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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=-0.

Latest revision as of 11:58, 17 September 2013


Full id: C2083_Placental_acantholytic_Amniotic_Endothelial_Tracheal_Urothelial_Fibroblast



Phase1 CAGE Peaks

Hg19::chr10:97050727..97050740,-p3@PDLIM1
Hg19::chr10:97050749..97050772,-p1@PDLIM1
Hg19::chr10:97050777..97050806,-p2@PDLIM1
Hg19::chr10:97050816..97050825,-p4@PDLIM1


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
endoderm-derived structure4.32e-21160
endoderm4.32e-21160
presumptive endoderm4.32e-21160
digestive system5.42e-17145
digestive tract5.42e-17145
primitive gut5.42e-17145
epithelial tube1.30e-16117
organism subdivision5.69e-14264
anatomical cluster1.45e-13373
circulatory system1.81e-13112
subdivision of digestive tract3.35e-13118
unilaminar epithelium1.76e-12148
splanchnic layer of lateral plate mesoderm1.84e-1283
surface structure2.00e-1299
cardiovascular system2.70e-12109
vasculature6.86e-1278
vascular system6.86e-1278
primordium2.30e-11160
multi-tissue structure8.25e-10342
vessel8.32e-1068
anatomical conduit3.14e-09240
endo-epithelium5.16e-0982
trunk5.72e-09199
compound organ7.39e-0968
cell layer2.24e-08309
orifice3.69e-0836
foregut4.01e-0887
trunk mesenchyme4.01e-08122
organ component layer5.02e-0866
subdivision of trunk5.33e-08112
epithelium5.56e-08306
mesenchyme8.16e-08160
entire embryonic mesenchyme8.16e-08160
epithelial tube open at both ends1.60e-0759
blood vessel1.60e-0759
blood vasculature1.60e-0759
vascular cord1.60e-0759
gut epithelium1.62e-0754
renal system1.70e-0748
primary circulatory organ1.74e-0727
urinary system structure2.38e-0747
simple squamous epithelium6.11e-0722
blood vessel endothelium9.04e-0718
endothelium9.04e-0718
cardiovascular system endothelium9.04e-0718


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)
MA0003.110
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.11.34758
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
MA0048.12.82503
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
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
MA0073.11.93422
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.11.9583
MA0101.10.539569
MA0103.10.521546
MA0105.11.90157
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.12.01976
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
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.12.41215
MA0146.14.2865
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.26.36864
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.23.12566
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.61785
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.14.24646
MA0163.13.83423
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.23.5408
MA0102.21.75932
MA0258.11.07498
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
CCNT2#90546.336201576962630.0006203100587215640.00511161134786346
CTCF#1066445.360256373075030.001211145381643620.0081543845096363
E2F1#186944.907389214879320.001724022357361790.0106233506980062
E2F6#187645.017155731697390.00157802193473060.00994851097677949
EGR1#195844.988179094810140.001615011500076050.0101254764111204
ELF1#199744.258097958807540.003041525565781240.0160512323680963
HEY1#2346244.040111043105710.00375304636917980.0185466267507698
MAX#414946.452555509007120.0005767613195645490.00484409935295552
PAX5#507946.669565531177830.0005052774169483260.00443041458724424
TAF1#687243.343046285745290.008005664898701650.0321146009739006
TBP#690843.706770687096390.005296377814784350.0243431062182926
YY1#752844.911170749853860.00171871838055440.0106598508787173
ZBTB7A#5134147.35190930787590.000342223540015990.00345896489845446



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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