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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.473101572251134,

Latest revision as of 12:15, 17 September 2013


Full id: C2927_cholangiocellular_mesenchymal_Fibroblast_CD14_glioma_Preadipocyte_Melanocyte



Phase1 CAGE Peaks

Hg19::chr8:72756194..72756208,-p9@MSC
Hg19::chr8:72756213..72756243,-p5@MSC
Hg19::chr8:72756267..72756296,-p4@MSC
Hg19::chr8:72756380..72756427,-p8@MSC


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
multi fate stem cell5.82e-23427
somatic stem cell1.49e-22433
stem cell1.46e-20441
motile cell1.29e-14386
fibroblast3.04e-1476
mesenchymal cell4.26e-13354
stuff accumulating cell1.14e-1287
connective tissue cell1.51e-12361
muscle precursor cell2.23e-1258
myoblast2.23e-1258
multi-potent skeletal muscle stem cell2.23e-1258
muscle cell3.70e-1255
contractile cell3.23e-1159
non-terminally differentiated cell3.24e-11106
somatic cell1.00e-10588
monopoietic cell1.22e-1059
monocyte1.22e-1059
monoblast1.22e-1059
promonocyte1.22e-1059
smooth muscle cell2.34e-1043
smooth muscle myoblast2.34e-1043
macrophage dendritic cell progenitor7.64e-1061
electrically responsive cell8.62e-1061
electrically active cell8.62e-1061
defensive cell2.34e-0948
phagocyte2.34e-0948
vascular associated smooth muscle cell1.97e-0832
classical monocyte1.52e-0742
CD14-positive, CD16-negative classical monocyte1.52e-0742
myeloid lineage restricted progenitor cell2.91e-0766
cardiocyte3.63e-0716
granulocyte monocyte progenitor cell4.27e-0767
fat cell4.99e-0715
Uber Anatomy
Ontology termp-valuen
musculoskeletal system5.98e-16167
mesoderm1.70e-14315
mesoderm-derived structure1.70e-14315
presumptive mesoderm1.70e-14315
connective tissue3.06e-13371
somite2.23e-1271
presomitic mesoderm2.23e-1271
presumptive segmental plate2.23e-1271
dermomyotome2.23e-1271
trunk paraxial mesoderm2.23e-1271
paraxial mesoderm2.70e-1272
presumptive paraxial mesoderm2.70e-1272
dense mesenchyme tissue2.71e-1273
skeletal muscle tissue7.07e-1262
striated muscle tissue7.07e-1262
myotome7.07e-1262
muscle tissue1.24e-1164
musculature1.24e-1164
musculature of body1.24e-1164
epithelial vesicle2.09e-0978
multilaminar epithelium4.34e-0983
lateral plate mesoderm3.29e-08203
heart5.18e-0824
primitive heart tube5.18e-0824
primary heart field5.18e-0824
anterior lateral plate mesoderm5.18e-0824
heart tube5.18e-0824
heart primordium5.18e-0824
cardiac mesoderm5.18e-0824
cardiogenic plate5.18e-0824
heart rudiment5.18e-0824
primary circulatory organ1.45e-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)
MA0003.11.05935
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.10.244769
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.12.02223
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.11.98521
MA0058.10.605914
MA0059.11.47051
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.12.50276
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.14.40535
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.10.8309
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.20.10559
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.88496
MA0155.13.05999
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.11.57817
MA0163.10.918944
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.21.38179
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
BCLAF1#9774421.65264761012184.54636978835329e-060.000141991122705093
CTBP2#1488462.71700033932816.45042639894877e-083.96980602639841e-06
CTCF#1066445.360256373075030.001211145381643620.00820356783925535
CTCFL#140690314.80985576923080.0004996291767563340.00441125805995898
EBF1#187936.679850134926750.005184294118278910.024066250040845
ELF1#199744.258097958807540.003041525565781240.0161311135773221
MEF2A#4205418.74323090964418.0978922767748e-060.000224810146595982
NANOG#79923321.93358386075950.0001557535816382770.00196624541432612
PAX5#507935.002174148383370.01196533174786410.0435280672407669
POU2F2#545236.829593043306890.004860473775203740.0227776640316119
RAD21#5885410.35503389545638.6948481184721e-050.00130097599232823
SMC3#9126311.28369963369960.001115802366868050.00766061552677707
SPI1#668836.153242631392040.006580387113059030.0281152450376686
TAF1#687243.343046285745290.008005664898701650.0323456859590507
TCF12#693837.975848676639820.003090920396013070.0162905044024631
YY1#752844.911170749853860.00171871838055440.0107107362579343
ZNF143#7702310.12565741417090.001534861610688180.0097713752976936
ZNF263#1012748.221841637010680.0002187871180958320.00250108448191885



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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