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Coexpression cluster:C1527: Difference between revisions

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{{Coexpression_clusters
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|full_id=C1527_glioblastoma_Lens_mesothelioma_mesenchymal_granulosa_Ciliary_Smooth
|id=C1527
|ontology_enrichment_celltype=CL:0000055!2.37e-37!180;CL:0000393!1.18e-17!60;CL:0000211!1.18e-17!60;CL:0000222!1.73e-17!119;CL:0000192!4.71e-17!42;CL:0000514!4.71e-17!42;CL:0000183!6.36e-17!59;CL:0000359!1.45e-16!32;CL:0000187!2.19e-16!54;CL:0000680!1.94e-15!57;CL:0000056!1.94e-15!57;CL:0000355!1.94e-15!57;CL:0000057!1.57e-14!75;CL:0002321!4.52e-14!248;CL:0000220!6.89e-14!246;CL:0002319!5.64e-09!25;CL:0000133!7.10e-09!59;CL:0002494!1.75e-07!16;CL:0000243!4.62e-07!15;CL:0000125!4.62e-07!15;CL:0000030!4.62e-07!15;CL:0000339!4.62e-07!15;CL:0000095!8.18e-07!17;CL:0000123!8.18e-07!17;CL:0002539!8.79e-07!10
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004872!1.39e-27!84;UBERON:0001981!4.99e-25!60;UBERON:0007500!4.99e-25!60;UBERON:0004537!4.99e-25!60;UBERON:0006965!4.99e-25!60;UBERON:0002049!5.27e-25!79;UBERON:0007798!5.27e-25!79;UBERON:0003914!3.51e-23!118;UBERON:0000119!7.63e-23!312;UBERON:0000483!9.38e-23!309;UBERON:0001637!3.52e-22!42;UBERON:0003509!3.52e-22!42;UBERON:0004572!3.52e-22!42;UBERON:0000055!1.52e-21!69;UBERON:0000468!4.14e-21!659;UBERON:0000477!4.76e-21!286;UBERON:0004111!3.65e-20!241;UBERON:0000025!5.46e-20!194;UBERON:0004535!1.22e-19!110;UBERON:0000475!2.65e-19!365;UBERON:0001009!3.73e-19!113;UBERON:0000467!1.78e-18!625;UBERON:0000480!3.77e-18!626;UBERON:0000481!5.94e-18!347;UBERON:0004573!8.35e-18!33;UBERON:0004571!8.35e-18!33;UBERON:0000914!2.92e-16!83;UBERON:0002329!2.92e-16!83;UBERON:0003077!2.92e-16!83;UBERON:0003059!2.92e-16!83;UBERON:0007282!2.92e-16!83;UBERON:0009618!2.92e-16!83;UBERON:0007285!2.92e-16!83;UBERON:0004290!5.09e-16!70;UBERON:0002385!6.48e-16!63;UBERON:0001015!6.48e-16!63;UBERON:0000383!6.48e-16!63;UBERON:0000922!6.60e-16!612;UBERON:0005256!7.94e-16!143;UBERON:0001134!1.69e-15!61;UBERON:0002036!1.69e-15!61;UBERON:0003082!1.69e-15!61;UBERON:0000490!1.43e-14!138;UBERON:0002050!1.99e-14!605;UBERON:0005423!1.99e-14!605;UBERON:0000923!4.02e-14!604;UBERON:0005291!4.02e-14!604;UBERON:0006598!4.02e-14!604;UBERON:0002532!4.02e-14!604;UBERON:0000486!1.86e-13!82;UBERON:0000947!1.39e-11!21;UBERON:0010191!1.39e-11!21;UBERON:0004121!1.43e-10!169;UBERON:0000924!5.72e-10!173;UBERON:0006601!5.72e-10!173;UBERON:0002100!2.36e-09!216;UBERON:0000948!4.93e-09!24;UBERON:0005498!4.93e-09!24;UBERON:0004140!4.93e-09!24;UBERON:0009881!4.93e-09!24;UBERON:0004141!4.93e-09!24;UBERON:0003084!4.93e-09!24;UBERON:0007005!4.93e-09!24;UBERON:0004139!4.93e-09!24;UBERON:0004291!4.93e-09!24;UBERON:0003104!2.40e-08!238;UBERON:0009142!2.40e-08!238;UBERON:0007100!3.82e-08!27;UBERON:0003103!7.64e-08!69;UBERON:0000064!9.03e-08!219;UBERON:0000033!1.25e-07!123;UBERON:0001135!2.94e-07!15;UBERON:0000153!4.65e-07!129;UBERON:0007811!4.65e-07!129;UBERON:0003075!7.76e-07!86;UBERON:0007284!7.76e-07!86;UBERON:0004237!8.79e-07!10;UBERON:0004695!8.79e-07!10;UBERON:0002111!8.79e-07!10;UBERON:0004178!8.79e-07!10
}}

