Coexpression cluster:C4437: Difference between revisions

Revision as of 16:44, 26 November 2012

Full id: C4437_astrocytoma_Endothelial_testicular_mesothelioma_Renal_teratocarcinoma_iPS

Phase1 CAGE Peaks

Hg19::chr4:85791617..85791626,-	p@chr4:85791617..85791626 -
Hg19::chr4:85791647..85791659,-	p@chr4:85791647..85791659 -
Hg19::chr4:85791667..85791699,-	p@chr4:85791667..85791699 -

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
endothelial cell of vascular tree	1.80e-61	24
endothelial cell	1.20e-47	36
blood vessel endothelial cell	6.56e-47	18
embryonic blood vessel endothelial progenitor cell	6.56e-47	18
meso-epithelial cell	1.21e-40	45
endothelial cell of artery	8.48e-35	9
lining cell	3.90e-33	58
barrier cell	3.90e-33	58
aortic endothelial cell	5.27e-24	6
vein endothelial cell	6.40e-17	6
lymphangioblast	6.13e-16	6
endothelial cell of lymphatic vessel	6.13e-16	6
vascular lymphangioblast	6.13e-16	6
squamous epithelial cell	3.48e-14	63
mesodermal cell	1.03e-12	121
embryonic cell	3.71e-12	250
embryonic stem cell	1.41e-11	5
epithelial cell	1.59e-09	253
thoracic aorta endothelial cell	3.24e-09	2

Uber Anatomy
Ontology term	p-value	n
blood vessel endothelium	6.56e-47	18
endothelium	6.56e-47	18
cardiovascular system endothelium	6.56e-47	18
simple squamous epithelium	7.15e-43	22
squamous epithelium	3.11e-37	25
endothelial tube	8.48e-35	9
arterial system endothelium	8.48e-35	9
endothelium of artery	8.48e-35	9
vessel	2.71e-20	68
vasculature	5.21e-17	78
vascular system	5.21e-17	78
epithelial tube open at both ends	2.15e-13	59
blood vessel	2.15e-13	59
blood vasculature	2.15e-13	59
vascular cord	2.15e-13	59
cardiovascular system	6.58e-12	109
lymphatic vessel	7.03e-12	8
lymph vasculature	7.03e-12	8
lymphatic part of lymphoid system	7.03e-12	8
circulatory system	1.90e-11	112
vein	3.68e-11	9
venous blood vessel	3.68e-11	9
venous system	3.68e-11	9
splanchnic layer of lateral plate mesoderm	6.42e-11	83
epithelial tube	1.75e-09	117
lymphoid system	1.94e-09	10
segment of aorta	3.24e-09	2
thoracic aorta	3.24e-09	2
aorta	2.51e-08	21
aortic system	2.51e-08	21
artery	1.84e-07	42
arterial blood vessel	1.84e-07	42
arterial system	1.84e-07	42

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
BCL11A#53335	3	28.3694551036071	4.37778126761649e-05	0.000779425669636206
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115605338865871
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0168101562368828
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00900618569439385
GATA2#2624	3	12.744931733554	0.000482952770428379	0.00438372191819655
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00392821309691786
JUN#3725	3	12.5128291923363	0.000510331399272625	0.00445714174683339
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157369178700531
POU5F1#5460	3	335.439201451906	2.63510205045339e-08	1.82377351257324e-06
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00667090375976095
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247537044124613
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00616313413673078
TRIM28#10155	3	18.5905250452625	0.000155596929725528	0.00197693281552365

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=BCL11A#53335;3:28.3694551036071:4.37778126761649e-05:0.000779425669636206!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115605338865871!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168101562368828!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00900618569439385!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00438372191819655!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00392821309691786!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00445714174683339!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157369178700531!POU5F1#5460;3:335.439201451906:2.63510205045339e-08:1.82377351257324e-06!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00667090375976095!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247537044124613!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00616313413673078!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00197693281552365
 |tfbs_overrepresentation=0.147255,0.0586687,0.716932,0.0477154,0.199763,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.688181,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.608896,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.58489,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.596561,0.0693171,0.0988228,0.0842275,0.0389418,0.0076135,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.46397,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.569726,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.582402,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.584917,0.0381789,0.782949,0.635872,0.563047,0.823736,0.807281,0.335423,0.629514,0.261553,0.446302,0.0806291,0.309233,0.49143,0.330703,0.395854,0.329568,0.53472,0.248224,0.271958,0.292154,0.405773,0.39729,0.581713,0.597171,0.187251,0.0756284,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.376924,0.463191,0.647576,0.528324,0.520763,0.370782,0.415647,0.484505,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.503224,0.603208,0.283727,0.314747,0.21363,0.291709,0.448095,0.0563639,0.416816,0.292835,0.476744,0.439556,0.373868,0.57762,0.608919,0.18237,0.706298,0.513427,0.747852,0.275351,0.236471,0.185661,0.346319,0.535598,0.270984,0.625945,0.503058,0.513852,0.522083,0.248634,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.230427,0.762864,0.581837,0.412837,0.671377,0.188159,0.551561,0.448039,0.218623,0.312808,0.695172,0.0451077,0.0747529,0.229003,0.28275,0.589326,0.50215,0.294698,0.34331,0.477304,0.289204,0.327108,0.683186,0.278044,0.807485,0.428671,0.228096,0.336314,0.19763,0.15631,0.567452,0.421464,0.48267,0.420626,0.516462,0.858756,0.335105,0.144809,0.0111455,0.385517,0.376191,0.119597,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.18767,0.293698,0.284593,0.343734,0.306556,0.305777,0.601433,0.503082,0.522888,0.284629,0.262537,0.0741332,0.226257,0.405955,0.41707,0.363685,0.464871,0.166672,0.206222,0.525396,0.651524,0.020698,0.269226,0.339277,0.552319,0.281425,0.141758,0.455379,0.520495,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.625309,0.347298,0.539392,0.34988,0.475069,0.404569,0.273024,0.630264,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.441735,0.191777,0.111931,0.046606,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.517717,0.137332,0.0145999,0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+|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,1.54806,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,1.54465,1.60265,1.17594,0.575162,0.452865,0.305559,1.65118,0.242883,0.845342,0.635379,0.743951,1.00973,1.05396,0.842925,0.645155,1.00813,0.795576,1.21459,2.27558,0.439574,0.599922,0.137917,0.596053,0.855276,1.39264,0.469078,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,1.81344,1.12884,1.20029,5.62051,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,1.34254,0.642354,0.560075,1.14422,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,2.82056,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,1.98143,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,3.03644,2.09999,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,1.69998,1.11698,0.960047,0.524529,2.15653,0.0768232
 }}

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Coexpression cluster:C4437: Difference between revisions

From FANTOM5_SSTAR

Revision as of 16:44, 26 November 2012

Phase1 CAGE Peaks

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