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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.414845407810641

Latest revision as of 11:31, 17 September 2013


Full id: C832_Neutrophils_CD14_Preadipocyte_Olfactory_tenocyte_mixed_Adipocyte



Phase1 CAGE Peaks

Hg19::chr14:62187163..62187261,+p@chr14:62187163..62187261
+
Hg19::chr14:62188445..62188464,+p@chr14:62188445..62188464
+
Hg19::chr14:62193465..62193490,+p7@HIF1A
Hg19::chr14:62200863..62200874,+p2@ENST00000555937
Hg19::chr14:62200903..62200934,+p1@ENST00000555937
Hg19::chr14:62203595..62203676,+p4@HIF1A
Hg19::chr14:62203749..62203798,+p5@HIF1A
Hg19::chr14:62204889..62204963,+p@chr14:62204889..62204963
+
Hg19::chr14:62205037..62205056,+p@chr14:62205037..62205056
+
Hg19::chr14:62207483..62207506,+p@chr14:62207483..62207506
+


Enriched pathways on this co-expression cluster<b>Summary:</b><br>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.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> 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. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0033483gas homeostasis0.00220770045920169
GO:0032906transforming growth factor-beta2 production0.00220770045920169
GO:0032364oxygen homeostasis0.00220770045920169
GO:0032909regulation of transforming growth factor-beta2 production0.00220770045920169
GO:0035035histone acetyltransferase binding0.00220770045920169
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.00993465206640763
GO:0001817regulation of cytokine production0.0129308169753242
GO:0001666response to hypoxia0.0132462027552102
GO:0046982protein heterodimerization activity0.0249470151889792
GO:0001816cytokine production0.0249470151889792
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0278973058026396
GO:0005667transcription factor complex0.0374082577809176
GO:0045893positive regulation of transcription, DNA-dependent0.0374082577809176
GO:0003702RNA polymerase II transcription factor activity0.0374082577809176
GO:0045941positive regulation of transcription0.0374082577809176
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0374082577809176
GO:0048878chemical homeostasis0.0374082577809176
GO:0019899enzyme binding0.0374082577809176
GO:0031325positive regulation of cellular metabolic process0.040400918403391
GO:0046983protein dimerization activity0.040400918403391
GO:0009893positive regulation of metabolic process0.0411052799784697
GO:0006357regulation of transcription from RNA polymerase II promoter0.0424480588291962
GO:0044451nucleoplasm part0.0433861133721377
GO:0042592homeostatic process0.0441540091840339
GO:0005654nucleoplasm0.0458318615330272



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>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. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
musculoskeletal system2.45e-11167
mesoderm4.39e-10315
mesoderm-derived structure4.39e-10315
presumptive mesoderm4.39e-10315
connective tissue6.66e-08371
bone marrow8.62e-0876
skeletal system1.99e-07100
skeletal element2.08e-0790


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>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. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.000221536
MA0004.10.380329
MA0006.10.236135
MA0007.10.363007
MA0009.11.93562
MA0014.10.0036779
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.11.60734
MA0038.10.477043
MA0040.11.77386
MA0041.11.02846
MA0042.10.963243
MA0043.10.828925
MA0046.10.817858
MA0048.10.0613414
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.0662377
MA0056.10
MA0057.10.211138
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.10.118318
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.0911063
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.11.11021e-05
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.0309101
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.11.2287
MA0101.10.241637
MA0103.10.228129
MA0105.10.0508589
MA0106.10.516528
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.11.31824
MA0114.10.174997
MA0115.11.06753
MA0116.10.182037
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.109245
MA0140.10.437738
MA0141.10.290336
MA0142.11.54256
MA0143.12.26801
MA0144.10.163394
MA0145.10.0359093
MA0146.10.00275056
MA0147.10.184931
MA0148.11.04145
MA0149.10.428597
MA0062.20.114378
MA0035.20.437071
MA0039.20.000314573
MA0138.20.569505
MA0002.20.129981
MA0137.20.255808
MA0104.20.138396
MA0047.21.25985
MA0112.20.0329985
MA0065.20.0371828
MA0150.11.52802
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.0494985
MA0155.10.030416
MA0156.10.257809
MA0157.11.4867
MA0158.10
MA0159.10.185458
MA0160.10.417847
MA0161.10
MA0162.10.00711618
MA0163.10.00405048
MA0164.10.544294
MA0080.20.671553
MA0018.20.517858
MA0099.21.12985
MA0079.26.56091e-07
MA0102.21.36707
MA0258.10.155735
MA0259.10.191914
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> 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. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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