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{{Coexpression_clusters
{
|full_id=C3310_Keratinocyte_Bronchial_Corneal_Small_Tracheal_Mammary_Prostate
|

Latest revision as of 12:23, 17 September 2013


Full id: C3310_Keratinocyte_Bronchial_Corneal_Small_Tracheal_Mammary_Prostate



Phase1 CAGE Peaks

Hg19::chr12:58159332..58159353,-p3@CYP27B1
Hg19::chr12:58159361..58159394,-p2@CYP27B1
Hg19::chr17:28898830..28898835,-p1@ENST00000420566


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:0004498calcidiol 1-monooxygenase activity0.00167785234899329
GO:0016709oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen0.0212527964205816
GO:0009110vitamin biosynthetic process0.0212527964205816
GO:0019825oxygen binding0.0218120805369128
GO:0006766vitamin metabolic process0.0218120805369128
GO:0006874cellular calcium ion homeostasis0.0218120805369128
GO:0055074calcium ion homeostasis0.0218120805369128
GO:0006875cellular metal ion homeostasis0.0218120805369128
GO:0055065metal ion homeostasis0.0218120805369128
GO:0016705oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen0.0218120805369128
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0218120805369128
GO:0055066di-, tri-valent inorganic cation homeostasis0.0218120805369128
GO:0006816calcium ion transport0.0218120805369128
GO:0030003cellular cation homeostasis0.0218120805369128
GO:0055080cation homeostasis0.0218120805369128
GO:0004497monooxygenase activity0.0218120805369128
GO:0055082cellular chemical homeostasis0.0218120805369128
GO:0006873cellular ion homeostasis0.0218120805369128
GO:0015674di-, tri-valent inorganic cation transport0.0218120805369128
GO:0050801ion homeostasis0.0220309308433032
GO:0020037heme binding0.0220309308433032
GO:0046906tetrapyrrole binding0.0220309308433032
GO:0048878chemical homeostasis0.0220309308433032
GO:0019725cellular homeostasis0.0262164429530201
GO:0042592homeostatic process0.0322147651006711
GO:0005506iron ion binding0.0324599896747548
GO:0030001metal ion transport0.0423813074819786
GO:0006118electron transport0.0434443911792905
GO:0006812cation transport0.0491205739412173
GO:0006091generation of precursor metabolites and energy0.0499685402684563
GO:0006629lipid metabolic process0.0499685402684563
GO:0065008regulation of biological quality0.0499685402684563



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
epithelial cell5.46e-26253
endo-epithelial cell2.17e-2242
respiratory epithelial cell1.72e-1813
general ecto-epithelial cell4.00e-1614
endodermal cell7.43e-1658
mammary gland epithelial cell1.92e-104
epithelial cell of tracheobronchial tree4.36e-109
epithelial cell of lower respiratory tract4.36e-109
transitional epithelial cell6.49e-104
urothelial cell6.49e-104
bronchial epithelial cell1.14e-083
duct epithelial cell1.23e-083
branched duct epithelial cell1.23e-083
tracheal epithelial cell1.23e-083
tracheoblast1.23e-083
gingival epithelial cell2.48e-083
ecto-epithelial cell7.70e-0834
epithelial cell of alimentary canal8.37e-0820
epithelial cell of Malassez9.97e-083
epithelial cell of prostate1.41e-073
stratified squamous epithelial cell4.25e-076
keratin accumulating cell4.25e-076
stratified epithelial cell4.25e-076
keratinizing barrier epithelial cell4.25e-076
epithelial fate stem cell4.25e-076
stratified epithelial stem cell4.25e-076
surface ectodermal cell4.25e-076
epidermal cell5.11e-079
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure8.32e-14160
endoderm8.32e-14160
presumptive endoderm8.32e-14160
urothelium9.62e-125
endo-epithelium7.92e-1182
respiratory system1.35e-1074
mammary gland1.92e-104
mammary bud1.92e-104
mammary ridge1.92e-104
mammary placode1.92e-104
transitional epithelium1.03e-096
respiratory tract1.62e-0954
mucosa2.35e-0920
epithelial fold4.35e-0947
digestive system9.52e-09145
digestive tract9.52e-09145
primitive gut9.52e-09145
lower respiratory tract epithelium1.14e-083
epithelium of bronchus1.14e-083
gingival epithelium2.48e-083
surface structure4.02e-0899
epithelial bud5.89e-0837
epithelium of mucosa2.11e-078
tracheobronchial tree2.67e-0715
lower respiratory tract2.67e-0715


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
MA0014.10.118426
MA0017.10.686276
MA0019.12.26702
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
MA0057.10.333427
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
MA0073.10.668628
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
MA0105.11.5295
MA0106.10.986396
MA0107.11.36919
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.13.4624
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
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.11.37817
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
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
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.10.256269
MA0156.11.60572
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.69213
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
SUZ12#23512233.41052060737530.00117826764536030.00799643216672844



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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