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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.689746179538143

Latest revision as of 11:44, 17 September 2013


Full id: C1417_Mesenchymal_leiomyoblastoma_chorionic_alveolar_uterus_extraskeletal_mesenchymal



Phase1 CAGE Peaks

Hg19::chr15:96869114..96869160,+p11@NR2F2
Hg19::chr15:96869165..96869183,+p20@NR2F2
Hg19::chr15:96869206..96869220,+p21@NR2F2
Hg19::chr15:96869222..96869251,+p18@NR2F2
Hg19::chr15:96869255..96869291,+p6@NR2F2
Hg19::chr15:96869292..96869320,+p15@NR2F2


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
organism subdivision5.64e-19264
trunk7.90e-17199
mesenchyme5.00e-14160
entire embryonic mesenchyme5.00e-14160
multi-tissue structure1.54e-13342
anatomical cluster8.10e-13373
cell layer4.71e-12309
multi-cellular organism7.90e-12656
vasculature3.90e-1178
vascular system3.90e-1178
epithelium4.03e-11306
trunk mesenchyme2.10e-10122
unilaminar epithelium4.32e-10148
muscle tissue9.72e-1064
musculature9.72e-1064
musculature of body9.72e-1064
skeletal muscle tissue1.97e-0962
striated muscle tissue1.97e-0962
myotome1.97e-0962
splanchnic layer of lateral plate mesoderm2.63e-0983
anatomical system3.00e-09624
anatomical group4.93e-09625
multilaminar epithelium5.57e-0983
anatomical conduit7.46e-09240
epithelial vesicle8.43e-0978
body cavity precursor9.04e-0954
dense mesenchyme tissue1.56e-0873
reproductive structure1.62e-0859
reproductive system1.62e-0859
somite1.85e-0871
presomitic mesoderm1.85e-0871
presumptive segmental plate1.85e-0871
dermomyotome1.85e-0871
trunk paraxial mesoderm1.85e-0871
paraxial mesoderm2.71e-0872
presumptive paraxial mesoderm2.71e-0872
body cavity3.73e-0846
anatomical space4.24e-0895
epithelial tube5.37e-08117
renal system7.27e-0848
vessel7.49e-0868
body cavity or lining9.98e-0849
urinary system structure1.05e-0747
organ component layer1.12e-0766
epithelial tube open at both ends1.55e-0759
blood vessel1.55e-0759
blood vasculature1.55e-0759
vascular cord1.55e-0759
artery3.00e-0742
arterial blood vessel3.00e-0742
arterial system3.00e-0742
systemic artery7.16e-0733
systemic arterial system7.16e-0733
anatomical cavity7.51e-0761


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)
MA0003.10.00461978
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.0254709
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
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
MA0057.10.450439
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
MA0073.10.00076337
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.11.15882
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.16.71165
MA0091.10.561458
MA0092.11.29635
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
MA0108.23.33678
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
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
MA0146.10.0213085
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.00570825
MA0138.20.765223
MA0002.20.709311
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.11.52275
MA0153.11.13732
MA0154.10.132326
MA0155.13.55553
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.0270301
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.27.22997e-05
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
E2F1#186964.907389214879327.15746523583771e-050.00112713888987584
EP300#203355.644951438519330.0003688138931814860.00366983176352717
GATA2#2624612.7449317335542.33109997620343e-071.22648740763078e-05
GATA3#2625418.15767757147072.56597141799789e-050.000554724671753843
HDAC2#306648.94374682441750.0004094079565307180.00390271609822121
POLR2A#543062.147453176558070.01019570676818780.03802283232147
SUZ12#23512650.11578091106296.2866744827465e-116.98482974791024e-09
TCF7L2#693447.180117708758230.0009553297120679730.0068747798386734
ZNF263#1012768.221841637010683.23542093046082e-060.000108720761440283



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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