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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.264767995087781,

Latest revision as of 11:40, 17 September 2013


Full id: C1220_Mesenchymal_Fibroblast_Renal_Alveolar_Trabecular_Smooth_Hepatic



Phase1 CAGE Peaks

Hg19::chr16:31483374..31483390,+p2@TGFB1I1
Hg19::chr19:4400432..4400570,-p1@SH3GL1
Hg19::chr8:22423168..22423206,+p4@SORBS3
Hg19::chr8:22423219..22423330,+p1@SORBS3
Hg19::chr8:22423457..22423476,+p9@SORBS3
Hg19::chr8:22423479..22423528,+p2@SORBS3
Hg19::chr8:22423529..22423543,+p7@SORBS3


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:0051496positive regulation of stress fiber formation0.00953586230242861
GO:0051495positive regulation of cytoskeleton organization and biogenesis0.00953586230242861
GO:0032233positive regulation of actin filament bundle formation0.00953586230242861
GO:0017166vinculin binding0.00953586230242861
GO:0030054cell junction0.00953586230242861
GO:0008134transcription factor binding0.00953586230242861
GO:0051492regulation of stress fiber formation0.00953586230242861
GO:0032231regulation of actin filament bundle formation0.00953586230242861
GO:0043149stress fiber formation0.00988875127094105
GO:0043410positive regulation of MAPKKK cascade0.0101709875930319
GO:0006366transcription from RNA polymerase II promoter0.0137426466736377
GO:0051130positive regulation of cellular component organization and biogenesis0.0146666708048605
GO:0043408regulation of MAPKKK cascade0.0146666708048605
GO:0031901early endosome membrane0.0154340161621278
GO:0051017actin filament bundle formation0.016098849256612
GO:0050681androgen receptor binding0.0174741809876831
GO:0048522positive regulation of cellular process0.0177970360144775
GO:0022610biological adhesion0.0177970360144775
GO:0007155cell adhesion0.0177970360144775
GO:0035258steroid hormone receptor binding0.0179571336086724
GO:0048518positive regulation of biological process0.0179571336086724
GO:0030521androgen receptor signaling pathway0.0179571336086724
GO:0005925focal adhesion0.0179571336086724
GO:0048523negative regulation of cellular process0.0179571336086724
GO:0005924cell-substrate adherens junction0.0179571336086724
GO:0007165signal transduction0.0179571336086724
GO:0030055cell-matrix junction0.0179571336086724
GO:0048519negative regulation of biological process0.0179571336086724
GO:0007015actin filament organization0.0179571336086724
GO:0016363nuclear matrix0.0182556209063587
GO:0005769early endosome0.0182556209063587
GO:0007154cell communication0.0182556209063587
GO:0030518steroid hormone receptor signaling pathway0.0182556209063587
GO:0005912adherens junction0.0182556209063587
GO:0030522intracellular receptor-mediated signaling pathway0.0182556209063587
GO:0035257nuclear hormone receptor binding0.0182556209063587
GO:0051493regulation of cytoskeleton organization and biogenesis0.0182556209063587
GO:0033043regulation of organelle organization and biogenesis0.0182556209063587
GO:0051427hormone receptor binding0.0182556209063587
GO:0005856cytoskeleton0.0182556209063587
GO:0005200structural constituent of cytoskeleton0.0247925546529704
GO:0016323basolateral plasma membrane0.0247925546529704
GO:0044440endosomal part0.0247925546529704
GO:0010008endosome membrane0.0247925546529704
GO:0051128regulation of cellular component organization and biogenesis0.028176292534052
GO:0031589cell-substrate adhesion0.0283881677841821
GO:0007242intracellular signaling cascade0.0295528142016561
GO:0005737cytoplasm0.0320387244708274
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.032836619654347
GO:0016055Wnt receptor signaling pathway0.036521136109633
GO:0044459plasma membrane part0.036521136109633
GO:0000165MAPKKK cascade0.036521136109633
GO:0009967positive regulation of signal transduction0.036545466937897
GO:0003713transcription coactivator activity0.0427683417257407
GO:0005768endosome0.0427683417257407
GO:0010324membrane invagination0.0427683417257407
GO:0006897endocytosis0.0427683417257407
GO:0043231intracellular membrane-bound organelle0.0427683417257407
GO:0043227membrane-bound organelle0.0427683417257407
GO:0045892negative regulation of transcription, DNA-dependent0.0427683417257407
GO:0005515protein binding0.0439555903333185
GO:0045893positive regulation of transcription, DNA-dependent0.0451167438222109
GO:0008285negative regulation of cell proliferation0.0451167438222109
GO:0007417central nervous system development0.0455739196306436
GO:0043232intracellular non-membrane-bound organelle0.0455739196306436
GO:0043228non-membrane-bound organelle0.0455739196306436
GO:0030036actin cytoskeleton organization and biogenesis0.0465410336754617
GO:0030029actin filament-based process0.0482515979559621
GO:0016020membrane0.0492796510940489



