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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 12:23, 17 September 2013


Full id: C3302_Skeletal_diaphragm_skeletal_penis_throat_tongue_epididymis



Phase1 CAGE Peaks

Hg19::chr12:56547669..56547684,+p2@MYL6B
Hg19::chr1:201399016..201399025,-p4@TNNI1
Hg19::chr2:219696548..219696558,-p2@PRKAG3


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


p.valueFDRnGenesnPathwayName
8.64980401661253e-060.00547532594251573249Muscle contraction (Reactome):REACT_17044



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:0044449contractile fiber part0.000486784263842463
GO:0043292contractile fiber0.000486784263842463
GO:0003012muscle system process0.00163023820085446
GO:0006936muscle contraction0.00163023820085446
GO:0004679AMP-activated protein kinase activity0.00164252914164606
GO:0015629actin cytoskeleton0.00349803528037607
GO:0030049muscle filament sliding0.00513229919892161
GO:0033275actin-myosin filament sliding0.00513229919892161
GO:0005861troponin complex0.00547429132176457
GO:0016461unconventional myosin complex0.00574783667623449
GO:0006942regulation of striated muscle contraction0.00597160256409073
GO:0005865striated muscle thin filament0.00752604267770224
GO:0030048actin filament-based movement0.0101034090920804
GO:0005523tropomyosin binding0.0123117172763509
GO:0044430cytoskeletal part0.0125512755839534
GO:0005859muscle myosin complex0.0125512755839534
GO:0016460myosin II complex0.0125512755839534
GO:0006941striated muscle contraction0.0168386859144542
GO:0006937regulation of muscle contraction0.0168386859144542
GO:0008307structural constituent of muscle0.0172257490857199
GO:0030017sarcomere0.018745801989806
GO:0030016myofibril0.019754740012505
GO:0005856cytoskeleton0.0205045017426492
GO:0007519skeletal muscle development0.0221987265916081
GO:0003008system process0.0221987265916081
GO:0006633fatty acid biosynthetic process0.0230097446059705
GO:0016053organic acid biosynthetic process0.0242859114184931
GO:0046394carboxylic acid biosynthetic process0.0242859114184931
GO:0014706striated muscle development0.0248573624476498
GO:0016459myosin complex0.0292004645054482
GO:0007517muscle development0.0453379495687452
GO:0006631fatty acid metabolic process0.0484986753684516
GO:0030705cytoskeleton-dependent intracellular transport0.0484986753684516



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
skeletal muscle tissue2.42e-1662
striated muscle tissue2.42e-1662
myotome2.42e-1662
muscle tissue9.91e-1664
musculature9.91e-1664
musculature of body9.91e-1664
somite7.33e-1471
presomitic mesoderm7.33e-1471
presumptive segmental plate7.33e-1471
dermomyotome7.33e-1471
trunk paraxial mesoderm7.33e-1471
paraxial mesoderm1.27e-1372
presumptive paraxial mesoderm1.27e-1372
dense mesenchyme tissue2.15e-1373
epithelial vesicle2.49e-1278
throat2.70e-122
muscle structure2.70e-122
muscle organ2.70e-122
multilaminar epithelium2.14e-1183
organism subdivision5.20e-11264
trunk mesenchyme2.13e-10122
unilaminar epithelium7.43e-09148
chordate pharynx1.19e-0810
pharyngeal region of foregut1.19e-0810
tongue3.19e-083
gustatory system3.19e-083
future tongue3.19e-083
pharynx7.17e-0811
trunk2.77e-07199
penis4.58e-071
intromittent organ4.58e-071
lateral plate mesenchyme4.58e-071
undifferentiated genital tubercle4.58e-071
somatopleure4.58e-071
pharyngeal arch system4.68e-0718
mesenchyme4.97e-07160
entire embryonic mesenchyme4.97e-07160
hindlimb bud5.13e-071
soleus muscle5.13e-071
appendage5.13e-071
lower limb segment5.13e-071
multi-limb segment region5.13e-071
hindlimb muscle5.13e-071
hindlimb zeugopod muscle5.13e-071
paired limb/fin5.13e-071
limb5.13e-071
pelvic appendage5.13e-071
limb segment5.13e-071
paired limb/fin segment5.13e-071
limb muscle5.13e-071
pelvic complex muscle5.13e-071
zeugopod5.13e-071
muscle of leg5.13e-071
paired limb/fin bud5.13e-071
limb bud5.13e-071
pelvic appendage bud5.13e-071
limb/fin field5.13e-071
subdivision of organism along appendicular axis5.13e-071
appendage girdle complex5.13e-071
leg5.13e-071
hindlimb5.13e-071
triceps surae5.13e-071
hindlimb zeugopod5.13e-071
posterior region of body5.13e-071
pelvic complex5.13e-071
limb field5.13e-071
hindlimb/pelvic fin field5.13e-071
multi-tissue structure5.73e-07342
chest muscle6.08e-071
respiratory system muscle6.08e-071
skeletal muscle of trunk6.08e-071
respiratory system skeletal muscle6.08e-071
thoracic segment muscle6.08e-071
chest organ6.08e-071
muscle of trunk6.08e-071
diaphragm6.08e-071
future diaphragm6.08e-071


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)
MA0003.10.401049
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.11.23283
MA0061.10.456531
MA0063.10
MA0066.12.1667
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0834661
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.846801
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.12.29491
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.22.88736
MA0065.21.39232
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.12.48891
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.941469
MA0102.21.88331
MA0258.12.22591
MA0259.10.575594
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.