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Coexpression cluster:C283: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:13, 17 September 2013


Full id: C283_tenocyte_Chondrocyte_mesenchymal_Macrophage_pleomorphic_Synoviocyte_cholangiocellular



Phase1 CAGE Peaks

Hg19::chr1:203148057..203148072,+p@chr1:203148057..203148072
+
Hg19::chr1:203148146..203148212,+p1@CU678996
Hg19::chr1:203148270..203148291,-p@chr1:203148270..203148291
-
Hg19::chr1:203148271..203148296,+p7@CU678996
Hg19::chr1:203148336..203148348,-p@chr1:203148336..203148348
-
Hg19::chr1:203148357..203148383,-p@chr1:203148357..203148383
-
Hg19::chr1:203148373..203148396,+p3@CU678996
Hg19::chr1:203148394..203148401,-p10@CHI3L1
Hg19::chr1:203148408..203148431,+p2@CU678996
Hg19::chr1:203148428..203148437,-p11@CHI3L1
Hg19::chr1:203148455..203148477,-p5@CHI3L1
Hg19::chr1:203148495..203148505,-p13@CHI3L1
Hg19::chr1:203148522..203148550,-p4@CHI3L1
Hg19::chr1:203148531..203148567,+p4@CU678996
Hg19::chr1:203148907..203148922,+p@chr1:203148907..203148922
+
Hg19::chr1:203148919..203148937,-p16@CHI3L1
Hg19::chr1:203148938..203148988,-p6@CHI3L1
Hg19::chr1:203149716..203149729,-p19@CHI3L1
Hg19::chr1:203149741..203149762,-p14@CHI3L1
Hg19::chr1:203149809..203149816,-p@chr1:203149809..203149816
-
Hg19::chr1:203150031..203150040,-p@chr1:203150031..203150040
-
Hg19::chr1:203150041..203150049,-p@chr1:203150041..203150049
-
Hg19::chr1:203150369..203150408,-p@chr1:203150369..203150408
-
Hg19::chr1:203151897..203151908,-p15@CHI3L1
Hg19::chr1:203151934..203151947,-p7@CHI3L1
Hg19::chr1:203151964..203151973,-p21@CHI3L1
Hg19::chr1:203152777..203152814,+p@chr1:203152777..203152814
+
Hg19::chr1:203152791..203152804,-p@chr1:203152791..203152804
-
Hg19::chr1:203152808..203152846,-p@chr1:203152808..203152846
-
Hg19::chr1:203152845..203152866,+p@chr1:203152845..203152866
+
Hg19::chr1:203152849..203152863,-p@chr1:203152849..203152863
-
Hg19::chr1:203152872..203152879,-p@chr1:203152872..203152879
-
Hg19::chr1:203152908..203152924,-p@chr1:203152908..203152924
-
Hg19::chr1:203153416..203153419,-p@chr1:203153416..203153419
-
Hg19::chr1:203153711..203153722,+p@chr1:203153711..203153722
+
Hg19::chr1:203154299..203154330,+p@chr1:203154299..203154330
+
Hg19::chr1:203154334..203154339,+p@chr1:203154334..203154339
+
Hg19::chr1:203154342..203154363,-p9@CHI3L1
Hg19::chr1:203154349..203154356,+p@chr1:203154349..203154356
+
Hg19::chr1:203154383..203154466,-p3@CHI3L1
Hg19::chr1:203154393..203154416,+p@chr1:203154393..203154416
+
Hg19::chr1:203154486..203154506,-p8@CHI3L1
Hg19::chr1:203154508..203154518,-p20@CHI3L1
Hg19::chr1:203155464..203155497,-p@chr1:203155464..203155497
-
Hg19::chr1:203155823..203155838,-p1@CHI3L1
Hg19::chr1:203155868..203155882,-p2@CHI3L1