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
mesodermal cell2.30e-29121
embryonic cell3.30e-27250
contractile cell2.79e-2059
muscle precursor cell6.89e-1958
myoblast6.89e-1958
multi-potent skeletal muscle stem cell6.89e-1958
muscle cell1.31e-1855
fibroblast2.77e-1876
non-terminally differentiated cell2.28e-17106
smooth muscle cell2.80e-1643
smooth muscle myoblast2.80e-1643
electrically responsive cell4.49e-1661
electrically active cell4.49e-1661
somatic cell2.62e-13588
vascular associated smooth muscle cell2.42e-1232
meso-epithelial cell3.22e-1145
endothelial cell3.07e-1036
lining cell4.81e-1058
barrier cell4.81e-1058
animal cell3.97e-09679
eukaryotic cell3.97e-09679
blood vessel endothelial cell1.36e-0818
embryonic blood vessel endothelial progenitor cell1.36e-0818
endothelial cell of vascular tree2.74e-0824
cardiocyte5.79e-0716
Uber Anatomy
Ontology termp-valuen
splanchnic layer of lateral plate mesoderm2.90e-2583
vasculature9.75e-2478
vascular system9.75e-2478
epithelial vesicle1.67e-2378
epithelial tube7.43e-22117
mesenchyme2.66e-21160
entire embryonic mesenchyme2.66e-21160
vessel4.29e-2168
epithelial tube open at both ends6.21e-2159
blood vessel6.21e-2159
blood vasculature6.21e-2159
vascular cord6.21e-2159
unilaminar epithelium3.33e-20148
somite6.08e-2071
presomitic mesoderm6.08e-2071
presumptive segmental plate6.08e-2071
dermomyotome6.08e-2071
trunk paraxial mesoderm6.08e-2071
multilaminar epithelium7.05e-2083
dense mesenchyme tissue9.55e-2073
paraxial mesoderm2.07e-1972
presumptive paraxial mesoderm2.07e-1972
organism subdivision2.03e-18264
cardiovascular system4.97e-18109
circulatory system7.51e-18112
trunk mesenchyme1.26e-17122
skeletal muscle tissue1.58e-1762
striated muscle tissue1.58e-1762
myotome1.58e-1762
artery2.65e-1742
arterial blood vessel2.65e-1742
arterial system2.65e-1742
cell layer3.14e-17309
muscle tissue7.27e-1764
musculature7.27e-1764
musculature of body7.27e-1764
epithelium1.31e-16306
trunk4.65e-16199
multi-cellular organism6.83e-16656
anatomical system1.57e-13624
anatomical group3.12e-13625
multi-tissue structure4.69e-13342
anatomical cluster5.70e-13373
systemic artery1.04e-1233
systemic arterial system1.04e-1233
surface structure8.47e-1199
anatomical conduit2.08e-09240
compound organ3.70e-0968
blood vessel endothelium1.36e-0818
endothelium1.36e-0818
cardiovascular system endothelium1.36e-0818
squamous epithelium1.75e-0825
integument1.97e-0846
integumental system1.97e-0846
mesoderm2.51e-08315
mesoderm-derived structure2.51e-08315
presumptive mesoderm2.51e-08315
simple squamous epithelium2.94e-0822
developing anatomical structure3.16e-08581
embryo4.18e-08592
tube1.76e-07192
aorta2.72e-0721
aortic system2.72e-0721
skin of body4.98e-0741
embryonic structure7.75e-07564


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)
MA0003.15.48657
MA0004.10.502801
MA0006.10.341337
MA0007.13.11883
MA0009.10.973289
MA0014.14.31657
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.12.53091
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.766755
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.0407081
MA0056.10
MA0057.10.744639
MA0058.10.406232
MA0059.11.04442
MA0060.10.224688
MA0061.12.43031
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.672652
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.11.37625
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
MA0105.12.96525
MA0106.10.648997
MA0107.10.752965
MA0108.20.806528
MA0109.10
MA0111.11.14351
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.760835
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.11.65047
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.0807715
MA0146.14.0644
MA0147.11.40486
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.21.4671
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.21.85658
MA0047.20.636643
MA0112.20.262665
MA0065.20.591589
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.685508
MA0155.11.36741
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.13.0847
MA0163.18.64005
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.26.42888
MA0102.21.51913
MA0258.10.245543
MA0259.10.787775
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
CCNT2#90554.525858269259020.00155157330626470.009856737502006
E2F1#186964.206333612753710.0004135232017007640.00393799121568579
FOSL1#8061528.36684265455222.03338323682158e-071.09862654873466e-05
POLR2A#543072.147453176558070.004747636447610280.0223431147689244
ZBTB7A#5134166.301636549607913.91424956694869e-050.000731437306356332
ZNF143#7702611.57217990190961.08146108094101e-064.49986907698796e-05



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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