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{{Coexpression_clusters
{
|full_id=C395_Synoviocyte_Cardiac_Fibroblast_mesothelioma_Endothelial_Chondrocyte_tenocyte

Latest revision as of 11:22, 17 September 2013


Full id: C395_Synoviocyte_Cardiac_Fibroblast_mesothelioma_Endothelial_Chondrocyte_tenocyte



Phase1 CAGE Peaks

Hg19::chr2:56094041..56094058,-p@chr2:56094041..56094058
-
Hg19::chr2:56094202..56094227,-p@chr2:56094202..56094227
-
Hg19::chr2:56098185..56098199,-p@chr2:56098185..56098199
-
Hg19::chr2:56102125..56102145,-p@chr2:56102125..56102145
-
Hg19::chr2:56102173..56102210,-p@chr2:56102173..56102210
-
Hg19::chr2:56103806..56103824,-p@chr2:56103806..56103824
-
Hg19::chr2:56104899..56104948,-p@chr2:56104899..56104948
-
Hg19::chr2:56104927..56104972,+p@chr2:56104927..56104972
+
Hg19::chr2:56104951..56104962,-p@chr2:56104951..56104962
-
Hg19::chr2:56104999..56105010,-p@chr2:56104999..56105010
-
Hg19::chr2:56108781..56108808,-p@chr2:56108781..56108808
-
Hg19::chr2:56108835..56108875,-p@chr2:56108835..56108875
-
Hg19::chr2:56144804..56144841,+p@chr2:56144804..56144841
+
Hg19::chr2:56144851..56144902,-p@chr2:56144851..56144902
-
Hg19::chr2:56144905..56144921,-p@chr2:56144905..56144921
-
Hg19::chr2:56144922..56144937,+p@chr2:56144922..56144937
+
Hg19::chr2:56144928..56144943,-p@chr2:56144928..56144943
-
Hg19::chr2:56144945..56144975,-p@chr2:56144945..56144975
-
Hg19::chr2:56145005..56145022,-p@chr2:56145005..56145022
-
Hg19::chr2:56145014..56145064,+p@chr2:56145014..56145064
+
Hg19::chr2:56145124..56145158,+p@chr2:56145124..56145158
+
Hg19::chr2:56145348..56145379,+p@chr2:56145348..56145379
+
Hg19::chr2:56149625..56149641,-p11@EFEMP1
Hg19::chr2:56149661..56149678,-p10@EFEMP1
Hg19::chr2:56150184..56150209,-p6@EFEMP1
Hg19::chr2:56150883..56150896,-p2@EFEMP1
Hg19::chr2:56150910..56150938,-p1@EFEMP1


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

No GOStat results

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 cell2.99e-25121
lining cell1.04e-1858
barrier cell1.04e-1858
endothelial cell of vascular tree1.45e-1824
blood vessel endothelial cell2.80e-1318
embryonic blood vessel endothelial progenitor cell2.80e-1318
meso-epithelial cell4.14e-1345
endothelial cell1.27e-1236
embryonic cell1.30e-11250
squamous epithelial cell9.93e-1163
muscle cell4.54e-1055
muscle precursor cell6.07e-0958
myoblast6.07e-0958
multi-potent skeletal muscle stem cell6.07e-0958
fibroblast1.19e-0876
contractile cell1.34e-0859
vascular associated smooth muscle cell1.64e-0832
endothelial cell of artery2.23e-089
electrically responsive cell5.96e-0861
electrically active cell5.96e-0861
smooth muscle cell6.53e-0843
smooth muscle myoblast6.53e-0843
lymphangioblast6.23e-076
endothelial cell of lymphatic vessel6.23e-076
vascular lymphangioblast6.23e-076
cardiocyte7.51e-0716
Uber Anatomy
Ontology termp-valuen
vasculature6.81e-2778
vascular system6.81e-2778
splanchnic layer of lateral plate mesoderm3.56e-2683
cardiovascular system1.37e-24109
vessel1.51e-2468
circulatory system6.66e-24112
epithelial tube open at both ends8.06e-2259
blood vessel8.06e-2259
blood vasculature8.06e-2259
vascular cord8.06e-2259
epithelial tube8.74e-18117
artery2.23e-1742
arterial blood vessel2.23e-1742
arterial system2.23e-1742
squamous epithelium2.79e-1425
blood vessel endothelium2.80e-1318
endothelium2.80e-1318
cardiovascular system endothelium2.80e-1318
simple squamous epithelium2.40e-1222
systemic artery4.99e-1233
systemic arterial system4.99e-1233
anatomical conduit6.08e-12240
unilaminar epithelium1.57e-10148
aorta1.58e-1021
aortic system1.58e-1021
anatomical cluster2.17e-10373
tube9.29e-10192
epithelium1.45e-09306
cell layer3.73e-09309
muscle tissue1.69e-0864
musculature1.69e-0864
musculature of body1.69e-0864
endothelial tube2.23e-089
arterial system endothelium2.23e-089
endothelium of artery2.23e-089
skeletal muscle tissue4.19e-0862
striated muscle tissue4.19e-0862
myotome4.19e-0862
heart1.50e-0724
primitive heart tube1.50e-0724
primary heart field1.50e-0724
anterior lateral plate mesoderm1.50e-0724
heart tube1.50e-0724
heart primordium1.50e-0724
cardiac mesoderm1.50e-0724
cardiogenic plate1.50e-0724
heart rudiment1.50e-0724
multi-cellular organism2.75e-07656
anatomical system3.28e-07624
anatomical group4.13e-07625
primary circulatory organ9.39e-0727


