Coexpression cluster:C2671: Difference between revisions

Revision as of 15:39, 26 November 2012

Full id: C2671_skeletal_smooth_heart_CD14_left_bladder_mature

Phase1 CAGE Peaks

Hg19::chr2:173940557..173940625,+	p1@ZAK
Hg19::chr2:173940628..173940639,+	p4@ZAK
Hg19::chr2:173940642..173940663,+	p2@ZAK
Hg19::chr2:173940668..173940682,+	p3@ZAK

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
fibroblast	6.08e-10	76
skin fibroblast	3.14e-09	23
classical monocyte	1.04e-07	42
CD14-positive, CD16-negative classical monocyte	1.04e-07	42

Uber Anatomy
Ontology term	p-value	n
surface structure	3.27e-13	99
musculoskeletal system	2.94e-09	167
multi-cellular organism	1.60e-08	656
anatomical system	1.37e-07	624
skin of body	1.61e-07	41
organ	1.84e-07	503
anatomical group	2.03e-07	625
integument	5.01e-07	46
integumental system	5.01e-07	46

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	4	6.33620157696263	0.000620310058721564	0.00512779501526211
CTCF#10664	4	5.36025637307503	0.00121114538164362	0.00818392938104803
CTCFL#140690	4	19.7464743589744	6.5732084880439e-06	0.000193216808692039
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106610913008768
E2F4#1874	4	12.6680603152844	3.88145892637771e-05	0.000727784001457741
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00997862877460214
EGR1#1958	4	4.98817909481014	0.00161501150007605	0.0101541259440397
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0161090262470017
HDAC2#3066	4	13.4156202366263	3.0859005065161e-05	0.000627264233164724
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0186356872415143
MYC#4609	4	5.2222818716094	0.00134430939527274	0.00888540781804249
PAX5#5079	4	6.66956553117783	0.000505277416948326	0.00444384573883505
RAD21#5885	4	10.3550338954563	8.6948481184721e-05	0.00129633296594591
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00797195215009284
SMC3#9126	4	15.0449328449328	1.95092670935632e-05	0.000438649805378826
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0322720254884785
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0244604405500249
YY1#7528	4	4.91117074985386	0.0017187183805544	0.0106960570222096
ZBTB7A#51341	4	7.3519093078759	0.00034222354001599	0.00346971015393942

