Coexpression cluster:C4849: Difference between revisions

Revision as of 17:00, 26 November 2012

Full id: C4849_CD14_Mesothelial_Mast_acute_lymphoma_rhabdomyosarcoma_H9

Phase1 CAGE Peaks

Hg19::chrX:131157290..131157309,+	p2@MST4
Hg19::chrX:131157322..131157339,+	p1@MST4
Hg19::chrX:131157354..131157369,+	p3@MST4

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
hematopoietic stem cell	1.66e-53	168
angioblastic mesenchymal cell	1.66e-53	168
hematopoietic oligopotent progenitor cell	2.32e-50	161
hematopoietic multipotent progenitor cell	2.32e-50	161
hematopoietic cell	9.80e-50	177
leukocyte	4.69e-39	136
nongranular leukocyte	1.51e-33	115
hematopoietic lineage restricted progenitor cell	2.62e-33	120
myeloid cell	2.17e-31	108
common myeloid progenitor	2.17e-31	108
myeloid leukocyte	6.41e-21	72
classical monocyte	2.44e-18	42
CD14-positive, CD16-negative classical monocyte	2.44e-18	42
granulocyte monocyte progenitor cell	1.82e-17	67
myeloid lineage restricted progenitor cell	9.47e-17	66
lymphocyte	1.28e-16	53
common lymphoid progenitor	1.28e-16	53
lymphoid lineage restricted progenitor cell	1.37e-16	52
defensive cell	2.48e-16	48
phagocyte	2.48e-16	48
nucleate cell	4.26e-16	55
monopoietic cell	1.58e-15	59
monocyte	1.58e-15	59
monoblast	1.58e-15	59
promonocyte	1.58e-15	59
macrophage dendritic cell progenitor	2.89e-15	61
lymphocyte of B lineage	1.71e-08	24
pro-B cell	1.71e-08	24
T cell	5.07e-08	25
pro-T cell	5.07e-08	25

Uber Anatomy
Ontology term	p-value	n
hematopoietic system	2.78e-20	98
blood island	2.78e-20	98
hemolymphoid system	4.08e-15	108
bone marrow	1.16e-14	76
bone element	3.41e-14	82
skeletal element	4.48e-13	90
immune system	1.66e-11	93
skeletal system	1.36e-10	100

Disease
Ontology term	p-value	n
hematologic cancer	1.27e-17	51
immune system cancer	1.27e-17	51
leukemia	7.78e-15	39
cancer	2.26e-13	235
myeloid leukemia	4.91e-13	31
disease of cellular proliferation	5.48e-13	239
organ system cancer	4.41e-11	137
carcinoma	7.31e-08	106

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	0.001645929477598
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0191448772552931
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00663388208036691
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0328313895106942
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0324828718471938
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.032294909210877
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0465459863634522
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0109367567132284
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0296526165078351
TAL1#6886	3	29.8686166774402	3.75103522793067e-05	0.000723728742231389

