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Coexpression cluster:C950: Difference between revisions

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{{Coexpression_clusters
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|full_id=C950_liposarcoma_extraskeletal_Fibroblast_Smooth_Preadipocyte_neuroblastoma_mesenchymal
|id=C950
|ontology_enrichment_celltype=CL:0000055!4.66e-27!180;CL:0000183!4.48e-18!59;CL:0000680!4.51e-18!57;CL:0000056!4.51e-18!57;CL:0000355!4.51e-18!57;CL:0000187!2.14e-16!54;CL:0000057!4.71e-16!75;CL:0000393!1.76e-14!60;CL:0000211!1.76e-14!60;CL:0000192!1.33e-12!42;CL:0000514!1.33e-12!42;CL:0000359!3.68e-10!32;CL:0000222!1.58e-08!119;CL:0002620!2.63e-08!23
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!8.98e-27!365;UBERON:0004290!3.26e-23!70;UBERON:0000914!3.02e-22!83;UBERON:0002329!3.02e-22!83;UBERON:0003077!3.02e-22!83;UBERON:0003059!3.02e-22!83;UBERON:0007282!3.02e-22!83;UBERON:0009618!3.02e-22!83;UBERON:0007285!3.02e-22!83;UBERON:0000119!1.10e-21!312;UBERON:0000483!2.81e-20!309;UBERON:0002385!1.94e-19!63;UBERON:0001015!1.94e-19!63;UBERON:0000383!1.94e-19!63;UBERON:0001134!2.63e-19!61;UBERON:0002036!2.63e-19!61;UBERON:0003082!2.63e-19!61;UBERON:0000481!2.14e-18!347;UBERON:0000073!2.89e-17!94;UBERON:0001016!2.89e-17!94;UBERON:0000486!4.04e-17!82;UBERON:0005743!9.43e-17!86;UBERON:0001017!1.86e-16!82;UBERON:0003075!2.20e-16!86;UBERON:0007284!2.20e-16!86;UBERON:0002346!5.64e-16!90;UBERON:0000955!1.05e-15!69;UBERON:0006238!1.05e-15!69;UBERON:0002616!2.07e-15!59;UBERON:0000153!7.45e-15!129;UBERON:0007811!7.45e-15!129;UBERON:0000033!1.61e-14!123;UBERON:0000468!1.75e-14!659;UBERON:0007023!2.02e-14!115;UBERON:0004121!3.11e-14!169;UBERON:0000924!3.91e-14!173;UBERON:0006601!3.91e-14!173;UBERON:0001049!1.04e-13!57;UBERON:0005068!1.04e-13!57;UBERON:0006241!1.04e-13!57;UBERON:0007135!1.04e-13!57;UBERON:0000025!1.68e-13!194;UBERON:0000477!1.84e-13!286;UBERON:0003056!2.40e-13!61;UBERON:0005256!1.61e-12!143;UBERON:0000467!6.84e-12!625;UBERON:0003080!8.68e-12!42;UBERON:0002780!8.83e-12!41;UBERON:0001890!8.83e-12!41;UBERON:0006240!8.83e-12!41;UBERON:0000480!1.10e-11!626;UBERON:0001893!4.27e-11!34;UBERON:0004111!5.68e-11!241;UBERON:0001869!7.89e-11!32;UBERON:0002791!1.02e-10!33;UBERON:0002049!1.21e-10!79;UBERON:0007798!1.21e-10!79;UBERON:0002020!1.46e-10!34;UBERON:0003528!1.46e-10!34;UBERON:0002619!3.01e-10!22;UBERON:0004872!3.26e-10!84;UBERON:0000479!3.74e-10!787;UBERON:0000956!5.63e-10!25;UBERON:0000203!5.63e-10!25;UBERON:0001950!9.78e-10!20;UBERON:0000922!1.33e-09!612;UBERON:0002050!1.46e-09!605;UBERON:0005423!1.46e-09!605;UBERON:0000923!2.69e-09!604;UBERON:0005291!2.69e-09!604;UBERON:0006598!2.69e-09!604;UBERON:0002532!2.69e-09!604;UBERON:0001637!7.28e-09!42;UBERON:0003509!7.28e-09!42;UBERON:0004572!7.28e-09!42;UBERON:0004573!1.45e-08!33;UBERON:0004571!1.45e-08!33;UBERON:0001009!1.70e-08!113;UBERON:0004535!2.56e-08!110;UBERON:0001981!8.80e-08!60;UBERON:0007500!8.80e-08!60;UBERON:0004537!8.80e-08!60;UBERON:0006965!8.80e-08!60;UBERON:0002100!2.32e-07!216;UBERON:0002199!2.44e-07!45;UBERON:0002416!2.44e-07!45;UBERON:0001135!2.85e-07!15;UBERON:0001013!5.74e-07!14;UBERON:0000948!8.09e-07!24;UBERON:0005498!8.09e-07!24;UBERON:0004140!8.09e-07!24;UBERON:0009881!8.09e-07!24;UBERON:0004141!8.09e-07!24;UBERON:0003084!8.09e-07!24;UBERON:0007005!8.09e-07!24;UBERON:0004139!8.09e-07!24;UBERON:0004291!8.09e-07!24;UBERON:0007100!8.28e-07!27;UBERON:0000055!8.42e-07!69;UBERON:0000064!8.43e-07!219
}}

