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{{Coexpression_clusters
{
|full_id=C1972_Fibroblast_Synoviocyte_Endothelial_osteosarcoma_mature_cerebellum_alveolar
 

Latest revision as of 11:56, 17 September 2013


Full id: C1972_Fibroblast_Synoviocyte_Endothelial_osteosarcoma_mature_cerebellum_alveolar



Phase1 CAGE Peaks

Hg19::chr6:151646636..151646655,+p5@AKAP12
Hg19::chr6:151646657..151646671,+p8@AKAP12
Hg19::chr6:151646675..151646705,+p4@AKAP12
Hg19::chr6:151646706..151646717,+p11@AKAP12
Hg19::chr6:151646718..151646731,+p10@AKAP12


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>

Uber Anatomy
Ontology termp-valuen
cell layer8.03e-22309
epithelium1.05e-20306
vasculature2.43e-2078
vascular system2.43e-2078
anatomical cluster1.41e-17373
unilaminar epithelium4.29e-17148
epithelial tube4.40e-17117
vessel6.94e-1668
mesenchyme1.02e-14160
entire embryonic mesenchyme1.02e-14160
anatomical conduit2.45e-14240
multi-tissue structure8.29e-14342
epithelial tube open at both ends9.96e-1459
blood vessel9.96e-1459
blood vasculature9.96e-1459
vascular cord9.96e-1459
cardiovascular system1.02e-13109
circulatory system1.04e-13112
splanchnic layer of lateral plate mesoderm1.49e-1383
trunk mesenchyme6.06e-13122
multilaminar epithelium9.54e-1383
epithelial vesicle9.84e-1378
organism subdivision3.98e-12264
tube4.29e-12192
multi-cellular organism9.18e-12656
trunk1.19e-11199
somite1.75e-1171
presomitic mesoderm1.75e-1171
presumptive segmental plate1.75e-1171
dermomyotome1.75e-1171
trunk paraxial mesoderm1.75e-1171
dense mesenchyme tissue1.97e-1173
paraxial mesoderm2.68e-1172
presumptive paraxial mesoderm2.68e-1172
skeletal muscle tissue6.64e-1162
striated muscle tissue6.64e-1162
myotome6.64e-1162
muscle tissue7.13e-1164
musculature7.13e-1164
musculature of body7.13e-1164
anatomical system9.20e-11624
anatomical group1.53e-10625
squamous epithelium8.02e-1025
blood vessel endothelium3.36e-0918
endothelium3.36e-0918
cardiovascular system endothelium3.36e-0918
artery3.88e-0942
arterial blood vessel3.88e-0942
arterial system3.88e-0942
simple squamous epithelium2.67e-0822
systemic artery2.42e-0733
systemic arterial system2.42e-0733


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)
MA0003.10.136928
MA0004.13.75179
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.10.161847
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.12.63789
MA0042.12.52778
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.15.68124
MA0059.12.23433
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.14.57459
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.114.4978
MA0074.17.05643
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.14.06535
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.11.00065
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.11.25946
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.11.76068
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.938075
MA0145.10.442008
MA0146.10.0359558
MA0147.11.00307
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.22.8814
MA0138.20.837782
MA0002.20.30855
MA0137.22.08722
MA0104.22.35335
MA0047.20.767096
MA0112.20.136971
MA0065.20.449243
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.98952
MA0155.10.813062
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.13.53221
MA0163.10.168633
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.823998
MA0102.21.66336
MA0258.10.345771
MA0259.11.02361
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
ATF3#467522.46317452600871.74638470646713e-079.5793420356471e-06
E2F1#186943.925911371903460.007214984547106360.029882843080395
E2F6#187655.017155731697390.0003144978599297790.00323254030048284
EGR1#195854.988179094810140.0003237398000590710.00331123895586812
GTF2B#2959531.94382993432423.00149609204784e-082.03951366530504e-06
MAX#414956.452555509007128.93743970843928e-050.00130803989028824
POLR3A#111285339.1321100917432.18870993324884e-133.30327567512392e-11
STAT1#6772520.70658749719922.62418353652031e-071.35542583763919e-05
STAT3#6774510.51946499715427.759040745861e-060.000220682586181094
TCF7L2#6934510.77017656313736.89693748574565e-060.000200141498770155
USF1#739156.361499277207969.59569864925045e-050.00137076346769124
USF2#7392512.99219738506962.69963551658264e-069.43914408156594e-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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