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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=1.20626728614416

Latest revision as of 11:23, 17 September 2013


Full id: C470_Adipocyte_Preadipocyte_Smooth_Fibroblast_aorta_normal_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr14:92336119..92336144,-p18@FBLN5
Hg19::chr14:92336334..92336351,-p22@FBLN5
Hg19::chr14:92336363..92336402,-p17@FBLN5
Hg19::chr14:92343879..92343891,-p@chr14:92343879..92343891
-
Hg19::chr14:92347684..92347698,-p@chr14:92347684..92347698
-
Hg19::chr14:92349351..92349365,-p@chr14:92349351..92349365
-
Hg19::chr14:92361339..92361353,-p@chr14:92361339..92361353
-
Hg19::chr14:92403359..92403409,+p@chr14:92403359..92403409
+
Hg19::chr14:92403378..92403403,-p@chr14:92403378..92403403
-
Hg19::chr14:92403405..92403440,-p@chr14:92403405..92403440
-
Hg19::chr14:92403450..92403483,-p@chr14:92403450..92403483
-
Hg19::chr14:92413677..92413688,-p12@FBLN5
Hg19::chr14:92413727..92413738,-p7@FBLN5
Hg19::chr14:92413748..92413762,-p1@FBLN5
Hg19::chr14:92413764..92413794,-p2@FBLN5
Hg19::chr14:92413800..92413837,-p4@FBLN5
Hg19::chr14:92414294..92414355,-p9@FBLN5
Hg19::chr15:89442263..89442298,-p@chr15:89442263..89442298
-
Hg19::chr19:38812519..38812533,-p@chr19:38812519..38812533
-
Hg19::chr4:88928828..88928841,+p3@PKD2
Hg19::chr5:151047146..151047178,-p4@SPARC


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:0007160cell-matrix adhesion0.00182617469241869
GO:0031589cell-substrate adhesion0.00182617469241869
GO:0005509calcium ion binding0.00352400893404339
GO:0050982detection of mechanical stimulus0.0088744333492283
GO:0005932basal body0.0101810085027996
GO:0005578proteinaceous extracellular matrix0.0101810085027996
GO:0009612response to mechanical stimulus0.0204284640188069
GO:0007368determination of left/right symmetry0.0204284640188069
GO:0009799determination of symmetry0.0204284640188069
GO:0009855determination of bilateral symmetry0.0204284640188069
GO:0005518collagen binding0.0204284640188069
GO:0005248voltage-gated sodium channel activity0.0209774322652129
GO:0044421extracellular region part0.0209774322652129
GO:0022610biological adhesion0.0209774322652129
GO:0007155cell adhesion0.0209774322652129
GO:0048513organ development0.0241483101232616
GO:0007259JAK-STAT cascade0.0241483101232616
GO:0005247voltage-gated chloride channel activity0.0241483101232616
GO:0005178integrin binding0.0241483101232616
GO:0005929cilium0.0241483101232616
GO:0022844voltage-gated anion channel activity0.0241483101232616
GO:0009582detection of abiotic stimulus0.0241483101232616
GO:0044463cell projection part0.0241483101232616
GO:0009581detection of external stimulus0.0246171127198746
GO:0005272sodium channel activity0.0269354144139597
GO:0048731system development0.0305550245877575
GO:0008022protein C-terminus binding0.0305550245877575
GO:0005604basement membrane0.0305550245877575
GO:0043169cation binding0.0305550245877575
GO:0051606detection of stimulus0.0305550245877575
GO:0005254chloride channel activity0.0305550245877575
GO:0001503ossification0.0305550245877575
GO:0031214biomineral formation0.0305550245877575
GO:0046872metal ion binding0.0305550245877575
GO:0046849bone remodeling0.0305550245877575
GO:0043167ion binding0.0305550245877575
GO:0005253anion channel activity0.0305550245877575
GO:0007050cell cycle arrest0.0305550245877575
GO:0032403protein complex binding0.0305550245877575
GO:0048771tissue remodeling0.030967346229515
GO:0048856anatomical structure development0.0311067998750359
GO:0006874cellular calcium ion homeostasis0.0311067998750359
GO:0055074calcium ion homeostasis0.0311067998750359
GO:0005507copper ion binding0.0311067998750359
GO:0006875cellular metal ion homeostasis0.0311067998750359
GO:0055065metal ion homeostasis0.0311067998750359
GO:0007389pattern specification process0.0311067998750359
GO:0044420extracellular matrix part0.0321715484447625
GO:0005815microtubule organizing center0.0351465779076556
GO:0007275multicellular organismal development0.0351465779076556
GO:0009628response to abiotic stimulus0.0380995966342028
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0398871888862169
GO:0055066di-, tri-valent inorganic cation homeostasis0.0398871888862169
GO:0006816calcium ion transport0.0398871888862169
GO:0030003cellular cation homeostasis0.0415848374287668
GO:0055080cation homeostasis0.0415848374287668
GO:0001501skeletal development0.0415848374287668
GO:0008509anion transmembrane transporter activity0.0415848374287668
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0415848374287668
GO:0005515protein binding0.0415848374287668
GO:0045786negative regulation of progression through cell cycle0.0433601492881494
GO:0005625soluble fraction0.0435163738114841
GO:0055082cellular chemical homeostasis0.0435163738114841
GO:0006873cellular ion homeostasis0.0435163738114841
GO:0015674di-, tri-valent inorganic cation transport0.0446416026002452
GO:0022843voltage-gated cation channel activity0.0453784752599863
GO:0050801ion homeostasis0.0467881969022059



