Coexpression cluster:C4801: Difference between revisions

Revision as of 16:58, 26 November 2012

Full id: C4801_Trabecular_Wilms_parotid_MCF7_salivary_breast_submaxillary

Phase1 CAGE Peaks

Hg19::chr9:129376073..129376080,-	p2@ENST00000451449
Hg19::chr9:129376201..129376225,+	p1@LMX1B
Hg19::chr9:129376233..129376251,+	p2@LMX1B

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

GO ID	GO name	FDR corrected p-value
GO:0009953	dorsal/ventral pattern formation	0.0313199105145414
GO:0001701	in utero embryonic development	0.0313199105145414
GO:0003002	regionalization	0.0313199105145414
GO:0009792	embryonic development ending in birth or egg hatching	0.0313199105145414
GO:0043009	chordate embryonic development	0.0313199105145414
GO:0007389	pattern specification process	0.0340672710859924
GO:0030182	neuron differentiation	0.0431885081832097
GO:0009790	embryonic development	0.0431885081832097
GO:0048699	generation of neurons	0.0431885081832097
GO:0022008	neurogenesis	0.0431885081832097

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
epithelial cell	4.43e-08	253
embryonic stem cell	2.62e-07	5
mammary gland epithelial cell	2.78e-07	4

Uber Anatomy
Ontology term	p-value	n
cavitated compound organ	1.76e-07	31
mammary gland	2.78e-07	4
mammary bud	2.78e-07	4
mammary ridge	2.78e-07	4
mammary placode	2.78e-07	4
stroma	3.06e-07	4

Disease
Ontology term	p-value	n
cell type cancer	9.01e-13	143
carcinoma	2.41e-10	106
cancer	1.43e-08	235
disease of cellular proliferation	4.42e-08	239
thoracic cancer	9.29e-08	4
breast cancer	9.29e-08	4
disease of anatomical entity	9.87e-08	39

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	0.00663201679649783
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0465315758413582
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157784164642296
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0296406298409631
SUZ12#23512	3	50.1157809110629	7.93834897779404e-06	0.000223831865251574
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00617908073943542

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 9: / Line 9: @@
 |tf_chipseq_enrich=CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00663201679649783!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0465315758413582!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157784164642296!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0296406298409631!SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000223831865251574!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00617908073943542
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+|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,1.23863,0.491742,1.84557,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.824321,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,2.07812,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,1.5923,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,4.62073,0.303648,0.381882,3.90735,2.0169,1.63834,1.36973,1.23218,1.34254,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,3.73269,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,1.66424,1.86486,1.10778,1.35006,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,2.79286,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,2.84192,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,6.28676
 }}

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Coexpression cluster:C4801: Difference between revisions

From FANTOM5_SSTAR

Revision as of 16:58, 26 November 2012

Phase1 CAGE Peaks

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