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{{Coexpression_clusters
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|full_id=C4329_mesenchymal_epithelioid_meningioma_Smooth_embryonic_Bronchial_Gingival
|id=C4329
|ontology_enrichment_celltype=CL:0002321!2.53e-22!248;CL:0000220!2.99e-22!246;CL:0000066!1.20e-21!254;CL:0000680!1.21e-14!57;CL:0000056!1.21e-14!57;CL:0000355!1.21e-14!57;CL:0000192!1.41e-14!42;CL:0000514!1.41e-14!42;CL:0000187!1.92e-14!54;CL:0000393!2.23e-14!60;CL:0000211!2.23e-14!60;CL:0000183!2.33e-14!59;CL:0002076!1.90e-13!43;CL:0000359!1.73e-12!32;CL:0000548!3.80e-10!679;CL:0000004!3.80e-10!679;CL:0000255!3.80e-10!679;CL:0000012!4.42e-10!682;CL:0000222!8.19e-10!119;CL:0000223!1.40e-08!59;CL:0002368!2.21e-07!13;CL:0002539!2.90e-07!10;CL:0000055!5.43e-07!180
|ontology_enrichment_disease=DOID:193!1.35e-11!29;DOID:120!3.53e-11!27;DOID:2394!1.01e-09!14;DOID:305!3.42e-09!106
|ontology_enrichment_uberon=UBERON:0003104!2.96e-19!238;UBERON:0009142!2.96e-19!238;UBERON:0000481!1.04e-18!347;UBERON:0000486!1.69e-16!82;UBERON:0000467!3.67e-16!625;UBERON:0005256!4.07e-16!143;UBERON:0000922!7.00e-16!612;UBERON:0000480!7.72e-16!626;UBERON:0002050!2.88e-15!605;UBERON:0005423!2.88e-15!605;UBERON:0000923!4.18e-15!604;UBERON:0005291!4.18e-15!604;UBERON:0006598!4.18e-15!604;UBERON:0002532!4.18e-15!604;UBERON:0002100!9.78e-15!216;UBERON:0004119!2.36e-14!169;UBERON:0000925!2.36e-14!169;UBERON:0006595!2.36e-14!169;UBERON:0000483!4.34e-14!309;UBERON:0004290!5.37e-14!70;UBERON:0000119!6.19e-14!312;UBERON:0000468!2.47e-13!659;UBERON:0000914!4.28e-13!83;UBERON:0002329!4.28e-13!83;UBERON:0003077!4.28e-13!83;UBERON:0003059!4.28e-13!83;UBERON:0007282!4.28e-13!83;UBERON:0009618!4.28e-13!83;UBERON:0007285!4.28e-13!83;UBERON:0000464!1.14e-12!104;UBERON:0000926!3.01e-12!448;UBERON:0004120!3.01e-12!448;UBERON:0006603!3.01e-12!448;UBERON:0001637!3.89e-12!42;UBERON:0003509!3.89e-12!42;UBERON:0004572!3.89e-12!42;UBERON:0001134!3.93e-12!61;UBERON:0002036!3.93e-12!61;UBERON:0003082!3.93e-12!61;UBERON:0002385!6.05e-12!63;UBERON:0001015!6.05e-12!63;UBERON:0000383!6.05e-12!63;UBERON:0001007!1.36e-11!155;UBERON:0001555!1.36e-11!155;UBERON:0007026!1.36e-11!155;UBERON:0004573!1.46e-11!33;UBERON:0004571!1.46e-11!33;UBERON:0000490!2.13e-11!138;UBERON:0001048!3.59e-11!168;UBERON:0000466!3.75e-10!126;UBERON:0003914!2.12e-09!118;UBERON:0000475!5.23e-09!365;UBERON:0000062!6.41e-09!511;UBERON:0004921!1.26e-08!129;UBERON:0004185!1.26e-08!129;UBERON:0005156!5.44e-08!59;UBERON:0000990!5.44e-08!59;UBERON:0001004!8.53e-08!72;UBERON:0002553!8.67e-08!70;UBERON:0001981!1.22e-07!60;UBERON:0007500!1.22e-07!60;UBERON:0004537!1.22e-07!60;UBERON:0006965!1.22e-07!60;UBERON:0003886!1.66e-07!63;UBERON:0003100!2.72e-07!41;UBERON:0004237!2.90e-07!10;UBERON:0004695!2.90e-07!10;UBERON:0002111!2.90e-07!10;UBERON:0004178!2.90e-07!10;UBERON:0005153!4.93e-07!37;UBERON:0001135!6.38e-07!15;UBERON:0000058!9.22e-07!26
}}

