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

Latest revision as of 11:21, 17 September 2013


Full id: C365_trachea_throat_aorta_lung_parotid_salivary_umbilical



Phase1 CAGE Peaks

Hg19::chr10:13276329..13276338,-p3@UCMA
Hg19::chr10:13276352..13276361,-p2@UCMA
Hg19::chr10:13276368..13276379,-p1@UCMA
Hg19::chr11:34909983..34910006,-p@chr11:34909983..34910006
-
Hg19::chr12:10998450..10998451,+p@chr12:10998450..10998451
+
Hg19::chr12:119772810..119772834,+p4@CCDC60
Hg19::chr12:48390329..48390340,+p@chr12:48390329..48390340
+
Hg19::chr16:78056435..78056451,+p1@CLEC3A
Hg19::chr17:10276319..10276324,-p1@MYH13
Hg19::chr19:41620335..41620338,+p1@CYP2F1
Hg19::chr1:31196427..31196433,-p1@MATN1
Hg19::chr22:37215541..37215544,-p3@PVALB
Hg19::chr2:180524914..180524925,-p17@ZNF385B
Hg19::chr5:147261651..147261660,+p@chr5:147261651..147261660
+
Hg19::chr5:147526410..147526417,+p@chr5:147526410..147526417
+
Hg19::chr5:180017106..180017107,+p@chr5:180017106..180017107
+
Hg19::chr5:180017127..180017161,-p@chr5:180017127..180017161
-
Hg19::chr5:180017171..180017202,+p@chr5:180017171..180017202
+
Hg19::chr5:180017205..180017215,-p@chr5:180017205..180017215
-
Hg19::chr5:180017253..180017257,-p@chr5:180017253..180017257
-
Hg19::chr5:180017672..180017683,-p11@SCGB3A1
Hg19::chr5:180017691..180017700,-p8@SCGB3A1
Hg19::chr5:180017732..180017767,-p3@SCGB3A1
Hg19::chr5:180017818..180017830,-p7@SCGB3A1
Hg19::chr5:180018490..180018505,-p1@SCGB3A1
Hg19::chr5:180018695..180018706,-p9@SCGB3A1
Hg19::chr6:70937124..70937126,-p@chr6:70937124..70937126
-
Hg19::chr6:71012780..71012794,-p2@COL9A1
Hg19::chr7:75368627..75368651,+p@chr7:75368627..75368651
+
Hg19::chr9:38720126..38720131,-p@chr9:38720126..38720131
-


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:0005201extracellular matrix structural constituent0.000213322837143487
GO:0044421extracellular region part0.00111610238361664
GO:0005578proteinaceous extracellular matrix0.00282570299014515
GO:0048856anatomical structure development0.0121855798442595
GO:0005594collagen type IX0.0164400489879395
GO:0001501skeletal development0.017181818860989
GO:0048513organ development0.0205446175102198
GO:0005593FACIT collagen0.0205446175102198
GO:0030934anchoring collagen0.0273855671839068
GO:0001502cartilage condensation0.0291932207385848
GO:0032502developmental process0.0291932207385848
GO:0000146microfilament motor activity0.0291932207385848
GO:0048731system development0.0291932207385848
GO:0032982myosin filament0.0291932207385848
GO:0005863striated muscle thick filament0.0291932207385848
GO:0032501multicellular organismal process0.0351270622408377
GO:0005859muscle myosin complex0.0374187747719306
GO:0016460myosin II complex0.0374187747719306
GO:0050381unspecific monooxygenase activity0.0374187747719306
GO:0030424axon0.0459438181410297
GO:0051216cartilage development0.0459438181410297
GO:0006941striated muscle contraction0.0459438181410297



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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
open tracheal system trachea3.99e-412
throat8.98e-412
surface4.22e-211
trachea1.59e-127
respiratory airway1.59e-127
thoracic cavity element9.38e-1034
thoracic cavity9.38e-1034
thoracic segment organ1.74e-0935
neck5.57e-0910
respiratory primordium9.23e-0938
endoderm of foregut9.23e-0938
Disease
Ontology termp-valuen
vascular disease7.72e-211
ischemia7.72e-211
extrinsic cardiomyopathy7.72e-211
myocardial ischemia7.72e-211
myocardial infarction7.72e-211
heart disease4.09e-112


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)
MA0003.10.461974
MA0004.10.0961566
MA0006.10.134363
MA0007.13.40339
MA0009.11.07184
MA0014.10.563835
MA0017.10.391994
MA0019.10.180682
MA0024.10.332558
MA0025.10.531977
MA0027.11.95983
MA0028.10.0380705
MA0029.10.347825
MA0030.10.338746
MA0031.10.288912
MA0038.10.15256
MA0040.10.352485
MA0041.10.105506
MA0042.10.300789
MA0043.10.417784
MA0046.10.408463
MA0048.10.246211
MA0050.10.0900741
MA0051.10.457885
MA0052.10.355576
MA0055.10.988598
MA0056.10
MA0057.10.0611057
MA0058.10.0546193
MA0059.10.199599
MA0060.10.26456
MA0061.10.366893
MA0063.10
MA0066.10.464855
MA0067.10.697961
MA0068.10.134205
MA0069.10.405267
MA0070.10.396023
MA0071.10.407159
MA0072.10.392323
MA0073.10.0127432
MA0074.10.456761
MA0076.10.060743
MA0077.11.00303
MA0078.10.213745
MA0081.10.441387
MA0083.10.423797
MA0084.10.873335
MA0087.10.390315
MA0088.10.941584
MA0089.10
MA0090.10.066597
MA0091.10.0974512
MA0092.10.574995
MA0093.10.0341631
MA0095.10
MA0098.10
MA0100.10.161006
MA0101.10.327739
MA0103.11.25547
MA0105.10.309448
MA0106.11.60312
MA0107.10.0779652
MA0108.21.42513
MA0109.10
MA0111.10.252572
MA0113.10.55303
MA0114.10.0743075
MA0115.10.62811
MA0116.10.969948
MA0117.10.449155
MA0119.12.6433
MA0122.10.471243
MA0124.10.590699
MA0125.10.516292
MA0130.10
MA0131.10.226279
MA0132.10
MA0133.10
MA0135.10.443024
MA0136.10.156833
MA0139.10.0271546
MA0140.10.128473
MA0141.10.437416
MA0142.11.34679
MA0143.10.188919
MA0144.10.338277
MA0145.10.309666
MA0146.15.79754
MA0147.10.40624
MA0148.10.352161
MA0149.10.779104
MA0062.20.0300684
MA0035.20.402308
MA0039.21.84905
MA0138.21.806
MA0002.20.238419
MA0137.20.643617
MA0104.20.262823
MA0047.20.508505
MA0112.20.995408
MA0065.20.322824
MA0150.10.495826
MA0151.10
MA0152.10.412817
MA0153.10.501603
MA0154.10.636726
MA0155.11.72898
MA0156.10.15867
MA0157.10.245386
MA0158.10
MA0159.10.0835942
MA0160.10.751346
MA0161.10
MA0162.11.324
MA0163.12.01698
MA0164.10.196993
MA0080.20.585263
MA0018.20.179075
MA0099.20.132386
MA0079.22.82896
MA0102.20.908736
MA0258.11.51248
MA0259.10.0202561
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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