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;4:6.33620157696263:0.000620310058721564:0.00512779501526211!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00818392938104803!CTCFL#140690;4:19.7464743589744:6.5732084880439e-06:0.000193216808692039!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106610913008768!E2F4#1874;4:12.6680603152844:3.88145892637771e-05:0.000727784001457741!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00997862877460214!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101541259440397!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0161090262470017!HDAC2#3066;4:13.4156202366263:3.0859005065161e-05:0.000627264233164724!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186356872415143!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00888540781804249!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00444384573883505!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129633296594591!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00797195215009284!SMC3#9126;4:15.0449328449328:1.95092670935632e-05:0.000438649805378826!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322720254884785!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244604405500249!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106960570222096!ZBTB7A#51341;4:7.3519093078759:0.00034222354001599:0.00346971015393942
 |tfbs_overrepresentation=0.191353,0.0774498,0.814139,0.0631091,0.257053,0.00122022,0.0569281,0.510252,0.043387,0.0341265,5.70614e-05,0.288577,0.243414,0.164339,0.193153,0.0816702,0.183412,0.128744,0.0698403,0.141416,0.243245,0.172742,0.107781,0.124486,0.0550418,0.276459,0.268949,0.119094,0.186914,0.122514,0.26347,0.149094,0.0239693,0.267529,0.0877018,0.111013,0.00526413,0.0568767,0.157159,0.0879352,0.126525,0.0326801,0.00116753,0.2375,0.157881,0.0480278,0.0503649,0.234372,0.145553,0.0132389,0.19996,0.0715789,0.0924421,0.12203,0.0359423,0.0508907,0.140644,0.00426281,0.103044,0.138225,0.0390464,0.194086,0.0106139,0.0999599,0.0720888,0.0667453,0.439574,0.0792005,0.113084,0.216289,0.00410045,0.0892037,0.116917,0.155921,0.00995563,0.0227583,0.126543,0.0578308,0.0493551,0.00965832,0.125428,0.290468,0.0562614,0.150119,0.368178,0.320801,0.0848546,0.268505,0.355976,0.0827752,0.112676,0.0655645,0.12511,0.0626609,0.112199,0.150351,0.327332,0.199405,0.121709,0.347653,0.0759036,0.350158,0.184542,0.0491142,0.280878,0.0541957,0.0883058,1.87436e-06,0.187509,0.34189,0.0302681,0.0450707,0.194256,0.0235108,0.132631,0.0447483,0.0270258,0.0748174,0.180926,0.110194,0.000120021,0.275495,0.182323,0.00660477,0.134107,0.228632,0.119051,0.0196757,0.110868,0.016435,0.078637,0.0985137,0.0755515,0.0302655,0.164103,0.141472,0.085537,0.0730922,0.0438087,0.0052702,0.0302521,0.166414,0.262198,0.202388,0.122756,0.0913381,0.129544,7.18694e-06,0.0515825,0.157774,0.258146,0.00126344,0.233377,0.0352845,0.0565357,2.81932e-05,0.0984158,0.29227,0.0683304,0.0447121,0.291455,0.124982,0.152417,0.192028,0.346873,0.149398,0.0530169,0.166112,0.0534404,0.392741,0.2321,0.179282,0.564569,0.0715212,0.105131,0.118265,0.182591,0.234755,0.230552,0.0472274,0.205973,0.159869,0.0363736,0.15105,0.0001644,0.155237,0.236268,0.0532055,0.108938,0.00014203,0.140245,0.241581,3.42283e-08,0.000455619,0.147332,0.0622664,0.102951,0.0795624,0.0891668,0.14349,0.117261,0.0797088,0.0408965,0.0799774,0.177664,4.06631e-06,0.346995,0.00149829,0.265132,0.230439,0.0606832,0.136664,0.0132285,0.147626,0.0143681,0.218801,0.21271,0.132273,0.0830988,0.134907,0.184613,0.462724,0.202467,0.208718,0.0972471,1.37409e-06,0.180711,0.112956,0.0797807,0.0790532,0.309911,0.00439336,0.0553945,0.10068,0.125804,0.122288,0.0624687,0.334388,0.21183,0.275612,0.235571,0.0204686,0.128998,0.109226,0.151958,0.0169062,0.107176,0.146021,0.0253438,0.15291,0.206234,0.238926,0.00279479,0.128521,0.1286,0.207017,0.14037,0.259646,0.0916845,0.00685525,0.0816983,0.226367,0.211672,0.167038,0.0457509,0.106603,0.106727,0.12083,0.154253,0.0993998,0.0711631,0.0834863,0.0594434,0.18736,0.113754,0.0504034,0.169684,0.114577,0.495926,0.869559,0.0479295,0.668426,0.0307547,9.91914e-05,0.018014,0.148431,0.332539,0.545329,0.464128,0.0881702,0.594055,0.414547,0.489273,0.413223,0.639461,0.0406667,0.0678774,0.369161,0.0334148,0.00507494,0.0305759,0.123196,0.241524,0.45167,0.234628,0.520726,0.143893,0.41477,0.00462477,0.170724,0.467825,0.201843,0.751064,0.632838,0.624969,0.460819,0.511459,2.86054e-09,0.322903,0.350886,0.380582,0.583749,0.398372,0.286293,0.0151426,0.34907,0.0739876,0.395864,0.683133,0.368633,0.188516,0.682118,0.512763,0.369971,0.214221,0.537928,0.00386096,0.683088,0.714007,0.235444,0.0255809,0.0297312,0.114723,0.349116,0.302142,0.239545,0.432689,0.640367,0.343881,0.145459,0.606382,0.617741,0.626346,0.316925,0.356561,0.573659,0.211506,0.0883859,0.0962508,0.238465,0.70198,0.301365,0.6873,0.508325,0.773224,0.651927,0.28972,0.046332,0.280307,0.090261,0.076625,0.0596868,0.0984075,0.293026,0.00320607,0.117621,0.0678767,0.372182,0.429205,0.0118001,0.0769243,0.0988815,0.784024,0.35234,0.00740524,0.525923,0.0474911,0.421082,0.25441,0.202782,2.24726e-05,0.517933,0.584705,0.517001,0.620475,0.12395,0.419676,0.188259,0.189182,0.138387,0.46699,0.546448,0.560187,0.321282,0.198207,0.0616078,0.178485,0.329745,0.175552,0.129238,0.651295,0.370995,0.360161,0.429696,0.386216,0.385297,0.706685,0.606408,0.627185,0.360203,0.333725,0.447838,0.289666,0.500627,0.513045,0.452694,0.565545,0.00014407,0.265037,0.000575107,0.754776,0.53531,0.341771,0.424526,0.290547,0.356381,0.184395,0.194887,0.0766597,0.206945,0.304719,0.462531,0.296994,0.0326312,0.00713433,0.0786167,0.629381,0.376317,0.433821,0.64428,0.436806,0.0563264,0.499072,0.0498754,0.0115505,0.397546,0.0919254,0.0735469,0.248103,0.102621,0.0760107,0.187642,0.286156,0.261868,0.541583,0.183047,0.247151,0.146385,0.365815,0.0576261,0.382413,0.164977,0.175633,0.139918,0.34669,2.17369e-06,0.135364,0.0238089,1.16898e-05,0.354433,0.00468928,0.0614918,0.219485,0.149782,0.136923,0.118103,0.113892,0.207214,0.140201,0.0580534,0.00518407,0.161297,0.168389,0.0403091,0.249506,0.432751,0.0660736,0.108971,0.0879235,0.0301295,0.145546,0.28124,0.417003,0.251882,0.172263,0.0323461,0.0637178,0.257309,0.00559963,0.166608,0.227224,0.238082,0.000127796,0.115115,0.00814887,0.0149794,0.28498,0.140114,0.348988,0.00641248,0.224626,0.183585,0.000326913,0.03989,0.000963352,0.05892,0.0691994,0.268299,0.198844,0.00571021,0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+|tfbs_overrepresentation_for_novel_motifs=0.590005,1.03954,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,1.01802,0.462021,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.635753,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,0.316693,1.72987,0.537869,0.297585,1.63433,1.09415,1.10579,0.344471,0.49475,0.0842336,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.183156,0.53106,0.314427,0.61613,0.822818,0.694903,0.173425,1.33034,0.90714,1.94963,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,1.8276,1.13655,0.825354,1.0193,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.692875,1.32819,2.42873,0.321165,0.823598,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,1.17995,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,2.27689,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,1.67377,1.04326,0.805616,0.632569,0.516141,1.44917,1.14697,0.575476,0.717043,1.46636,0.489254,0.393155,0.681522,0.988625,1.97727,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.774456,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,2.68745,3.82793,1.24902,0.383416,0.824835,1.65997,0.917558,1.28873,0.632914,1.4628,1.44595,1.23002,1.07918,1.47036,0.997702,0.843324,0.423521,0.820225,0.644569
 }}

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Coexpression cluster:C2671: Difference between revisions

From FANTOM5_SSTAR

Revision as of 15:39, 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