Latest revision as of 12:43, 17 September 2013


Full id: C4329_mesenchymal_epithelioid_meningioma_Smooth_embryonic_Bronchial_Gingival



Phase1 CAGE Peaks

Hg19::chr3:45187813..45187824,-p3@CDCP1
Hg19::chr3:45187843..45187907,-p1@CDCP1
Hg19::chr3:45187930..45187949,-p2@CDCP1


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
organism subdivision4.04e-19264
multilaminar epithelium5.26e-1883
anatomical system2.83e-17624
anatomical group5.50e-17625
somite1.08e-1571
presomitic mesoderm1.08e-1571
presumptive segmental plate1.08e-1571
dermomyotome1.08e-1571
trunk paraxial mesoderm1.08e-1571
trunk2.39e-15199
paraxial mesoderm2.54e-1572
presumptive paraxial mesoderm2.54e-1572
epithelial vesicle2.90e-1578
multi-tissue structure5.63e-15342
embryo6.00e-15592
dense mesenchyme tissue1.17e-1473
trunk mesenchyme2.06e-14122
unilaminar epithelium3.69e-14148
multi-cellular organism4.89e-14656
epithelium1.45e-13306
skeletal muscle tissue2.45e-1362
striated muscle tissue2.45e-1362
myotome2.45e-1362
cell layer2.51e-13309
artery3.26e-1342
arterial blood vessel3.26e-1342
arterial system3.26e-1342
developing anatomical structure5.22e-13581
muscle tissue7.87e-1364
musculature7.87e-1364
musculature of body7.87e-1364
mesenchyme2.08e-12160
entire embryonic mesenchyme2.08e-12160
systemic artery2.67e-1233
systemic arterial system2.67e-1233
embryonic structure1.44e-11564
endoderm-derived structure5.42e-11160
endoderm5.42e-11160
presumptive endoderm5.42e-11160
germ layer1.17e-10560
germ layer / neural crest1.17e-10560
embryonic tissue1.17e-10560
presumptive structure1.17e-10560
germ layer / neural crest derived structure1.17e-10560
epiblast (generic)1.17e-10560
epithelial tube3.76e-09117
digestive system6.33e-09145
digestive tract6.33e-09145
primitive gut6.33e-09145
anatomical space6.36e-0995
organ9.88e-09503
epithelial tube open at both ends2.22e-0859
blood vessel2.22e-0859
blood vasculature2.22e-0859
vascular cord2.22e-0859
anatomical cluster9.16e-08373
blood vessel smooth muscle9.78e-0810
arterial system smooth muscle9.78e-0810
artery smooth muscle tissue9.78e-0810
aorta smooth muscle tissue9.78e-0810
surface structure1.11e-0799
primordium3.27e-07160
reproductive structure4.65e-0759
reproductive system4.65e-0759
smooth muscle tissue5.29e-0715
immaterial anatomical entity6.10e-07117
respiratory system6.42e-0774
Disease
Ontology termp-valuen
reproductive organ cancer1.82e-1129
female reproductive organ cancer4.86e-1127
ovarian cancer1.16e-0914
carcinoma1.83e-07106


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)
MA0003.11.54338
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.14.37851
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.12.84236
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.11.3784
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.11.76247
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.181755
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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#90536.336201576962630.003930750035764890.0190666296495866
E2F1#186934.907389214879320.008460985347239390.0326723673992581
NRF1#4899312.21027944771090.0005492172401020010.00472485167537174
ZNF263#1012738.221841637010680.001799043925565870.010974903536342



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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