Coexpression cluster:C4750: Difference between revisions

Revision as of 16:56, 26 November 2012

Full id: C4750_testicular_mesothelioma_chronic_teratocarcinoma_Reticulocytes_Mesothelial_Hepatic

Phase1 CAGE Peaks

Hg19::chr8:37963407..37963454,+	p2@ASH2L
Hg19::chr8:37963466..37963506,+	p3@ASH2L
Hg19::chr8:37963511..37963523,+	p4@ASH2L

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 disease_data

Cell Type
Ontology term	p-value	n
mesothelial cell	1.86e-08	19
native cell	2.34e-08	722
lining cell	7.58e-07	58
barrier cell	7.58e-07	58

Disease
Ontology term	p-value	n
cancer	2.91e-20	235
disease of cellular proliferation	3.72e-20	239
hematologic cancer	2.80e-10	51
immune system cancer	2.80e-10	51
leukemia	5.15e-10	39
organ system cancer	1.31e-08	137
myeloid leukemia	2.29e-07	31

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	0.0191288198585923
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.0066306185218201
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0327924017026138
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00439149833234319
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0324535505735484
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0465155746117016
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.0076567452183828
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154881911861855
GATA1#2623	3	13.5603081438004	0.000400961596378263	0.00389580688102609
GATA2#2624	3	12.744931733554	0.000482952770428379	0.0043917374306286
GTF2B#2959	3	31.9438299343242	3.06634405746243e-05	0.000629909337170179
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00436111744757719
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00393751233578883
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0109286169160525
HNF4A#3172	3	23.1322903629537	8.07584663437677e-05	0.00123525680528365
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128788367760796
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270922550362452
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0278411268148606
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0248015670857847
THAP1#55145	3	31.3691446028513	3.23800758564397e-05	0.000649460868517516
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0331385188108222
ZBTB33#10009	2	21.1098166866541	0.00292859706060324	0.0156433995710077
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0141022401820241

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;3:6.33620157696263:0.00393075003576489:0.0191288198585923!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.0066306185218201!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327924017026138!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00439149833234319!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0324535505735484!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0465155746117016!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.0076567452183828!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154881911861855!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00389580688102609!GATA2#2624;3:12.744931733554:0.000482952770428379:0.0043917374306286!GTF2B#2959;3:31.9438299343242:3.06634405746243e-05:0.000629909337170179!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00436111744757719!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00393751233578883!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109286169160525!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00123525680528365!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128788367760796!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270922550362452!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0278411268148606!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0248015670857847!THAP1#55145;3:31.3691446028513:3.23800758564397e-05:0.000649460868517516!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0331385188108222!ZBTB33#10009;2:21.1098166866541:0.00292859706060324:0.0156433995710077!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0141022401820241
 |tfbs_overrepresentation=0.147255,0.0586687,0.716932,0.0477154,0.199763,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.0190579,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.0226057,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.688181,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.00315066,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.0831028,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,1.34634e-05,0.064341,0.209032,0.0693924,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.21992,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.00117529,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.230347,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.0172085,0.137725,0.46397,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.569726,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.000171422,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.582402,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.584917,0.713218,0.198118,0.635872,0.563047,0.823736,0.00690237,0.335423,0.629514,0.261553,0.446302,0.373681,0.309233,0.49143,0.330703,0.395854,0.329568,0.178727,0.615744,0.271958,0.292154,0.405773,0.39729,0.581713,0.597171,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.107929,0.376924,0.463191,0.647576,0.528324,0.520763,0.370782,0.415647,0.0297533,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.503224,0.603208,0.283727,0.314747,0.577664,0.291709,0.448095,0.576651,0.416816,0.292835,0.137839,0.439556,0.0120909,0.213592,0.608919,0.18237,0.706298,0.00847576,0.161148,0.275351,0.236471,0.185661,0.346319,0.535598,0.270984,0.625945,0.503058,0.513852,0.522083,0.248634,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.596648,0.176034,0.581837,0.412837,0.102184,0.546839,0.0477082,0.448039,0.218623,0.312808,0.695172,0.0451077,0.0747529,0.229003,0.650179,0.589326,0.50215,0.294698,0.34331,0.477304,0.289204,0.327108,0.683186,0.278044,0.229008,0.0193295,0.228096,0.0642385,0.19763,0.15631,0.20495,0.421464,0.48267,0.420626,0.516462,0.135248,0.335105,0.144809,0.145539,0.385517,0.376191,0.447325,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.305777,0.2348,0.155572,0.169823,0.284629,0.262537,0.359455,0.226257,0.405955,0.0175765,0.363685,0.464871,0.00320894,0.206222,0.525396,0.651524,0.437176,0.269226,0.339277,0.552319,0.281425,0.141758,0.124432,0.520495,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.257493,0.347298,0.182325,0.34988,0.475069,0.404569,0.6408,0.630264,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.441735,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.0413156,0.0627924,0.381386,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.0238665,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.166024,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+|tfbs_overrepresentation_for_novel_motifs=1.66899,0.869629,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,1.11328,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,1.00813,0.795576,1.21459,0.534793,0.439574,0.599922,0.427404,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,1.32383,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,2.20718,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,1.87308,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.507157,0.82001,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,1.7605,0.622396,1.67826,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.951408
 }}

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Coexpression cluster:C4750: Difference between revisions

From FANTOM5_SSTAR

Revision as of 16:56, 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