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{{Coexpression_clusters
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|full_id=C2195_liposarcoma_Smooth_Fibroblast_CD14_giant_Hepatic_mesothelioma
|id=C2195
|ontology_enrichment_celltype=CL:0000222!7.88e-14!119;CL:0000055!4.67e-13!180;CL:0002057!5.04e-10!42;CL:0000057!1.04e-08!75;CL:0000359!2.07e-08!32;CL:0000860!7.70e-08!45;CL:0000183!1.19e-07!59;CL:0000192!1.44e-07!42;CL:0000514!1.44e-07!42;CL:0000077!1.45e-07!19;CL:0002009!2.48e-07!65;CL:0000680!4.65e-07!57;CL:0000056!4.65e-07!57;CL:0000355!4.65e-07!57;CL:0002194!8.94e-07!63;CL:0000576!8.94e-07!63;CL:0000040!8.94e-07!63;CL:0000559!8.94e-07!63
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000468!4.67e-17!659;UBERON:0000467!8.40e-17!625;UBERON:0000480!1.89e-16!626;UBERON:0000475!1.58e-14!365;UBERON:0000025!2.09e-14!194;UBERON:0003081!2.78e-14!216;UBERON:0001637!4.24e-14!42;UBERON:0003509!4.24e-14!42;UBERON:0004572!4.24e-14!42;UBERON:0003914!4.62e-14!118;UBERON:0000926!4.98e-13!448;UBERON:0004120!4.98e-13!448;UBERON:0006603!4.98e-13!448;UBERON:0000062!6.72e-13!511;UBERON:0000119!7.95e-13!312;UBERON:0000483!4.10e-12!309;UBERON:0000923!5.22e-12!604;UBERON:0005291!5.22e-12!604;UBERON:0006598!5.22e-12!604;UBERON:0002532!5.22e-12!604;UBERON:0002050!6.50e-12!605;UBERON:0005423!6.50e-12!605;UBERON:0001981!1.29e-11!60;UBERON:0007500!1.29e-11!60;UBERON:0004537!1.29e-11!60;UBERON:0006965!1.29e-11!60;UBERON:0004573!3.63e-11!33;UBERON:0004571!3.63e-11!33;UBERON:0002049!6.41e-11!79;UBERON:0007798!6.41e-11!79;UBERON:0000922!6.57e-11!612;UBERON:0004111!9.26e-11!241;UBERON:0004872!1.26e-10!84;UBERON:0002100!2.27e-10!216;UBERON:0002204!2.74e-10!167;UBERON:0000477!8.47e-10!286;UBERON:0000055!3.10e-09!69;UBERON:0005256!3.44e-09!143;UBERON:0004290!3.19e-08!70;UBERON:0001134!4.89e-08!61;UBERON:0002036!4.89e-08!61;UBERON:0003082!4.89e-08!61;UBERON:0000481!6.55e-08!347;UBERON:0002385!6.99e-08!63;UBERON:0001015!6.99e-08!63;UBERON:0000383!6.99e-08!63;UBERON:0000490!2.68e-07!138;UBERON:0001009!4.74e-07!113;UBERON:0000914!5.20e-07!83;UBERON:0002329!5.20e-07!83;UBERON:0003077!5.20e-07!83;UBERON:0003059!5.20e-07!83;UBERON:0007282!5.20e-07!83;UBERON:0009618!5.20e-07!83;UBERON:0007285!5.20e-07!83;UBERON:0004535!8.89e-07!110
}}

Latest revision as of 12:00, 17 September 2013


Full id: C2195_liposarcoma_Smooth_Fibroblast_CD14_giant_Hepatic_mesothelioma



Phase1 CAGE Peaks

Hg19::chr12:124873357..124873401,-p1@NCOR2
Hg19::chr12:124873824..124873833,-p19@NCOR2
Hg19::chr12:124873852..124873881,-p3@NCOR2
Hg19::chr12:124873905..124873916,-p@chr12:124873905..124873916
-


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
multi-cellular organism2.44e-17656
anatomical system7.90e-17624
anatomical group1.75e-16625
epithelial tube2.05e-14117
lateral plate mesoderm2.62e-14203
tube4.62e-14192
mesoderm5.84e-14315
mesoderm-derived structure5.84e-14315
presumptive mesoderm5.84e-14315
organ2.65e-13503
artery1.04e-1242
arterial blood vessel1.04e-1242
arterial system1.04e-1242
embryo1.51e-12592
developing anatomical structure2.80e-12581
cell layer9.20e-12309
germ layer1.89e-11560
germ layer / neural crest1.89e-11560
embryonic tissue1.89e-11560
presumptive structure1.89e-11560
germ layer / neural crest derived structure1.89e-11560
epiblast (generic)1.89e-11560
epithelium4.51e-11306
embryonic structure5.30e-11564
trunk7.58e-11199
musculoskeletal system2.12e-10167
systemic artery2.75e-1033
systemic arterial system2.75e-1033
anatomical conduit3.12e-10240
epithelial tube open at both ends3.54e-1059
blood vessel3.54e-1059
blood vasculature3.54e-1059
vascular cord3.54e-1059
vasculature1.10e-0978
vascular system1.10e-0978
splanchnic layer of lateral plate mesoderm2.26e-0983
organism subdivision2.98e-09264
epithelial vesicle8.11e-0978
trunk mesenchyme1.38e-08122
mesenchyme3.12e-08160
entire embryonic mesenchyme3.12e-08160
multi-tissue structure6.52e-08342
vessel7.50e-0868
tissue3.19e-07773
unilaminar epithelium4.37e-07148
somite4.75e-0771
presomitic mesoderm4.75e-0771
presumptive segmental plate4.75e-0771
dermomyotome4.75e-0771
trunk paraxial mesoderm4.75e-0771
paraxial mesoderm6.70e-0772
presumptive paraxial mesoderm6.70e-0772
dense mesenchyme tissue9.32e-0773


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)
MA0003.11.45381
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.11.86845
MA0017.12.4142
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
MA0048.11.30988
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.13.6449
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.12.31526
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.599068
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.13.07281
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
MA0105.10.656404
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
MA0117.12.78257
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
MA0139.10.912459
MA0140.10.779643
MA0141.11.46638
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.11.75643
MA0147.10.46175
MA0148.10.739888
MA0149.15.7925
MA0062.20.353589
MA0035.20.778873
MA0039.21.5472
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.21.65877
MA0065.21.7213
MA0150.11.53138
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.11.78721
MA0161.10
MA0162.10.640035
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.29.35212
MA0102.21.75932
MA0258.12.82128
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
E2F1#186944.907389214879320.001724022357361790.0106302497922132
ESR1#2099323.07645247211590.0001339105244968570.00175719076114176
TAF1#687243.343046285745290.008005664898701650.0321405257305874



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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