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Coexpression cluster:C2918

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Full id: C2918_Mast_mesothelioma_spindle_mesodermal_myxofibrosarcoma_lens_neurofibroma



Phase1 CAGE Peaks

  Short description
Hg19::chr8:13133974..13133985,- p13@DLC1
Hg19::chr8:13134001..13134011,- p14@DLC1
Hg19::chr8:13134015..13134038,- p2@DLC1
Hg19::chr8:13134045..13134063,- p5@DLC1


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Uber Anatomy
Ontology termp-valuen
cell layer2.44e-24309
vasculature2.45e-2378
vascular system2.45e-2378
epithelial tube4.20e-23117
epithelium4.39e-23306
anatomical conduit4.50e-20240
vessel3.16e-1968
unilaminar epithelium6.23e-19148
tube7.78e-19192
epithelial tube open at both ends2.85e-1759
blood vessel2.85e-1759
blood vasculature2.85e-1759
vascular cord2.85e-1759
splanchnic layer of lateral plate mesoderm6.28e-1783
circulatory system3.36e-16112
cardiovascular system4.31e-16109
anatomical cluster8.87e-16373
epithelial vesicle1.10e-1578
trunk mesenchyme3.41e-15122
artery2.02e-1442
arterial blood vessel2.02e-1442
arterial system2.02e-1442
mesenchyme2.25e-14160
entire embryonic mesenchyme2.25e-14160
multi-cellular organism3.54e-14656
anatomical system6.90e-14624
multi-tissue structure7.61e-14342
organism subdivision9.82e-14264
anatomical group1.25e-13625
dense mesenchyme tissue2.94e-1373
somite5.67e-1371
presomitic mesoderm5.67e-1371
presumptive segmental plate5.67e-1371
dermomyotome5.67e-1371
trunk paraxial mesoderm5.67e-1371
paraxial mesoderm6.96e-1372
presumptive paraxial mesoderm6.96e-1372
trunk1.41e-12199
multilaminar epithelium2.10e-1183
systemic artery8.81e-1133
systemic arterial system8.81e-1133
blood vessel endothelium3.18e-1018
endothelium3.18e-1018
cardiovascular system endothelium3.18e-1018
skeletal muscle tissue4.03e-1062
striated muscle tissue4.03e-1062
myotome4.03e-1062
muscle tissue7.67e-1064
musculature7.67e-1064
musculature of body7.67e-1064
simple squamous epithelium5.73e-0922
aorta9.48e-0921
aortic system9.48e-0921
integument2.12e-0846
integumental system2.12e-0846
squamous epithelium3.15e-0825
surface structure7.26e-0899
structure with developmental contribution from neural crest7.99e-08132
skin of body4.44e-0741
germ layer4.60e-07560
germ layer / neural crest4.60e-07560
embryonic tissue4.60e-07560
presumptive structure4.60e-07560
germ layer / neural crest derived structure4.60e-07560
epiblast (generic)4.60e-07560
developing anatomical structure8.02e-07581


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.16.84463
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.896009
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
MA0055.12.526
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.214613
MA0074.11.91637
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
MA0093.11.32557
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.12.23207
MA0105.10.656404
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
MA0119.18.90259
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.13.39971
MA0140.10.779643
MA0141.11.46638
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.10.061409
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.21.66396
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.79838
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.12.98688
MA0161.10
MA0162.11.06783
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.21.85039
MA0079.20.00910927
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CEBPB#105147.971147625824820.0002476385788090830.0026881951493859
CHD2#1106410.34402283411698.73193255208051e-050.00129391927327857
E2F1#186944.907389214879320.001724022357361790.0106838646520209
ELF1#199744.258097958807540.003041525565781240.0161302944480083
EP300#203346.77394172622320.0004748459821442640.00435594550102458
FOS#235348.99795530889440.0001525147711168630.00195561573734488
FOSL2#2355416.93020060456171.2165416097647e-050.000304467743067854
FOXA1#3169411.08141974938556.62943068949433e-050.0010737765381205
HDAC2#3066413.41562023662633.0859005065161e-050.000628855342439093
HEY1#2346244.040111043105710.00375304636917980.0186685278029515
HNF4A#3172423.13229036295373.48990320893214e-060.000115892528215473
JUN#3725412.51282919233634.07770316866756e-050.000745572901317352
JUND#372746.994663941871030.000417684217818580.00392748014988338
RAD21#5885410.35503389545638.6948481184721e-050.0013006033266186
REST#597849.650028716128020.0001152825614219170.0015761219311878
RXRA#6256420.07461713913336.1537798808435e-060.000182635583113218
SP1#666745.69838137814090.0009482606065333980.00685888146587309
TAF1#687243.343046285745290.008005664898701650.0323419323980931
TBP#690843.706770687096390.005296377814784350.0245124702028832
TCF7L2#6934410.77017656313737.42969445082454e-050.00115813411753681
USF1#739146.361499277207960.0006105011399140830.00509266202487915
ZNF263#1012748.221841637010680.0002187871180958320.00250081075044441



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.