Coexpression cluster:C3805: Difference between revisions

Revision as of 16:21, 26 November 2012

Full id: C3805_Mammary_skeletal_Mesenchymal_Osteoblast_Corneal_Pericytes_Fibroblast

Phase1 CAGE Peaks

Hg19::chr19:46916678..46916710,-	p3@CCDC8
Hg19::chr19:46916779..46916800,-	p4@CCDC8
Hg19::chr19:46916805..46916852,-	p1@CCDC8

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	6.23e-09	76
contractile cell	2.66e-08	59
non-terminally differentiated cell	7.69e-08	106
muscle precursor cell	3.77e-07	58
myoblast	3.77e-07	58
multi-potent skeletal muscle stem cell	3.77e-07	58
electrically responsive cell	5.67e-07	61
electrically active cell	5.67e-07	61

Uber Anatomy
Ontology term	p-value	n
multi-tissue structure	4.46e-14	342
compound organ	6.02e-14	68
organism subdivision	7.73e-14	264
multi-cellular organism	1.05e-12	656
mesenchyme	6.07e-11	160
entire embryonic mesenchyme	6.07e-11	160
cell layer	2.53e-10	309
epithelium	1.38e-09	306
anatomical system	2.47e-08	624
multilaminar epithelium	2.91e-08	83
trunk	3.30e-08	199
anatomical group	3.65e-08	625
epithelial vesicle	5.45e-08	78
embryo	5.58e-08	592
primary circulatory organ	7.23e-08	27
urinary system structure	7.30e-08	47
muscle tissue	7.35e-08	64
musculature	7.35e-08	64
musculature of body	7.35e-08	64
skeletal muscle tissue	7.47e-08	62
striated muscle tissue	7.47e-08	62
myotome	7.47e-08	62
renal system	1.18e-07	48
dense mesenchyme tissue	2.43e-07	73
anatomical cluster	3.54e-07	373
somite	4.46e-07	71
presomitic mesoderm	4.46e-07	71
presumptive segmental plate	4.46e-07	71
dermomyotome	4.46e-07	71
trunk paraxial mesoderm	4.46e-07	71
paraxial mesoderm	4.52e-07	72
presumptive paraxial mesoderm	4.52e-07	72

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	3	6.33620157696263	0.00393075003576489	0.0190013239058204
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00660370063323148
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00437131612724136
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322183615917562
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0320586590177623
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0462246833786106
ESR1#2099	3	30.7686032961545	3.43136389821584e-05	0.000676421695292118
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00762175236437044
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00897348513283915
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154083177201526
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00433863746073401
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108694995827747
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128063730927006
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156770909025533
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.00199626449348886
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.0024580724186981
REST#5978	3	9.65002871612802	0.00111263624711459	0.00767419211546696
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276730153480148
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246477622763611
SP2#6668	3	26.1535304938446	5.58768218891694e-05	0.000940032120052023
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0109077377773907
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00542944996512892
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0329367188868051
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140172416146799

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;3:6.33620157696263:0.00393075003576489:0.0190013239058204!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00660370063323148!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00437131612724136!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322183615917562!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320586590177623!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0462246833786106!ESR1#2099;3:30.7686032961545:3.43136389821584e-05:0.000676421695292118!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00762175236437044!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00897348513283915!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154083177201526!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00433863746073401!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108694995827747!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128063730927006!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156770909025533!NFYA#4800;3:18.4255806998305:0.000159813550781416:0.00199626449348886!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.0024580724186981!REST#5978;3:9.65002871612802:0.00111263624711459:0.00767419211546696!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276730153480148!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246477622763611!SP2#6668;3:26.1535304938446:5.58768218891694e-05:0.000940032120052023!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109077377773907!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00542944996512892!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329367188868051!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140172416146799
 |tfbs_overrepresentation=0.147255,0.0586687,0.00948065,0.0477154,0.199763,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.00198832,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.688181,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.00762432,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.00252127,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.0126543,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.241734,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.0594776,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.00954291,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.596561,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.0255071,0.0541353,0.0799324,0.090079,0.0103428,0.181817,0.178449,0.0356339,0.0133424,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.0413967,0.15185,0.206299,0.178359,0.0458667,0.104357,0.0076549,0.1129,0.0549274,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.0538541,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.014161,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.0133783,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.21774,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.584917,0.00183105,0.000191546,0.635872,0.563047,0.00879988,0.807281,0.00083951,0.261644,0.261553,0.000368869,0.373681,0.309233,0.49143,0.330703,0.395854,0.000775053,0.042539,0.615744,0.271958,0.292154,0.405773,0.39729,0.581713,0.230901,0.187251,0.0109219,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.376924,0.463191,0.280025,0.528324,0.520763,0.370782,0.415647,0.484505,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.503224,0.0669244,0.283727,0.0557438,0.0567394,0.291709,0.448095,0.576651,0.416816,0.00535876,0.137839,0.439556,0.373868,0.57762,0.241757,0.18237,0.126021,0.00847576,0.0133926,0.275351,0.236471,0.185661,0.346319,0.535598,0.270984,0.625945,0.155555,0.000896465,0.169228,0.248634,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.00243366,0.0158541,0.0121151,0.412837,0.102184,0.546839,0.551561,0.120021,0.218623,0.312808,0.333034,0.0451077,0.0747529,0.229003,0.00449125,0.223844,0.50215,0.294698,0.34331,0.0282052,0.289204,0.327108,0.683186,0.278044,0.000315884,0.428671,0.228096,0.336314,0.19763,0.15631,0.567452,0.421464,0.00466824,0.420626,0.516462,0.000203002,0.335105,0.144809,0.145539,0.385517,0.0818086,0.447325,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.0673219,0.306556,0.000553055,0.601433,0.503082,0.522888,0.284629,0.262537,0.359455,0.226257,0.405955,0.102469,0.363685,0.464871,0.00320894,0.206222,0.525396,0.00455998,0.437176,0.269226,0.00872205,0.192529,0.281425,0.141758,0.455379,0.0385377,0.159617,0.238587,0.372281,0.232251,0.0192138,0.0891382,0.0595618,0.524997,0.0769581,0.347298,0.182325,0.34988,0.475069,0.404569,0.6408,0.630264,0.0562865,0.0697683,0.0556835,0.0198561,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.441735,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.0413156,0.0627924,0.000143044,0.0179103,0.0517437,0.279795,0.0140073,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.0190418,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0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+|tfbs_overrepresentation_for_novel_motifs=0.699513,1.40091,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.824321,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.843849,0.596053,0.855276,1.39264,0.469078,0.598234,0.777097,1.32383,0.63803,0.151453,0.726632,0.939121,0.808003,1.28131,0.645308,1.02504,0.951993,0.893117,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,1.5923,1.45054,1.10051,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.977977,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,3.81931,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,1.05469,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,1.54007,3.66389,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,3.62109,1.3017,0.936473,1.42224
 }}

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Coexpression cluster:C3805: Difference between revisions

From FANTOM5_SSTAR

Revision as of 16:21, 26 November 2012

Phase1 CAGE Peaks

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