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;3:20.1842306432238:0.000121570486027164:0.001645929477598!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0191448772552931!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00663388208036691!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0328313895106942!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0324828718471938!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.032294909210877!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0465459863634522!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109367567132284!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0296526165078351!TAL1#6886;3:29.8686166774402:3.75103522793067e-05:0.000723728742231389
 |tfbs_overrepresentation=0.147255,0.0586687,0.134243,0.0477154,0.199763,0.287811,0.0430074,2.07206e-05,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.000616359,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.00920475,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,4.37092e-06,0.114046,0.0180314,0.0233668,0.0665252,0.0844722,3.84895e-06,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.0175714,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.00599201,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.00234531,0.0425,0.114846,0.291327,0.251834,0.064341,0.0235519,5.63916e-05,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.58489,0.0124568,0.0927458,0.27413,0.0574857,0.0422457,0.141874,0.0370665,0.219088,0.0409286,0.00229559,0.0649715,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.013844,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.00847953,0.0403542,0.312091,0.179689,0.137725,0.46397,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.00109304,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,6.74839e-08,0.0458667,0.104357,0.121154,0.1129,0.0549274,0.169057,0.0142864,0.100942,0.062995,0.10299,0.14193,0.37245,0.000717242,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.569726,0.0133328,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.00377835,0.163502,0.214803,0.182472,0.00958651,0.000171422,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.0585224,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.003405,0.00320178,0.0865903,0.0380459,0.130174,0.059488,0.131316,0.0199061,0.000626254,0.051522,0.0986134,0.00156905,0.0638737,0.0185583,0.261553,0.118991,0.373681,0.309233,0.49143,0.330703,0.395854,0.061507,0.0078057,0.0724671,0.271958,0.292154,0.405773,0.39729,0.581713,0.000362379,0.187251,0.0756284,0.181715,0.0186051,0.109988,0.000789293,0.218329,0.427027,0.376924,0.463191,0.000107655,0.00107382,0.168255,0.370782,0.101703,0.142924,0.253571,0.276829,0.301787,0.0291592,0.316882,0.223503,0.0340949,0.236436,0.283727,0.314747,0.0567394,0.291709,0.448095,0.0115542,0.0175396,0.292835,0.476744,0.0210941,0.0807167,0.213592,0.00280546,0.18237,4.27123e-05,1.33224e-05,2.75136e-08,0.275351,0.236471,0.185661,0.00934251,0.179399,0.270984,0.0179843,0.0340542,0.513852,0.169228,0.248634,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.0641718,0.0582356,0.217247,0.0021959,0.00570056,0.546839,0.551561,0.0225539,0.218623,0.312808,0.117923,0.0451077,0.0747529,0.229003,0.000764752,0.061213,0.50215,0.294698,0.00907354,0.477304,0.289204,0.327108,0.109738,0.0428373,0.0015747,0.428671,0.228096,0.336314,0.19763,0.15631,0.000235935,0.104858,0.141711,0.104399,0.00092633,6.80909e-06,0.0637439,0.144809,0.145539,0.08628,0.376191,0.0032214,0.459928,0.0348837,0.152681,0.0465712,0.00985947,0.0369524,0.134788,0.0985856,0.00870714,0.293698,0.0450006,0.343734,0.306556,0.305777,4.97127e-05,0.503082,0.0391885,0.284629,0.262537,0.359455,0.226257,0.405955,0.00230458,0.363685,0.130283,0.00320894,0.206222,0.00713629,0.0905337,0.020698,0.269226,0.339277,0.552319,0.281425,0.141758,4.166e-05,0.00680512,0.159617,0.238587,0.0119179,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.0769581,0.347298,0.539392,0.00966846,0.0277379,0.404569,0.000670954,0.0186811,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,4.2235e-06,0.0216577,0.00303204,0.0196924,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.00184145,0.00141596,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.026047,0.332809,0.19559,0.000427374,0.188694,0.0481795,0.199971,0.0966069,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.0160457,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.0443426,0.000112257,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.02609,0.0394698,0.0596469,0.0178982,0.000337112,0.108872,0.11002,0.26144,0.0286025,0.190156,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.0458479,0.0473033,0.094881,0.118532,0.132886,0.0774373,0.00619136,0.128564,0.131452,0.00681584,0.0226843,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,1.59254e-06,0.