Coexpression cluster:C4541: Difference between revisions

Revision as of 16:48, 26 November 2012

Full id: C4541_parotid_salivary_Smooth_submaxillary_Mast_Hepatocyte_liver

Phase1 CAGE Peaks

Hg19::chr6:108279263..108279284,-	p4@SEC63
Hg19::chr6:108279288..108279308,-	p3@SEC63
Hg19::chr6:108279309..108279366,-	p2@SEC63

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 disease_data

Cell Type
Ontology term	p-value	n
fibroblast	4.40e-08	76

Uber Anatomy
Ontology term	p-value	n
digestive system	2.11e-09	145
digestive tract	2.11e-09	145
primitive gut	2.11e-09	145
endoderm-derived structure	2.44e-08	160
endoderm	2.44e-08	160
presumptive endoderm	2.44e-08	160
gland	5.70e-08	59
gut epithelium	9.71e-08	54
surface structure	1.19e-07	99
subdivision of digestive tract	9.58e-07	118

Disease
Ontology term	p-value	n
cancer	1.80e-07	235
disease of cellular proliferation	5.53e-07	239
cell type cancer	5.86e-07	143

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
BRCA1#672	3	20.1842306432238	0.000121570486027164	0.00164507644340385
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190941210690814
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00662503131430224
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0327316682846366
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00438662264028405
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323988742943233
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0322157732054594
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00764693549760403
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.0039314270894517
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128632903064459
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157531657848433
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0187286417218432
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295796482716425
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270667203943637
PBX3#5090	3	21.9145126867441	9.49854535978121e-05	0.00137322616117136
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00885254695676155
REST#5978	3	9.65002871612802	0.00111263624711459	0.00770676595121373
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0278024211155351
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00631642755720001
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330962217299764
ZBTB33#10009	3	31.6647250299812	3.14815888737575e-05	0.00063473082246841

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=BRCA1#672;3:20.1842306432238:0.000121570486027164:0.00164507644340385!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190941210690814!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00662503131430224!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327316682846366!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00438662264028405!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323988742943233!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322157732054594!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00764693549760403!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.0039314270894517!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128632903064459!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157531657848433!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187286417218432!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295796482716425!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270667203943637!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00137322616117136!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00885254695676155!REST#5978;3:9.65002871612802:0.00111263624711459:0.00770676595121373!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0278024211155351!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00631642755720001!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330962217299764!ZBTB33#10009;3:31.6647250299812:3.14815888737575e-05:0.00063473082246841
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64,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.0445413,0.249955,0.164638,0.224257,0.0935776,0.327622,0.0276507,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.0133429,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.0750181
+|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,1.54806,0.853988,0.937929,1.23863,0.491742,1.18351,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,2.27558,0.439574,0.599922,1.36391,0.596053,1.99037,0.567465,3.05174,0.598234,1.82956,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,3.20105,0.928548,0.650353,0.892517,1.0078,0.891404,1.25741,0.941709,0.492369,1.14672,3.62494,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,3.32688,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.507157,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,6.47785,0.560075,1.14422,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,2.12604,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.553386,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,1.37952,1.37044,1.87432,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.853445,0.250511,1.37083,1.21015,0.941179,1.78371,1.03563,0.624795,0.744018,1.69223,1.56892,1.35169,1.19946,0.714443,1.11698,2.20464,0.524529,0.936473,0.56135
 }}

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Coexpression cluster:C4541: Difference between revisions

From FANTOM5_SSTAR

Revision as of 16:48, 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