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{{Coexpression_clusters
{
|full_id=C2097_amniotic_Urothelial_esophagus_trachea_Sebocyte_Small_Prostate
 

Latest revision as of 11:58, 17 September 2013


Full id: C2097_amniotic_Urothelial_esophagus_trachea_Sebocyte_Small_Prostate



Phase1 CAGE Peaks

Hg19::chr11:118134950..118134961,-p6@MPZL2
Hg19::chr11:118134962..118134971,-p5@MPZL2
Hg19::chr11:118134982..118134993,-p2@MPZL2
Hg19::chr11:118134997..118135052,-p1@MPZL2


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.15e-26160
endoderm2.15e-26160
presumptive endoderm2.15e-26160
digestive system9.25e-21145
digestive tract9.25e-21145
primitive gut9.25e-21145
subdivision of digestive tract7.24e-19118
respiratory system1.35e-1574
anatomical cluster8.29e-15373
foregut2.25e-1487
respiratory tract4.02e-1354
adult organism4.07e-13114
multi-cellular organism1.31e-12656
embryo3.02e-12592
anatomical group3.23e-12625
anatomical system4.91e-12624
anatomical conduit6.29e-12240
developing anatomical structure6.67e-12581
respiratory primordium1.17e-1038
endoderm of foregut1.17e-1038
renal system2.00e-1048
urinary system structure3.56e-1047
organ3.77e-10503
endo-epithelium4.01e-1082
organ system subdivision2.68e-09223
organ part3.28e-09218
embryonic structure4.58e-09564
segment of respiratory tract4.87e-0947
multi-tissue structure4.89e-08342
blood vessel endothelium6.22e-0818
endothelium6.22e-0818
cardiovascular system endothelium6.22e-0818
simple squamous epithelium7.25e-0822
orifice7.51e-0836
germ layer9.53e-08560
germ layer / neural crest9.53e-08560
embryonic tissue9.53e-08560
presumptive structure9.53e-08560
germ layer / neural crest derived structure9.53e-08560
epiblast (generic)9.53e-08560
trunk region element1.51e-07101
larynx6.62e-079
upper respiratory tract6.94e-0719
Disease
Ontology termp-valuen
carcinoma2.61e-17106
squamous cell carcinoma2.67e-1014
cell type cancer3.09e-07143


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
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
MA0048.10.25531
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
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.12.50276
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
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
MA0114.11.98562
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
MA0139.11.63368
MA0140.10.779643
MA0141.11.46638
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.8309
MA0147.10.46175
MA0148.10.739888
MA0149.14.36159
MA0062.20.353589
MA0035.20.778873
MA0039.20.10559
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.13.7809
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.13.02177
MA0160.11.78721
MA0161.10
MA0162.10.0928415
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.21.85039
MA0079.20.0021048
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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
CEBPB#105147.971147625824820.0002476385788090830.00267540348942193
CTCF#1066445.360256373075030.001211145381643620.00815543600989544
E2F1#186944.907389214879320.001724022357361790.0106246044126104
FOSL2#2355416.93020060456171.2165416097647e-050.000303160079174936
GATA3#2625427.2365163572061.81561517799785e-066.74807948665185e-05
GTF2F1#2962412.73966087675773.79492332235515e-050.000716575658765956
HEY1#2346244.040111043105710.00375304636917980.018550137707088
RAD21#5885410.35503389545638.6948481184721e-050.00129080489359646
SMARCB1#6598418.25271578115749.00423392720929e-060.000240694442570722
SMC3#9126415.04493284493281.95092670935632e-050.000437050267263974
TAF1#687243.343046285745290.008005664898701650.0321195357979141
TBP#690843.706770687096390.005296377814784350.0243463205368954
ZNF263#1012748.221841637010680.0002187871180958320.00248071955561943



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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