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Coexpression cluster:C3654: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3654_Alveolar_Renal_Smooth_Fibroblast_Mesenchymal_Keratinocyte_Hair
|id=C3654
}}

Latest revision as of 12:30, 17 September 2013


Full id: C3654_Alveolar_Renal_Smooth_Fibroblast_Mesenchymal_Keratinocyte_Hair



Phase1 CAGE Peaks

Hg19::chr17:48474828..48474914,-p1@LRRC59
Hg19::chr17:7210921..7210983,+p1@EIF5A
Hg19::chr19:36631867..36631919,+p2@CAPNS1


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>

Cell Type
Ontology termp-valuen
animal cell5.01e-59679
eukaryotic cell5.01e-59679
somatic cell9.92e-40588
native cell1.94e-38722
embryonic cell7.81e-32250
mesodermal cell3.92e-31121
contractile cell7.35e-2159
muscle precursor cell3.23e-1958
myoblast3.23e-1958
multi-potent skeletal muscle stem cell3.23e-1958
muscle cell6.08e-1955
epithelial cell3.37e-18253
electrically responsive cell3.87e-1861
electrically active cell3.87e-1861
smooth muscle cell2.72e-1743
smooth muscle myoblast2.72e-1743
non-terminally differentiated cell6.46e-16106
vascular associated smooth muscle cell3.83e-1532
stem cell4.39e-12441
lining cell1.27e-1158
barrier cell1.27e-1158
somatic stem cell1.49e-11433
fibroblast7.07e-1176
multi fate stem cell7.21e-11427
squamous epithelial cell7.00e-1063
endothelial cell5.32e-0936
meso-epithelial cell5.34e-0945
epithelial cell of nephron3.71e-0815
blood vessel endothelial cell1.90e-0718
embryonic blood vessel endothelial progenitor cell1.90e-0718
kidney cortical cell2.64e-0712
renal cortical epithelial cell2.64e-0712
endothelial cell of vascular tree2.97e-0724
kidney cell3.60e-0717
kidney epithelial cell3.60e-0717
Uber Anatomy
Ontology termp-valuen
epithelial vesicle7.84e-2378
unilaminar epithelium7.67e-22148
vasculature3.74e-2178
vascular system3.74e-2178
epithelial tube2.32e-20117
somite3.64e-1971
presomitic mesoderm3.64e-1971
presumptive segmental plate3.64e-1971
dermomyotome3.64e-1971
trunk paraxial mesoderm3.64e-1971
multilaminar epithelium6.00e-1983
vessel2.62e-1868
paraxial mesoderm3.31e-1872
presumptive paraxial mesoderm3.31e-1872
dense mesenchyme tissue4.76e-1873
artery3.48e-1742
arterial blood vessel3.48e-1742
arterial system3.48e-1742
epithelial tube open at both ends4.22e-1759
blood vessel4.22e-1759
blood vasculature4.22e-1759
vascular cord4.22e-1759
splanchnic layer of lateral plate mesoderm4.47e-1783
trunk mesenchyme6.63e-17122
trunk3.70e-16199
skeletal muscle tissue3.77e-1662
striated muscle tissue3.77e-1662
myotome3.77e-1662
mesenchyme1.15e-15160
entire embryonic mesenchyme1.15e-15160
muscle tissue1.78e-1464
musculature1.78e-1464
musculature of body1.78e-1464
organism subdivision2.48e-14264
cardiovascular system3.24e-13109
systemic artery1.12e-1233
systemic arterial system1.12e-1233
circulatory system3.37e-12112
nephron epithelium3.71e-0815
renal tubule3.71e-0815
nephron tubule3.71e-0815
nephron3.71e-0815
uriniferous tubule3.71e-0815
nephrogenic mesenchyme3.71e-0815
parenchyma1.21e-0715
cell layer1.26e-07309
blood vessel endothelium1.90e-0718
endothelium1.90e-0718
cardiovascular system endothelium1.90e-0718
simple squamous epithelium2.05e-0722
cortex of kidney2.64e-0712
renal parenchyma2.64e-0712
excretory tube4.20e-0716
kidney epithelium4.20e-0716
epithelium4.57e-07306
larynx5.88e-079
mesoderm6.00e-07315
mesoderm-derived structure6.00e-07315
presumptive mesoderm6.00e-07315
aorta7.92e-0721
aortic system7.92e-0721


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)
MA0003.10.708947
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
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
MA0055.10.557638
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.14.54482
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
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
MA0106.12.25834
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.11.3784
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.11.12079
MA0140.12.07172
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.22.74132
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.21.39232
MA0150.10.744617
MA0151.10
MA0152.10.902317
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
MA0162.13.52399
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.90288
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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
EGR1#195834.988179094810140.008056488137383440.0320257132638142
TRIM28#10155212.39368336350830.008368344129438470.0329022133243393



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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