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Coexpression cluster:C4454: Difference between revisions

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{{Coexpression_clusters
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cis-trans isomerase activity!0.000114914022548021!5480;11328$GO:0016859!cis-trans isomerase activity!0.000114914022548021!5480;11328$GO:0016853!isomerase activity!0.000796984349929822!5480;11328$GO:0006457!protein folding!0.000796984349929822!5480;11328$GO:0016018!cyclosporin A binding!0.002189877685791!5480$GO:0008144!drug binding!0.00608174002924203!5480$GO:0051082!unfolded protein binding!0.0473062726156019!5480$GO:0042277!peptide 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|full_id=C4454_Preadipocyte_Chondrocyte_Adipocyte_tenocyte_Ewing_Fibroblast_Smooth
|id=C4454
}}

Latest revision as of 12:46, 17 September 2013


Full id: C4454_Preadipocyte_Chondrocyte_Adipocyte_tenocyte_Ewing_Fibroblast_Smooth



Phase1 CAGE Peaks

Hg19::chr5:122372354..122372440,-p1@PPIC
Hg19::chr7:32996997..32997094,+p1@FKBP9
Hg19::chr7:32997098..32997114,+p2@FKBP9


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

GO IDGO nameFDR corrected p-value
GO:0003755peptidyl-prolyl cis-trans isomerase activity0.000114914022548021
GO:0016859cis-trans isomerase activity0.000114914022548021
GO:0016853isomerase activity0.000796984349929822
GO:0006457protein folding0.000796984349929822
GO:0016018cyclosporin A binding0.002189877685791
GO:0008144drug binding0.00608174002924203
GO:0051082unfolded protein binding0.0473062726156019
GO:0042277peptide binding0.0473062726156019



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 subdivision3.36e-16264
multi-cellular organism6.89e-16656
trunk6.94e-14199
mesenchyme7.17e-14160
entire embryonic mesenchyme7.17e-14160
surface structure2.03e-1399
multilaminar epithelium4.12e-1383
anatomical system9.66e-13624
anatomical group2.07e-12625
trunk mesenchyme2.44e-12122
splanchnic layer of lateral plate mesoderm3.53e-1283
dense mesenchyme tissue1.28e-1173
somite1.59e-1171
presomitic mesoderm1.59e-1171
presumptive segmental plate1.59e-1171
dermomyotome1.59e-1171
trunk paraxial mesoderm1.59e-1171
muscle tissue2.05e-1164
musculature2.05e-1164
musculature of body2.05e-1164
skeletal muscle tissue2.37e-1162
striated muscle tissue2.37e-1162
myotome2.37e-1162
paraxial mesoderm3.43e-1172
presumptive paraxial mesoderm3.43e-1172
multi-tissue structure3.50e-11342
epithelial vesicle8.57e-1178
epithelial tube1.43e-10117
integument2.14e-1046
integumental system2.14e-1046
vasculature4.33e-1078
vascular system4.33e-1078
unilaminar epithelium4.66e-10148
cell layer1.63e-09309
epithelium1.72e-09306
anatomical cluster4.81e-09373
skin of body7.36e-0941
primary circulatory organ1.59e-0827
vessel1.69e-0868
circulatory system2.36e-08112
artery3.48e-0842
arterial blood vessel3.48e-0842
arterial system3.48e-0842
epithelial tube open at both ends4.05e-0859
blood vessel4.05e-0859
blood vasculature4.05e-0859
vascular cord4.05e-0859
heart8.50e-0824
primitive heart tube8.50e-0824
primary heart field8.50e-0824
anterior lateral plate mesoderm8.50e-0824
heart tube8.50e-0824
heart primordium8.50e-0824
cardiac mesoderm8.50e-0824
cardiogenic plate8.50e-0824
heart rudiment8.50e-0824
cardiovascular system9.13e-08109
systemic artery1.45e-0733
systemic arterial system1.45e-0733
adipose tissue9.59e-0714


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
MA0007.11.88666
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.12.1667
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
MA0088.10.715722
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
MA0116.10.560723
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
MA0145.11.37817
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.22.15877
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.21.34467
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.23.61229
MA0102.21.88331
MA0258.11.29138
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
E2F1#186934.907389214879320.008460985347239390.0327025960800982
NR3C1#290829.982015554115360.01278474365547170.0460676870905951
SMARCB1#6598318.25271578115740.000164397760679890.00203671859165445
SMC3#9126210.02995522995520.0126656379767470.0457774973924931



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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