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
fibroblast2.41e-3276
skin fibroblast2.81e-1523
preadipocyte2.48e-1012
muscle precursor cell7.68e-0958
myoblast7.68e-0958
multi-potent skeletal muscle stem cell7.68e-0958
fat cell7.88e-0915
multi fate stem cell6.70e-08427
muscle cell1.20e-0755
somatic stem cell2.96e-07433
contractile cell6.54e-0759
Uber Anatomy
Ontology termp-valuen
surface structure3.81e-1499
integument3.36e-1346
integumental system3.36e-1346
dense mesenchyme tissue1.36e-1273
somite2.27e-1271
presomitic mesoderm2.27e-1271
presumptive segmental plate2.27e-1271
dermomyotome2.27e-1271
trunk paraxial mesoderm2.27e-1271
paraxial mesoderm5.59e-1272
presumptive paraxial mesoderm5.59e-1272
skin of body2.37e-1041
muscle tissue4.58e-1064
musculature4.58e-1064
musculature of body4.58e-1064
epithelial vesicle6.89e-1078
multilaminar epithelium7.99e-1083
organism subdivision1.37e-09264
skeletal muscle tissue1.45e-0962
striated muscle tissue1.45e-0962
myotome1.45e-0962
adipose tissue1.35e-0814
trunk mesenchyme1.84e-08122
organ component layer1.02e-0766
tissue2.06e-07773
mesenchyme2.29e-07160
entire embryonic mesenchyme2.29e-07160
omentum3.03e-076
peritoneum3.03e-076
abdominal cavity3.03e-076
visceral peritoneum3.03e-076
cavity lining4.46e-0712
serous membrane4.46e-0712
trunk5.56e-07199


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)
MA0003.10.0960623
MA0004.10.505176
MA0006.10.264032
MA0007.10.474974
MA0009.10.543169
MA0014.10.0296553
MA0017.10.0964051
MA0019.10.757112
MA0024.10.450307
MA0025.10.665335
MA0027.12.11401
MA0028.10.598774
MA0029.10.467171
MA0030.10.457153
MA0031.10.401568
MA0038.10.24162
MA0040.10.472301
MA0041.10.181587
MA0042.10.160318
MA0043.10.543454
MA0046.10.533373
MA0048.11.91674
MA0050.10.160894
MA0051.10.238478
MA0052.10.475699
MA0055.11.18698
MA0056.10
MA0057.10.00555109
MA0058.10.110291
MA0059.10.718209
MA0060.10.122116
MA0061.10.0219462
MA0063.10
MA0066.10.678752
MA0067.10.83875
MA0068.10.168508
MA0069.10.529912
MA0070.10.519883
MA0071.10.611515
MA0072.10.515863
MA0073.10.200932
MA0074.10.23792
MA0076.10.119431
MA0077.10.508982
MA0078.10.31524
MA0081.10.354412
MA0083.11.35561
MA0084.12.32484
MA0087.11.27862
MA0088.10.0904746
MA0089.10
MA0090.13.26896
MA0091.10.981778
MA0092.11.41571
MA0093.10.268179
MA0095.10
MA0098.10
MA0100.10.702151
MA0101.10.0794742
MA0103.10.536497
MA0105.10.0246233
MA0106.10.750238
MA0107.10.046982
MA0108.22.72787
MA0109.10
MA0111.10.423052
MA0113.10.779331
MA0114.10.17185
MA0115.10.766188
MA0116.10.719614
MA0117.10.577217
MA0119.10.100647
MA0122.10.600851
MA0124.12.8938
MA0125.10.648747
MA0130.10
MA0131.10.878923
MA0132.10
MA0133.10
MA0135.10.570637
MA0136.10.246897
MA0139.10.0845536
MA0140.10.606998
MA0141.10.351584
MA0142.10.374765
MA0143.10.285827
MA0144.10.64066
MA0145.10.543498
MA0146.10.0432698
MA0147.10.049714
MA0148.10.546085
MA0149.10.204488
MA0062.20.22708
MA0035.20.605801
MA0039.20.050501
MA0138.20.316226
MA0002.20.110362
MA0137.21.03083
MA0104.20.0293723
MA0047.20.728835
MA0112.20.328246
MA0065.20.0482045
MA0150.10.124469
MA0151.10
MA0152.10.618168
MA0153.10.633172
MA0154.10.299683
MA0155.10.0886229
MA0156.10.620624
MA0157.10.352016
MA0158.10
MA0159.10.417407
MA0160.11.08448
MA0161.10
MA0162.10.0647873
MA0163.10.715927
MA0164.10.295453
MA0080.20.268297
MA0018.20.274004
MA0099.20.216352
MA0079.20.00728329
MA0102.21.05522
MA0258.11.3635
MA0259.10.435255
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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