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)
MA0003.10.00741063
MA0004.10.115462
MA0006.10.167736
MA0007.10.105458
MA0009.10.45361
MA0014.10.000496059
MA0017.10.0582511
MA0019.10.596513
MA0024.10.959204
MA0025.10.570597
MA0027.12.00534
MA0028.10.0494049
MA0029.10.993942
MA0030.10.372472
MA0031.10.320773
MA0038.10.176878
MA0040.10.38667
MA0041.10.125771
MA0042.10.108251
MA0043.10.453881
MA0046.10.444311
MA0048.10.0995077
MA0050.10.108721
MA0051.10.174152
MA0052.11.01149
MA0055.10.0448426
MA0056.10
MA0057.10.18052
MA0058.10.0687016
MA0059.10.0681464
MA0060.10.0133608
MA0061.10.129432
MA0063.10
MA0066.10.177154
MA0067.10.739032
MA0068.10.00487684
MA0069.11.96401
MA0070.10.431528
MA0071.10.152483
MA0072.10.427724
MA0073.10.000409419
MA0074.10.173668
MA0076.10.0757217
MA0077.10.421218
MA0078.11.26004
MA0081.10.0682163
MA0083.10.460049
MA0084.10.916043
MA0087.10.425657
MA0088.10.0317537
MA0089.10
MA0090.10.280795
MA0091.10.116893
MA0092.10.659672
MA0093.10.0447606
MA0095.10
MA0098.10
MA0100.10.185942
MA0101.10.393842
MA0103.10.0405948
MA0105.10.26297
MA0106.10.204305
MA0107.10.472748
MA0108.20.853131
MA0109.10
MA0111.10.620854
MA0113.10.2156
MA0114.10.022641
MA0115.10.668285
MA0116.11.54613
MA0117.10.486035
MA0119.10.0614144
MA0122.10.50863
MA0124.10.630319
MA0125.10.554615
MA0130.10
MA0131.10.255226
MA0132.10
MA0133.10
MA0135.10.479757
MA0136.10.181467
MA0139.10.6495
MA0140.10.89891
MA0141.10.0674008
MA0142.11.45957
MA0143.10.215723
MA0144.10.0193859
MA0145.10.813115
MA0146.17.32986e-06
MA0147.10.0256229
MA0148.10.405671
MA0149.10.145006
MA0062.20.00844267
MA0035.20.150428
MA0039.22.9609e-08
MA0138.20.242899
MA0002.20.787856
MA0137.20.051801
MA0104.20.0630844
MA0047.21.08299
MA0112.20.0124735
MA0065.20.0157973
MA0150.10.273149
MA0151.10
MA0152.10.154883
MA0153.12.29145
MA0154.10.401974
MA0155.10.354736
MA0156.10.0526574
MA0157.10.755651
MA0158.10
MA0159.10.025786
MA0160.10.138224
MA0161.10
MA0162.10.0332526
MA0163.10.0292869
MA0164.10.63749
MA0080.20.0447905
MA0018.20.205249
MA0099.20.155103
MA0079.25.53526e-06
MA0102.20.951693
MA0258.10.201963
MA0259.10.0278251
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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