Latest revision as of 11:34, 17 September 2013


Full id: C950_liposarcoma_extraskeletal_Fibroblast_Smooth_Preadipocyte_neuroblastoma_mesenchymal



Phase1 CAGE Peaks

Hg19::chr5:14440817..14440832,+p24@TRIO
Hg19::chr5:14440848..14440864,+p22@TRIO
Hg19::chr5:14440872..14440890,+p13@TRIO
Hg19::chr5:14440903..14440920,+p6@TRIO
Hg19::chr5:14440934..14440949,+p10@TRIO
Hg19::chr5:14441117..14441141,+p5@TRIO
Hg19::chr5:14441157..14441216,+p3@TRIO
Hg19::chr5:14441222..14441241,+p4@TRIO
Hg19::chr5:14441335..14441346,+p18@TRIO


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
somite7.03e-2571
presomitic mesoderm7.03e-2571
presumptive segmental plate7.03e-2571
dermomyotome7.03e-2571
trunk paraxial mesoderm7.03e-2571
paraxial mesoderm2.97e-2472
presumptive paraxial mesoderm2.97e-2472
epithelial vesicle7.99e-2478
dense mesenchyme tissue1.20e-2373
skeletal muscle tissue2.10e-2262
striated muscle tissue2.10e-2262
myotome2.10e-2262
muscle tissue5.11e-2264
musculature5.11e-2264
musculature of body5.11e-2264
multilaminar epithelium1.35e-1983
trunk mesenchyme8.86e-15122
vasculature1.17e-1378
vascular system1.17e-1378
artery1.31e-1242
arterial blood vessel1.31e-1242
arterial system1.31e-1242
systemic artery3.00e-1233
systemic arterial system3.00e-1233
cell layer4.54e-12309
cardiovascular system1.68e-11109
epithelium8.38e-11306
circulatory system9.66e-11112
splanchnic layer of lateral plate mesoderm1.25e-1083
aorta2.25e-1021
aortic system2.25e-1021
smooth muscle tissue3.18e-1015
tissue3.63e-10773
unilaminar epithelium3.73e-10148
mesenchyme6.69e-10160
entire embryonic mesenchyme6.69e-10160
blood vessel smooth muscle9.64e-1010
arterial system smooth muscle9.64e-1010
artery smooth muscle tissue9.64e-1010
aorta smooth muscle tissue9.64e-1010
epithelial tube open at both ends1.67e-0959
blood vessel1.67e-0959
blood vasculature1.67e-0959
vascular cord1.67e-0959
multi-cellular organism1.67e-08656
vessel2.19e-0868
multi-tissue structure2.24e-08342
integument2.92e-0846
integumental system2.92e-0846
vasculature of organ3.25e-0811
anatomical system4.85e-08624
anatomical group6.01e-08625
organism subdivision6.75e-08264
epithelial tube1.14e-07117
mesoderm4.47e-07315
mesoderm-derived structure4.47e-07315
presumptive mesoderm4.47e-07315
trunk5.12e-07199
structure with developmental contribution from neural crest6.46e-07132
Disease
Ontology termp-valuen
ovarian cancer1.55e-0814


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)
MA0003.10.0416606
MA0004.10.415381
MA0006.10.733408
MA0007.10.397529
MA0009.10.870971
MA0014.10.00594475
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.13.75659
MA0027.12.48103
MA0028.10.280275
MA0029.11.84783
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.12.02319
MA0046.10.860127
MA0048.10.0764047
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.11.02363
MA0056.10
MA0057.10.0725989
MA0058.10.325084
MA0059.10.323879
MA0060.10.162248
MA0061.10.851955
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.109867
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.10.00642257
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.363555
MA0089.10
MA0090.11.66392
MA0091.12.81626
MA0092.10.993944
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.13.31755
MA0101.10.746654
MA0103.10.257174
MA0105.10.0643619
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.129876
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.11.53859
MA0146.10.0045741
MA0147.10.211483
MA0148.10.439278
MA0149.10.464973
MA0062.20.421263
MA0035.20.473658
MA0039.20.0006485
MA0138.20.608783
MA0002.20.152495
MA0137.20.28622
MA0104.20.161609
MA0047.20.542971
MA0112.20.166662
MA0065.20.0483532
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.062786
MA0155.10.0402662
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.10.0107891
MA0163.10.00648562
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.22.07833e-05
MA0102.21.41188
MA0258.10.180288
MA0259.10.218904
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
EP300#203396.77394172622323.3261238408136e-082.22963445321394e-06
GATA2#2624811.32882820760351.20057232306882e-088.94979106702244e-07
RAD21#5885910.35503389545637.29196863888313e-106.91703826227353e-08
YY1#752894.911170749853866.01179022795762e-072.76227610918463e-05



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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