0.000273537,0.241757,0.18237,0.706298,0.821217,0.00296206,0.275351,0.236471,0.185661,0.346319,0.535598,0.270984,0.625945,0.503058,0.513852,0.0389686,0.248634,0.281576,0.135034,0.163244,0.0670502,0.0730934,0.184794,0.596648,0.762864,0.581837,0.412837,0.305671,0.546839,0.551561,0.120021,0.218623,0.312808,0.333034,0.0451077,0.0747529,0.229003,0.650179,0.589326,0.50215,0.294698,0.34331,0.477304,0.0465597,0.327108,0.109738,0.278044,0.807485,0.108847,0.228096,0.336314,0.19763,0.15631,0.20495,0.421464,0.48267,0.420626,0.516462,0.582303,0.335105,0.144809,0.145539,0.385517,0.376191,0.119597,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.048108,0.284593,0.343734,0.306556,0.305777,0.2348,0.503082,0.00696513,0.0450125,0.262537,0.359455,0.226257,0.405955,0.41707,0.363685,0.000474832,0.753577,0.206222,0.525396,0.651524,0.437176,0.269226,0.00872205,0.552319,0.281425,0.141758,0.455379,0.520495,0.159617,0.238587,0.372281,0.232251,0.0192138,0.0891382,0.0595618,0.524997,0.0769581,0.347298,0.539392,0.34988,0.475069,0.404569,0.000670954,0.0186811,0.316179,0.00249247,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.441735,0.191777,0.111931,0.0051519,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.0129363,0.0179103,0.303939,0.279795,0.0886747,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.0200986,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.000924948,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.00187586,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.166024,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.016278,0.370421,0.0330727,0.00956472,0.02609,0.0394698,0.0596469,0.103658,0.122476,0.108872,0.11002,0.26144,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.0306378,0.00501606,0.0761239,0.172491,0.0818785,0.182701,0.0637246,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.000236316,0.128564,0.131452,0.323837,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.000147224,0.144075,0.0340203,0.0741807,0.277091,0.047822,0.655293,0.21727,0.289306,0.119215,0.192475,0.177967,0.188967,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.000216899,0.0225581,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,1.64212e-05,0.110216,0.070276,0.0277579,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,5.42792e-08,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.00771936,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.00490354,0.15503,0.0154015,0.00141547,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.0384217,0.249049,0.140533,0.0997756,0.257598,0.103667,0.00664782,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.0362615,0.0590944,0.247324,0.178389,0.218229,0.00248603,0.0161946,0.0170505,0.0360851,0.0168763,0.131093,0.0434602,0.133616,0.418146,0.36927,0.449036,0.407369,0.231447,0.544776,0.0210947,0.37006,0.0189483,0.022688,0.197484,0.396996,0.36145,0.406019,0.381071,0.0119618,0.643768,0.432035,0.722159,0.0140037,0.0305485,0.000757632,0.443185,0.522904,0.3468,0.336835,0.227104,0.00667974,0.617852,0.38649,0.284625,0.00583062,0.000187838,0.729153,0.28907,0.164197,0.462688,0.000422595,0.21103,0.478174,0.336276,0.0263888,0.258219,0.119142,0.243383,0.777351,0.0140783,0.73485,0.683217,0.161598,0.751174,0.000102726,0.496032,0.799185,0.37357,0.78509,0.0282154,0.452741,0.746954,0.185744,0.00165472,0.200493,0.20558,0.300504,0.25656,0.425963,0.349197,0.0131573,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.0513026,0.314429,0.181415,0.282286,0.194707,0.24884,0.0978616,0.00654592,0.322213,0.00480191,0.33942,0.0156581,0.387276,0.522605,0.802166,0.0433137,0.222037,0.102227,0.416292,0.128937,0.734551,0.215157,0.204817,0.452428,0.138871,0.027191,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.373557,0.00701509,0.408861,0.0111982,0.178743,0.39088,0.0109626,0.236011,0.203486,0.273398,0.0816179,0.4466,0.00977892,0.275347,0.269604,0.305885,0.241132,0.0795725,0.0527347,0.303709,0.15059,0.386538,0.508064,0.250964,0.0851927,0.0243456,0.156714,0.220231,0.509064,0.196976,0.191517,0.463751,0.235208,0.307334,0.459728,0.283463,0.0517073,0.00422311,0.399569,0.273281,0.0780405,0.275089,0.0858306,0.47795,0.359231,0.339729,0.197805,0.608187,0.387069,0.332774,0.52832,0.299887,0.0193657,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.0348699,0.012591,0.255516,0.20753,0.119514,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.00310436,0.222339,0.0673329,0.20847,0.0391817,0.113092,0.145701,0.0285999,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.00632223,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.0183464,0.0723291,0.258496,0.261744,0.203781,0.21382,0.0232077,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.036274,0.222798,0.172134,0.176789,0.0969345,0.0219648,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.00717361,0.261724,0.211332,0.187731,0.0025753,0.00132285,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.000241242,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.0457735,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.0203812,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.0232618,0.00475042,0.0859274,0.316866,0.171683,0.0133429,0.271275,0.071111,0.0404514,0.101021,0.222548,0.175934,0.157274,0.0251447,0.252796,0.205954,0.361435
+|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,1.94915,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.824321,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,3.63468,0.137917,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.151453,1.72524,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,1.87308,1.02656,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,2.15606,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,1.54991,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,2.12604,0.743661,0.622396,5.44379,1.26794,0.684398,3.21962,1.58942,0.594137,1.05469,0.794219,1.10778,0.547323,1.44203,1.0504,3.28248,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,1.87432,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,2.29164,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,1.3017,0.936473,0.265282
 }}

Personal tools

Coexpression cluster:C3605: Difference between revisions - resource_browser

Search

Human

Mouse

Rat

Dog

Chicken

Macaque

Cross species

Other

Tools

Coexpression cluster:C3605: Difference between revisions

From FANTOM5_SSTAR

Revision as of 16:14, 26 November 2012

Phase1 CAGE Peaks

	FAQ
	Mozilla Cavendish skin modified by DaSch for the Web Community Wiki GitHub project page – Report a bug – Skin version: 2.6.0