Latest revision as of 11:46, 17 September 2013


Full id: C1527_glioblastoma_Lens_mesothelioma_mesenchymal_granulosa_Ciliary_Smooth



Phase1 CAGE Peaks

Hg19::chr5:146889496..146889529,-p2@DPYSL3
Hg19::chr5:146889532..146889549,-p6@DPYSL3
Hg19::chr5:146889596..146889607,-p13@DPYSL3
Hg19::chr5:146889619..146889639,-p3@DPYSL3
Hg19::chr5:146889643..146889652,-p11@DPYSL3
Hg19::chr5:146889655..146889679,-p4@DPYSL3


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
anatomical cluster2.30e-29373
splanchnic layer of lateral plate mesoderm2.18e-2683
vasculature2.37e-2478
vascular system2.37e-2478
epithelial tube open at both ends3.56e-2459
blood vessel3.56e-2459
blood vasculature3.56e-2459
vascular cord3.56e-2459
epithelial tube4.25e-23117
cell layer8.12e-23309
epithelium1.05e-22306
artery1.00e-2142
arterial blood vessel1.00e-2142
arterial system1.00e-2142
multi-cellular organism1.27e-21656
vessel5.46e-2168
anatomical conduit2.28e-20240
tube9.30e-20192
multi-tissue structure1.08e-19342
anatomical system2.71e-19624
anatomical group5.72e-19625
cardiovascular system1.10e-18109
circulatory system2.89e-18112
systemic artery2.78e-1733
systemic arterial system2.78e-1733
epithelial vesicle9.98e-1778
dense mesenchyme tissue8.18e-1673
unilaminar epithelium1.77e-15148
paraxial mesoderm2.42e-1572
presumptive paraxial mesoderm2.42e-1572
somite2.48e-1571
presomitic mesoderm2.48e-1571
presumptive segmental plate2.48e-1571
dermomyotome2.48e-1571
trunk paraxial mesoderm2.48e-1571
embryo3.09e-15592
muscle tissue3.28e-1564
musculature3.28e-1564
musculature of body3.28e-1564
mesenchyme7.07e-15160
entire embryonic mesenchyme7.07e-15160
skeletal muscle tissue8.93e-1562
striated muscle tissue8.93e-1562
myotome8.93e-1562
trunk mesenchyme1.48e-14122
developing anatomical structure3.82e-14581
embryonic structure5.30e-14564
germ layer6.12e-14560
germ layer / neural crest6.12e-14560
embryonic tissue6.12e-14560
presumptive structure6.12e-14560
germ layer / neural crest derived structure6.12e-14560
epiblast (generic)6.12e-14560
multilaminar epithelium4.19e-1383
structure with developmental contribution from neural crest7.31e-13132
organism subdivision2.33e-12264
aorta2.49e-1121
aortic system2.49e-1121
ectoderm-derived structure8.74e-10171
ectoderm8.74e-10171
presumptive ectoderm8.74e-10171
heart1.75e-0824
primitive heart tube1.75e-0824
primary heart field1.75e-0824
anterior lateral plate mesoderm1.75e-0824
heart tube1.75e-0824
heart primordium1.75e-0824
cardiac mesoderm1.75e-0824
cardiogenic plate1.75e-0824
heart rudiment1.75e-0824
trunk2.76e-08199
organ part9.44e-08218
compound organ1.01e-0768
primary circulatory organ1.04e-0727
neural plate4.06e-0782
presumptive neural plate4.06e-0782
smooth muscle tissue5.18e-0715
tissue8.89e-07773


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)
MA0003.10.756372
MA0004.10.558729
MA0006.12.69125
MA0007.10.539222
MA0009.11.03681
MA0014.10.108006
MA0017.11.10421
MA0019.10.7124
MA0024.15.03465
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.51617
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.11.52717
MA0115.11.28169
MA0116.10.323925
MA0117.13.97537
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.093337
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.00570825
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.23.77022
MA0150.11.21643
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.413181
MA0155.10.65596
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.11.46233
MA0161.10
MA0162.10.150673
MA0163.10.0270301
MA0164.11.74929
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.00183606
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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
CTCF#1066465.360256373075034.21437267579784e-050.000756002864801873
POLR2A#543062.147453176558070.01019570676818780.0380704118399273
RAD21#5885610.35503389545638.10515055094479e-073.54329769104279e-05
TAF1#687263.343046285745290.0007162474284635620.0057369556853521
TBP#690863.706770687096390.000385416472907960.00378099859233838
ZNF263#1012768.221841637010683.23542093046082e-060.000108825805654234



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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