Coexpression cluster:C4308: Difference between revisions

Revision as of 16:40, 26 November 2012

Full id: C4308_Hepatocyte_gastrointestinal_anaplastic_liver_hepatocellular_smallcell_hepatoblastoma

Phase1 CAGE Peaks

Hg19::chr3:184095923..184095953,-	p1@THPO
Hg19::chr3:184095972..184095983,-	p3@THPO
Hg19::chr3:184095989..184096000,-	p2@THPO

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
metabolising cell	2.38e-17	12
endopolyploid cell	2.38e-17	12
parenchymal cell	2.38e-17	12
polyploid cell	2.38e-17	12
hepatocyte	2.38e-17	12
endodermal cell	8.99e-07	58

Uber Anatomy
Ontology term	p-value	n
liver	1.80e-16	19
digestive gland	1.80e-16	19
liver bud	1.80e-16	19
hepatic diverticulum	6.39e-14	22
liver primordium	6.39e-14	22
digestive tract diverticulum	3.22e-13	23
epithelial sac	5.51e-12	25
epithelium of foregut-midgut junction	5.51e-12	25
anatomical boundary	5.51e-12	25
hepatobiliary system	5.51e-12	25
foregut-midgut junction	5.51e-12	25
septum transversum	5.51e-12	25
abdomen element	5.68e-12	54
abdominal segment element	5.68e-12	54
sac	1.93e-11	26
endocrine gland	2.67e-11	35
abdominal segment of trunk	2.19e-10	60
abdomen	2.19e-10	60
endocrine system	9.94e-10	45
exocrine gland	3.01e-09	31
exocrine system	3.01e-09	31
gut epithelium	6.73e-09	54

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	0.00662038249575315
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.032167739594762
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0463863691131403
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154558195879282
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00392500435505252
HNF4A#3172	3	23.1322903629537	8.07584663437677e-05	0.00123146933369496
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0187088106529747
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295403231409937
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.0024640803726156
RXRA#6256	3	20.0746171391333	0.000123573034843222	0.00165650676241706
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247309259280539
STAT1#6772	3	20.7065874971992	0.000112599244104667	0.00155162322932409
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190864966542929

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;3:10.3440228341169:0.000903370110274688:0.00662038249575315!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.032167739594762!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0463863691131403!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154558195879282!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00392500435505252!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00123146933369496!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187088106529747!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295403231409937!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.0024640803726156!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00165650676241706!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247309259280539!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00155162322932409!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190864966542929
 |tfbs_overrepresentation=0.147255,0.0586687,0.039404,0.0477154,0.199763,0.287811,0.0430074,0.0172144,0.03272,0.0257057,0.139423,0.00229455,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.00920475,0.081977,0.0948982,0.0415721,0.0250931,0.0236364,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.688181,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.0279481,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.608896,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.58489,0.0124568,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.00056041,0.00407722,0.182599,0.000584565,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.00215071,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.0223702,0.155998,0.596561,0.0693171,0.0988228,0.0842275,1.01382e-05,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.0255071,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.00033709,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.0549274,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.569726,0.0859236,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.0802194,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.000770586,0.107242,0.201859,0.0695832,0.21774,0.001958,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.059488,0.0381789,0.0691572,0.268011,0.20128,0.000443992,0.807281,0.335423,0.00355277,0.261553,0.118991,0.373681,0.309233,0.49143,0.0619618,0.395854,0.00791734,0.0078057,0.0164332,0.271958,0.292154,0.0964816,0.0921263,3.66238e-07,5.1852e-06,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.376924,0.463191,0.647576,0.528324,0.520763,0.370782,0.0173702,0.484505,0.253571,0.276829,0.301787,0.481778,0.0565541,0.223503,0.503224,0.0026262,0.283727,0.000629694,0.00194826,0.291709,0.120054,0.212757,0.102333,0.292835,0.476744,0.439556,0.373868,0.213592,0.608919,0.18237,0.706298,0.248484,0.400457,0.275351,0.236471,0.185661,0.346319,0.535598,0.0405716,0.0772647,0.503058,0.513852,0.0389686,0.248634,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.230427,0.762864,0.0121151,0.412837,0.671377,0.546839,0.000186789,0.448039,0.218623,0.0550136,0.00743804,0.0451077,0.0747529,7.98829e-06,0.650179,0.589326,0.50215,0.294698,0.00907354,0.138202,0.289204,0.327108,0.109738,0.00452305,0.229008,0.00262586,0.0282539,0.336314,0.19763,0.15631,0.0530502,0.104858,0.00466824,0.420626,0.516462,0.858756,0.335105,0.144809,0.145539,0.385517,0.376191,0.0224279,0.459928,0.00329638,0.152681,0.0465712,0.137098,0.0369524,0.134788,0.0985856,0.00133722,0.048108,0.284593,0.343734,0.306556,0.0524121,0.00257275,0.0340602,0.00100376,0.00488238,0.262537,0.359455,0.226257,0.405955,0.41707,0.363685,0.130283,0.753577,0.206222,0.03988,0.0905337,0.113671,0.040018,0.0654598,0.552319,0.281425,0.141758,0.455379,0.520495,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.171389,0.257493,0.0688327,0.182325,0.34988,0.136757,0.404569,0.0847452,0.262389,0.316179,0.0697683,0.0556835,0.0198561,0.0779981,3.32302e-05,0.144322,0.223391,0.203656,0.116981,0.441735,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,1.13138e-05,0.0179103,0.0517437,0.279795,0.0140073,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.00220026,0.107043,0.0419304,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,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0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.00417402,0.071111,0.0404514,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435
+|tfbs_overrepresentation_for_novel_motifs=0.699513,2.70919,0.690871,0.855819,1.54806,0.853988,0.937929,0.494933,1.23181,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.824321,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,1.86765,1.21459,0.534793,0.439574,0.599922,0.427404,0.596053,0.855276,1.39264,0.469078,0.598234,0.777097,0.259059,0.63803,0.461452,0.726632,0.939121,0.808003,0.69206,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,1.0078,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,1.02656,1.12884,1.20029,0.73687,3.00588,1.14559,0.960908,0.498519,1.39759,0.507157,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,1.14422,1.27663,1.05794,1.68795,2.38768,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,4.08454,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,1.35006,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,1.87432,1.50051,0.969553,1.65144,0.372828,1.8537,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,3.23473,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,3.30166,0.936473,0.0768232
 }}

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Coexpression cluster:C4308: Difference between revisions

From FANTOM5_SSTAR

Revision as of 16:40, 26 November 2012

Phase1 CAGE Peaks

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