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:0006032chitin catabolic process0.00331155068880254
GO:0006046N-acetylglucosamine catabolic process0.00331155068880254
GO:0006043glucosamine catabolic process0.00331155068880254
GO:0046348amino sugar catabolic process0.00331155068880254
GO:0006030chitin metabolic process0.00331155068880254
GO:0004568chitinase activity0.00331155068880254
GO:0044247cellular polysaccharide catabolic process0.00347712822324267
GO:0000272polysaccharide catabolic process0.00347712822324267
GO:0006044N-acetylglucosamine metabolic process0.00463617096432356
GO:0006041glucosamine metabolic process0.00463617096432356
GO:0006040amino sugar metabolic process0.00493722102694197
GO:0044264cellular polysaccharide metabolic process0.00876287259190826
GO:0005976polysaccharide metabolic process0.00876287259190826
GO:0005201extracellular matrix structural constituent0.0116377352777918
GO:0044275cellular carbohydrate catabolic process0.0149604172294138
GO:0004553hydrolase activity, hydrolyzing O-glycosyl compounds0.0149604172294138
GO:0016052carbohydrate catabolic process0.0149604172294138
GO:0016798hydrolase activity, acting on glycosyl bonds0.0161898033674791
GO:0005529sugar binding0.0241917492424101
GO:0005578proteinaceous extracellular matrix0.0278832567997174
GO:0043285biopolymer catabolic process0.0279759802190039
GO:0030246carbohydrate binding0.0279759802190039
GO:0044262cellular carbohydrate metabolic process0.0279759802190039
GO:0044265cellular macromolecule catabolic process0.0279759802190039
GO:0005615extracellular space0.0279759802190039
GO:0009057macromolecule catabolic process0.0312021664900506
GO:0009308amine metabolic process0.0312021664900506
GO:0006807nitrogen compound metabolic process0.0320747338144018
GO:0005975carbohydrate metabolic process0.0357205934298834
GO:0044248cellular catabolic process0.0357205934298834
GO:0044421extracellular region part0.0388840145394879
GO:0009056catabolic process0.0402767352525609



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>

Cell Type
Ontology termp-valuen
GAG secreting cell5.51e-219
carbohydrate secreting cell5.51e-219
collagen secreting cell1.89e-166
chondroblast1.89e-166
chondrocyte1.89e-166
macrophage1.95e-166
fibrocyte1.20e-123
attachment cell1.20e-123
tendon cell1.20e-123
stromal cell2.88e-1228
extracellular matrix secreting cell3.75e-1215
Uber Anatomy
Ontology termp-valuen
dense regular connective tissue1.20e-123
tendon1.20e-123
regular connective tissue1.20e-123


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)
MA0003.10.022604
MA0004.10.0380427
MA0006.10.00805332
MA0007.10.573372
MA0009.10.282049
MA0014.10.0015719
MA0017.10.550825
MA0019.12.79538
MA0024.10.603486
MA0025.10.383675
MA0027.11.77546
MA0028.10.049363
MA0029.10.222602
MA0030.10.215031
MA0031.12.25373
MA0038.10.542133
MA0040.10.226506
MA0041.10.0434336
MA0042.10.138038
MA0043.10.282278
MA0046.10.274202
MA0048.12.12567
MA0050.10.0346399
MA0051.10.0713589
MA0052.10.2291
MA0055.11.26698
MA0056.10
MA0057.10.00172028
MA0058.10.0167504
MA0059.10.0165339
MA0060.10.0286759
MA0061.14.70701
MA0063.10
MA0066.10.0732172
MA0067.10.537012
MA0068.10.443922
MA0069.10.271442
MA0070.10.263481
MA0071.10.212157
MA0072.10.721253
MA0073.10.00072048
MA0074.10.907477
MA0076.10.0195703
MA0077.10.254892
MA0078.10.371676
MA0081.10.38039
MA0083.12.18698
MA0084.10.703837
MA0087.10.258584
MA0088.10.745766
MA0089.10
MA0090.10.240463
MA0091.19.77761
MA0092.10.119932
MA0093.10.00837134
MA0095.10
MA0098.10
MA0100.10.0787315
MA0101.11.72112
MA0103.11.60116
MA0105.12.08753
MA0106.10.0905927
MA0107.14.71372
MA0108.20.988321
MA0109.10
MA0111.10.107174
MA0113.10.0981023
MA0114.10.127493
MA0115.10.471806
MA0116.10.429698
MA0117.10.83365
MA0119.10.0660527
MA0122.10.329219
MA0124.10.437263
MA0125.10.36951
MA0130.10
MA0131.10.12559
MA0132.10
MA0133.10
MA0135.10.304312
MA0136.10.0759094
MA0139.10.585192
MA0140.10.797927
MA0141.15.00184
MA0142.10.155551
MA0143.12.87767
MA0144.10.108522
MA0145.13.70021
MA0146.10.328227
MA0147.10.003339
MA0148.10.390676
MA0149.10.0540502
MA0062.20.0160535
MA0035.20.457865
MA0039.20.0111986
MA0138.20.11686
MA0002.20.542307
MA0137.20.291852
MA0104.20.00110619
MA0047.21.01344
MA0112.21.66249
MA0065.22.12407
MA0150.12.91152
MA0151.10
MA0152.10.817398
MA0153.11.67346
MA0154.11.48306
MA0155.10.907055
MA0156.10.146275
MA0157.11.3775
MA0158.10
MA0159.12.35634
MA0160.11.13039
MA0161.10
MA0162.15.10396e-07
MA0163.12.10734
MA0164.10.103984
MA0080.20.253231
MA0018.20.0912146
MA0099.20.0598901
MA0079.26.56666e-05
MA0102.20.737926
MA0258.14.70528
MA0259.10.00382833
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

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