0926491,0.21727,0.0465945,0.119215,0.192475,0.0168693,1.97467e-05,0.057571,0.047591,1.40366e-05,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,4.67397e-05,0.00739585,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.00259914,0.0759837,0.0457643,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.0661495,0.151597,0.0626744,0.191335,0.000615006,0.034431,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.0154015,0.193653,0.137219,7.82592e-06,0.00326415,0.0461822,0.11903,0.0838874,6.31571e-05,0.113145,0.00659775,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.000258759,0.103667,0.113069,0.025556,0.16791,0.09066,0.0597157,0.166967,0.188651,0.0813902,0.184948,0.156261,0.0065917,0.0062542,0.0590944,0.247324,5.31e-05,0.0020701,0.231073,0.407281,8.59161e-07,0.0360851,0.0168763,0.131093,0.0434602,0.133616,0.418146,0.0785808,0.449036,0.407369,0.231447,0.0455669,0.0210947,0.37006,0.42622,0.448797,0.197484,0.0919774,0.36145,0.406019,0.381071,0.216033,0.000101057,2.24673e-06,0.366326,0.390366,0.0305485,0.000757632,0.00308025,0.522904,0.158867,5.69054e-05,0.227104,0.000113758,7.77002e-06,0.0135352,0.284625,7.91575e-07,2.10364e-06,0.00228337,0.00513616,0.164197,0.0252589,0.287881,0.000261949,0.478174,0.336276,5.16277e-05,0.258219,0.446557,0.243383,0.00448654,0.390974,1.07621e-05,0.029557,0.161598,0.00310283,0.000709044,0.000714735,0.00136122,0.37357,0.00106614,0.0282154,0.00492096,2.80567e-09,2.48085e-05,0.20342,0.200493,0.20558,0.300504,0.25656,0.425963,0.00960524,0.0851996,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.0448825,0.562405,0.314429,0.0175523,0.282286,0.0192486,0.0165273,0.408413,0.0374737,0.322213,0.000830547,0.33942,0.00285083,0.0136291,0.522605,0.000283063,0.537348,0.222037,0.416621,0.416292,0.0252635,1.84971e-09,0.0118519,0.204817,0.452428,0.138871,0.000165333,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.0120568,0.523625,0.0164118,0.0768488,0.000145338,0.39088,0.363192,0.236011,0.203486,0.00428131,0.375787,0.000370385,0.351067,0.275347,1.26519e-06,0.305885,0.241132,0.371414,0.00623664,0.303709,0.0323359,0.0135408,0.508064,0.250964,0.383276,2.84796e-07,0.504711,0.220231,0.509064,0.196976,0.191517,0.463751,0.235208,0.307334,0.459728,0.283463,0.0102434,5.01908e-06,0.399569,0.273281,0.368095,0.275089,0.384593,0.47795,0.359231,0.339729,0.197805,0.0690807,0.387069,0.332774,1.39598e-05,0.299887,8.64162e-05,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,7.52509e-05,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.000366137,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.00242972,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.0701861,0.154941,0.120196,0.0986735,0.00610703,0.0595618,0.0251995,0.158479,0.220319,0.195218,0.124213,0.00361981,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.00149718,0.240478,0.156465,0.13108,0.00350063,0.222798,0.172134,0.176789,0.0969345,0.202137,0.00649151,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.0056723,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.00954842,0.204393,0.295769,0.286691,0.347036,0.0005308,0.263159,0.00345643,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.0257187,0.223831,0.11528,0.194982,0.0195259,0.281727,0.283218,0.249955,0.00084829,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.056548,0.171683,0.0133429,0.271275,0.071111,0.270604,0.101021,0.0268373,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435
+|tfbs_overrepresentation_for_novel_motifs=0.699513,1.40091,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,2.59717,0.820209,0.985163,1.11328,0.925331,0.639839,0.667627,1.17594,0.575162,1.14835,0.824321,0.69094,1.26332,0.845342,0.635379,0.743951,2.30584,0.409304,0.842925,0.645155,1.00813,0.795576,1.21459,0.534793,0.439574,0.599922,2.64886,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,2.63353,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,2.13568,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,1.7986,0.502203,0.333216,1.45054,3.91579,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,1.24629,1.39759,0.169933,0.82001,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,1.68795,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,2.55998,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,1.66424,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,2.04753,1.08214,2.31409,0.773313,1.33389,0.318511,1.29196,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,1.69998,1.11698,0.960047,0.524529,0.936473,2.56478
 }}

Personal tools

Coexpression cluster:C4849: Difference between revisions - resource_browser

Search

Human

Mouse

Rat

Dog

Chicken

Macaque

Cross species

Other

Tools

Coexpression cluster:C4849: Difference between revisions

From FANTOM5_SSTAR

Revision as of 17:00, 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