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{{Coexpression_clusters
{
|full_id=C635_Fibroblast_Pericytes_Nucleus_Preadipocyte_Smooth_mesothelioma_Prostate

Latest revision as of 11:27, 17 September 2013


Full id: C635_Fibroblast_Pericytes_Nucleus_Preadipocyte_Smooth_mesothelioma_Prostate



Phase1 CAGE Peaks

Hg19::chr3:170136642..170136663,+p1@CLDN11
Hg19::chr3:170140945..170141037,+p@chr3:170140945..170141037
+
Hg19::chr3:170150373..170150387,+p@chr3:170150373..170150387
+
Hg19::chr3:170150429..170150439,+p@chr3:170150429..170150439
+
Hg19::chr3:170150498..170150515,+p@chr3:170150498..170150515
+
Hg19::chr3:170150547..170150552,+p@chr3:170150547..170150552
+
Hg19::chr3:170150588..170150600,+p@chr3:170150588..170150600
+
Hg19::chr3:170150614..170150632,+p@chr3:170150614..170150632
+
Hg19::chr3:170150675..170150707,+p6@CLDN11
Hg19::chr3:170150778..170150789,+p13@CLDN11
Hg19::chr3:170150980..170151004,+p12@CLDN11
Hg19::chr3:170151051..170151075,+p10@CLDN11
Hg19::chr3:170151355..170151372,+p8@CLDN11
Hg19::chr3:170151409..170151477,+p5@CLDN11


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
cell layer4.15e-19309
epithelial vesicle4.82e-1978
epithelium4.51e-18306
paraxial mesoderm6.56e-1772
presumptive paraxial mesoderm6.56e-1772
somite1.39e-1671
presomitic mesoderm1.39e-1671
presumptive segmental plate1.39e-1671
dermomyotome1.39e-1671
trunk paraxial mesoderm1.39e-1671
dense mesenchyme tissue1.97e-1673
multilaminar epithelium8.73e-1583
skeletal muscle tissue7.99e-1462
striated muscle tissue7.99e-1462
myotome7.99e-1462
vasculature1.40e-1378
vascular system1.40e-1378
trunk mesenchyme4.34e-13122
muscle tissue6.20e-1364
musculature6.20e-1364
musculature of body6.20e-1364
anatomical conduit8.36e-13240
anatomical cluster4.19e-12373
structure with developmental contribution from neural crest1.03e-11132
mesenchyme4.69e-11160
entire embryonic mesenchyme4.69e-11160
tube9.21e-11192
unilaminar epithelium1.03e-10148
cardiovascular system1.39e-10109
multi-tissue structure1.99e-10342
circulatory system7.78e-10112
neural plate2.45e-0982
presumptive neural plate2.45e-0982
vessel4.19e-0968
neural tube1.25e-0856
neural rod1.25e-0856
future spinal cord1.25e-0856
neural keel1.25e-0856
neurectoderm2.79e-0886
anatomical system1.32e-07624
anatomical group1.65e-07625
regional part of nervous system4.13e-0753
regional part of brain4.13e-0753
lymphatic vessel5.90e-078
lymph vasculature5.90e-078
lymphatic part of lymphoid system5.90e-078
articulation6.48e-078
skeletal joint6.48e-078
articular system6.48e-078
epithelial tube8.66e-07117
Disease
Ontology termp-valuen
ovarian cancer9.39e-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)
MA0003.10.210327
MA0004.10.275994
MA0006.10.152601
MA0007.10.260673
MA0009.10.695988
MA0014.10.00418733
MA0017.10.181071
MA0019.10.403106
MA0024.10.59663
MA0025.10.824398
MA0027.12.28954
MA0028.10.164086
MA0029.10.614815
MA0030.10.604021
MA0031.10.543644
MA0038.10.363295
MA0040.11.50383
MA0041.10.291389
MA0042.10.264992
MA0043.10.69629
MA0046.10.685589
MA0048.10.800598
MA0050.10.265714
MA0051.10.359609
MA0052.10.623986
MA0055.10.0654733
MA0056.10
MA0057.10.0243088
MA0058.10.200063
MA0059.10.199079
MA0060.10.564002
MA0061.10.487876
MA0063.10
MA0066.10.363668
MA0067.11.00375
MA0068.10.68421
MA0069.10.681911
MA0070.10.671241
MA0071.10.878639
MA0072.10.666958
MA0073.10.000107661
MA0074.10.943486
MA0076.10.212295
MA0077.10.65962
MA0078.11.13748
MA0081.10.578007
MA0083.10.703169
MA0084.11.18798
MA0087.10.664629
MA0088.10.0514785
MA0089.10
MA0090.11.85461
MA0091.18.11113
MA0092.11.28008
MA0093.10.154754
MA0095.10
MA0098.10
MA0100.10.375452
MA0101.10.1571
MA0103.10.146091
MA0105.10.430023
MA0106.14.80937
MA0107.10.348426
MA0108.22.29525
MA0109.10
MA0111.10.234271
MA0113.10.414278
MA0114.10.104181
MA0115.10.929032
MA0116.10.10959
MA0117.10.732
MA0119.10.18693
MA0122.10.756889
MA0124.10.888592
MA0125.10.807083
MA0130.10
MA0131.10.464307
MA0132.10
MA0133.10
MA0135.10.725055
MA0136.10.369468
MA0139.10.0564547
MA0140.10.327488
MA0141.11.08958
MA0142.10.514195
MA0143.10.414436
MA0144.10.0953756
MA0145.10.0609666
MA0146.10.548423
MA0147.11.19725
MA0148.10.296708
MA0149.10.319221
MA0062.20.0599644
MA0035.20.326883
MA0039.20.0118926
MA0138.20.44894
MA0002.21.36124
MA0137.20.168782
MA0104.21.96419
MA0047.20.388882
MA0112.20.0554275
MA0065.20.0133095
MA0150.14.28461
MA0151.10
MA0152.10.333125
MA0153.10.790794
MA0154.10.0872435
MA0155.10.138832
MA0156.10.170442
MA0157.10.489002
MA0158.10
MA0159.10.112236
MA0160.10.30953
MA0161.10
MA0162.10.165836
MA0163.10.106785
MA0164.10.425415
MA0080.20.154815
MA0018.20.400879
MA0099.20.333432
MA0079.20.000124295
MA0102.21.22472
MA0258.10.089643
MA0259.10.117259
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

No analysis results for this cluster

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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