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{{Coexpression_clusters
{
|full_id=C1113_heart_skeletal_smooth_bladder_penis_tongue_diaphragm
|

Latest revision as of 11:38, 17 September 2013


Full id: C1113_heart_skeletal_smooth_bladder_penis_tongue_diaphragm



Phase1 CAGE Peaks

Hg19::chr10:29923874..29923879,-p12@SVIL
Hg19::chr22:36291022..36291026,-p@chr22:36291022..36291026
-
Hg19::chr6:76203489..76203522,-p1@FILIP1
Hg19::chrX:33229600..33229611,-p7@DMD
Hg19::chrX:33229614..33229635,-p3@DMD
Hg19::chrX:33229636..33229651,-p4@DMD
Hg19::chrX:33229657..33229675,-p2@DMD


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:0043034costamere9.77416470118443e-07
GO:0030016myofibril8.2102983489949e-05
GO:0044449contractile fiber part8.2102983489949e-05
GO:0043292contractile fiber8.2102983489949e-05
GO:0007517muscle development0.00047912955365206
GO:0003779actin binding0.00259838023443736
GO:0043043peptide biosynthetic process0.00369591711616474
GO:0008092cytoskeletal protein binding0.00369591711616474
GO:0048513organ development0.00848267173866793
GO:0051693actin filament capping0.00848267173866793
GO:0051016barbed-end actin filament capping0.00848267173866793
GO:0030835negative regulation of actin filament depolymerization0.00848267173866793
GO:0016010dystrophin-associated glycoprotein complex0.00848267173866793
GO:0030834regulation of actin filament depolymerization0.00848267173866793
GO:0030042actin filament depolymerization0.00848267173866793
GO:0006518peptide metabolic process0.00961264662949734
GO:0005856cytoskeleton0.00961264662949734
GO:0005509calcium ion binding0.00961264662949734
GO:0048731system development0.00962668341602653
GO:0051015actin filament binding0.00962668341602653
GO:0005605basal lamina0.00962668341602653
GO:0008307structural constituent of muscle0.00962668341602653
GO:0008064regulation of actin polymerization and/or depolymerization0.00962668341602653
GO:0051261protein depolymerization0.00962668341602653
GO:0030832regulation of actin filament length0.00962668341602653
GO:0032535regulation of cellular component size0.00962668341602653
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.00962668341602653
GO:0051129negative regulation of cellular component organization and biogenesis0.0102696566719827
GO:0051493regulation of cytoskeleton organization and biogenesis0.0103217134077448
GO:0033043regulation of organelle organization and biogenesis0.0103217134077448
GO:0048856anatomical structure development0.010539812693488
GO:0008154actin polymerization and/or depolymerization0.010539812693488
GO:0007519skeletal muscle development0.0112247198530957
GO:0005604basement membrane0.0120315799077811
GO:0007275multicellular organismal development0.0122947402574183
GO:0005200structural constituent of cytoskeleton0.0130501615289126
GO:0014706striated muscle development0.0131450187455632
GO:0051128regulation of cellular component organization and biogenesis0.0145418564873345
GO:0051248negative regulation of protein metabolic process0.0147348790925255
GO:0043232intracellular non-membrane-bound organelle0.0169329059648885
GO:0043228non-membrane-bound organelle0.0169329059648885
GO:0044420extracellular matrix part0.0172276867122797
GO:0003012muscle system process0.0202706437938474
GO:0006936muscle contraction0.0202706437938474
GO:0032502developmental process0.0202706437938474
GO:0005886plasma membrane0.0253086085924412
GO:0032501multicellular organismal process0.0253086085924412
GO:0030036actin cytoskeleton organization and biogenesis0.0283737756670157
GO:0030029actin filament-based process0.0292519804867804
GO:0015629actin cytoskeleton0.0326188506973571
GO:0044444cytoplasmic part0.0336695570485764
GO:0005578proteinaceous extracellular matrix0.0437898899623931
GO:0051246regulation of protein metabolic process0.0437898899623931
GO:0009892negative regulation of metabolic process0.0443956015287848



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
muscle precursor cell7.57e-0758
myoblast7.57e-0758
multi-potent skeletal muscle stem cell7.57e-0758
Uber Anatomy
Ontology termp-valuen
adult organism1.67e-45114
multi-tissue structure3.20e-19342
structure with developmental contribution from neural crest2.36e-13132
anatomical cluster2.40e-13373
neural tube7.28e-1356
neural rod7.28e-1356
future spinal cord7.28e-1356
neural keel7.28e-1356
multi-cellular organism2.26e-12656
anatomical conduit3.02e-12240
regional part of nervous system2.89e-1153
regional part of brain2.89e-1153
primary circulatory organ3.25e-1127
neural plate4.16e-1182
presumptive neural plate4.16e-1182
organ system subdivision8.41e-11223
brain9.09e-1168
future brain9.09e-1168
central nervous system1.24e-1081
muscle tissue2.66e-1064
musculature2.66e-1064
musculature of body2.66e-1064
epithelium4.68e-10306
tube4.77e-10192
cell layer5.90e-10309
neurectoderm6.20e-1086
embryonic structure9.20e-10564
germ layer9.48e-10560
germ layer / neural crest9.48e-10560
embryonic tissue9.48e-10560
presumptive structure9.48e-10560
germ layer / neural crest derived structure9.48e-10560
epiblast (generic)9.48e-10560
nervous system1.44e-0989
regional part of forebrain2.15e-0941
forebrain2.15e-0941
anterior neural tube2.15e-0941
future forebrain2.15e-0941
skeletal muscle tissue4.13e-0962
striated muscle tissue4.13e-0962
myotome4.13e-0962
heart7.50e-0924
primitive heart tube7.50e-0924
primary heart field7.50e-0924
anterior lateral plate mesoderm7.50e-0924
heart tube7.50e-0924
heart primordium7.50e-0924
cardiac mesoderm7.50e-0924
cardiogenic plate7.50e-0924
heart rudiment7.50e-0924
developing anatomical structure9.08e-09581
embryo1.38e-08592
anatomical system1.71e-08624
anatomical group2.15e-08625
tissue6.24e-08773
organ1.15e-07503
ecto-epithelium2.27e-07104
dense mesenchyme tissue2.70e-0773
paraxial mesoderm6.72e-0772
presumptive paraxial mesoderm6.72e-0772
brain grey matter6.99e-0734
gray matter6.99e-0734


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)
MA0003.10.00215847
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0156227
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.12.23229
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.382278
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.362619
MA0056.10
MA0057.11.22064
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.11.51089
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.000265001
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.12.24713
MA0084.11.48179
MA0087.13.55906
MA0088.10.538456
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.340955
MA0106.10.648997
MA0107.10.752965
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.12.46913
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.0807715
MA0146.10.0127148
MA0147.10.281049
MA0148.12.2535
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.00276064
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.21.53797
MA0112.20.0758925
MA0065.20.0828768
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.071478
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.0249953
MA0163.10.0167306
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.21.40221
MA0079.20.000432051
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
FOS#235345.141688747939660.004042095865678250.0193470417101545
STAT1#6772411.83233571268530.0001690950295571690.00206647739198704
STAT3#677469.016684283275064.74133156431288e-060.000147155996209591



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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