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Coexpression cluster:C3101: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3101_Fibroblast_Adipocyte_tenocyte_Pancreatic_Smooth_extraskeletal_mesenchymal
|id=C3101
}}

Latest revision as of 12:19, 17 September 2013


Full id: C3101_Fibroblast_Adipocyte_tenocyte_Pancreatic_Smooth_extraskeletal_mesenchymal



Phase1 CAGE Peaks

Hg19::chr11:121971132..121971166,-p1@MIR100HG
Hg19::chr11:121971176..121971195,-p2@MIR100HG
Hg19::chr11:121971257..121971264,-p4@MIR100HG


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
dense mesenchyme tissue2.83e-1973
somite7.55e-1971
presomitic mesoderm7.55e-1971
presumptive segmental plate7.55e-1971
dermomyotome7.55e-1971
trunk paraxial mesoderm7.55e-1971
paraxial mesoderm7.61e-1972
presumptive paraxial mesoderm7.61e-1972
multi-tissue structure9.31e-19342
multilaminar epithelium1.17e-1783
epithelial vesicle3.69e-1778
structure with developmental contribution from neural crest4.51e-17132
muscle tissue9.39e-1764
musculature9.39e-1764
musculature of body9.39e-1764
skeletal muscle tissue1.00e-1662
striated muscle tissue1.00e-1662
myotome1.00e-1662
cell layer1.19e-15309
epithelium2.45e-15306
multi-cellular organism2.05e-13656
anatomical cluster5.03e-13373
mesenchyme5.77e-12160
entire embryonic mesenchyme5.77e-12160
trunk mesenchyme3.92e-11122
ectoderm-derived structure4.57e-11171
ectoderm4.57e-11171
presumptive ectoderm4.57e-11171
anatomical system1.81e-10624
neural plate2.36e-1082
presumptive neural plate2.36e-1082
anatomical group2.85e-10625
surface structure9.32e-1099
ecto-epithelium1.44e-09104
organism subdivision1.83e-09264
neurectoderm2.98e-0986
central nervous system1.05e-0881
nervous system1.44e-0889
integument2.14e-0846
integumental system2.14e-0846
tissue3.83e-08773
embryonic structure3.87e-08564
pre-chordal neural plate4.43e-0861
unilaminar epithelium4.91e-08148
artery1.00e-0742
arterial blood vessel1.00e-0742
arterial system1.00e-0742
skin of body1.36e-0741
germ layer1.43e-07560
germ layer / neural crest1.43e-07560
embryonic tissue1.43e-07560
presumptive structure1.43e-07560
germ layer / neural crest derived structure1.43e-07560
epiblast (generic)1.43e-07560
developing anatomical structure1.81e-07581
neural tube2.07e-0756
neural rod2.07e-0756
future spinal cord2.07e-0756
neural keel2.07e-0756
brain2.55e-0768
future brain2.55e-0768
splanchnic layer of lateral plate mesoderm3.11e-0783
regional part of nervous system4.10e-0753
regional part of brain4.10e-0753
anatomical conduit6.44e-07240
tube6.79e-07192
systemic artery6.80e-0733
systemic arterial system6.80e-0733
embryo8.87e-07592


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.12.44638
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.11.59304
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.84332
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.12.78116
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.12.19699
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
MA0116.10.560723
MA0117.11.36676
MA0119.11.66081
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
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
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
MA0150.10.744617
MA0151.10
MA0152.12.08673
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.76014
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.221.2156
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
RAD21#5885310.35503389545630.0009004912073565420.00661785948948771



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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