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{{Coexpression_clusters
{
|full_id=C2293_large_lung_nonsmall_throat_trachea_bronchioalveolar_thyroid
|

Latest revision as of 12:02, 17 September 2013


Full id: C2293_large_lung_nonsmall_throat_trachea_bronchioalveolar_thyroid



Phase1 CAGE Peaks

Hg19::chr14:36982935..36982943,-p9@SFTA3
Hg19::chr14:36982948..36982964,-p7@SFTA3
Hg19::chr8:55471706..55471714,+p3@RP1
Hg19::chr8:55471724..55471729,+p8@RP1


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:0007603phototransduction, visible light0.00508440105755542
GO:0007602phototransduction0.00508440105755542
GO:0050962detection of light stimulus during sensory perception0.00508440105755542
GO:0050908detection of light stimulus during visual perception0.00508440105755542
GO:0009584detection of visible light0.00508440105755542
GO:0009583detection of light stimulus0.00508440105755542
GO:0006228UTP biosynthetic process0.00508440105755542
GO:0046051UTP metabolic process0.00508440105755542
GO:0004550nucleoside diphosphate kinase activity0.00508440105755542
GO:0046036CTP metabolic process0.00508440105755542
GO:0009209pyrimidine ribonucleoside triphosphate biosynthetic process0.00508440105755542
GO:0009208pyrimidine ribonucleoside triphosphate metabolic process0.00508440105755542
GO:0006241CTP biosynthetic process0.00508440105755542
GO:0006183GTP biosynthetic process0.00508440105755542
GO:0046039GTP metabolic process0.00508440105755542
GO:0009220pyrimidine ribonucleotide biosynthetic process0.00508440105755542
GO:0009218pyrimidine ribonucleotide metabolic process0.00508440105755542
GO:0005929cilium0.00508440105755542
GO:0009582detection of abiotic stimulus0.00508440105755542
GO:0050906detection of stimulus during sensory perception0.00508440105755542
GO:0009581detection of external stimulus0.00508440105755542
GO:0009147pyrimidine nucleoside triphosphate metabolic process0.00508440105755542
GO:0006221pyrimidine nucleotide biosynthetic process0.0051551405505301
GO:0006220pyrimidine nucleotide metabolic process0.00626398210290828
GO:0016776phosphotransferase activity, phosphate group as acceptor0.00626398210290828
GO:0051606detection of stimulus0.00671140939597316
GO:0009416response to light stimulus0.00671140939597316
GO:0019205nucleobase, nucleoside, nucleotide kinase activity0.00727069351230425
GO:0009314response to radiation0.00779140631026768
GO:0009206purine ribonucleoside triphosphate biosynthetic process0.00820283370618941
GO:0009145purine nucleoside triphosphate biosynthetic process0.00820283370618941
GO:0009201ribonucleoside triphosphate biosynthetic process0.00820283370618941
GO:0009142nucleoside triphosphate biosynthetic process0.00820283370618941
GO:0009205purine ribonucleoside triphosphate metabolic process0.00820283370618941
GO:0009144purine nucleoside triphosphate metabolic process0.00820283370618941
GO:0009199ribonucleoside triphosphate metabolic process0.00820283370618941
GO:0009152purine ribonucleotide biosynthetic process0.00859263778726866
GO:0009141nucleoside triphosphate metabolic process0.00859263778726866
GO:0009150purine ribonucleotide metabolic process0.00859263778726866
GO:0009260ribonucleotide biosynthetic process0.00859263778726866
GO:0006164purine nucleotide biosynthetic process0.00859263778726866
GO:0009628response to abiotic stimulus0.00859263778726866
GO:0006163purine nucleotide metabolic process0.00859263778726866
GO:0009259ribonucleotide metabolic process0.00859263778726866
GO:0007601visual perception0.0108452485166813
GO:0050953sensory perception of light stimulus0.0108452485166813
GO:0005625soluble fraction0.0111380836784235
GO:0009165nucleotide biosynthetic process0.0118847874720358
GO:0042995cell projection0.0142902798703374
GO:0009117nucleotide metabolic process0.0152125279642058
GO:0055086nucleobase, nucleoside and nucleotide metabolic process0.0160986094661578
GO:0009605response to external stimulus0.0272328342798141
GO:0000267cell fraction0.0380735300325018
GO:0007600sensory perception0.0393570304084845



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>

Cell Type
Ontology termp-valuen
brush border epithelial cell4.95e-103
kidney cortex tubule cell4.95e-103
epithelial cell of proximal tubule4.95e-103
lung fibroblast1.41e-081
Uber Anatomy
Ontology termp-valuen
thyroid gland1.52e-225
pharyngeal pouch1.52e-225
thyroid diverticulum1.52e-225
pharyngeal pouch 21.52e-225
thyroid primordium1.52e-225
throat2.36e-152
lung2.72e-1522
respiratory tube2.72e-1522
respiration organ2.72e-1522
pair of lungs2.72e-1522
lung primordium2.72e-1522
lung bud2.72e-1522
epithelial bud4.39e-1437
endo-epithelium4.91e-1482
thoracic cavity element1.86e-1234
thoracic cavity1.86e-1234
thoracic segment organ4.55e-1235
respiratory primordium5.04e-1138
endoderm of foregut5.04e-1138
epithelial fold8.77e-1147
entire pharyngeal arch endoderm2.37e-1011
early pharyngeal endoderm2.37e-1011
renal cortex tubule4.95e-103
region of nephron tubule4.95e-103
proximal tubule4.95e-103
lower lobe of right lung1.13e-081
right lung lobe1.13e-081
lower lobe of lung1.13e-081
lobe of lung1.13e-081
right lung1.13e-081
digestive system6.87e-08145
digestive tract6.87e-08145
primitive gut6.87e-08145
trunk region element7.85e-08101
thoracic segment of trunk9.64e-0852
respiratory tract2.06e-0754
endoderm-derived structure6.86e-07160
endoderm6.86e-07160
presumptive endoderm6.86e-07160
subdivision of trunk7.50e-07112
Disease
Ontology termp-valuen
papillary adenocarcinoma4.72e-081
lung cancer7.62e-0815
lung carcinoma9.96e-089
respiratory system cancer2.33e-0716


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.524262
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.12.80052
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.599068
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.11.57689
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.12.2938
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.10.221129
MA0147.10.46175
MA0148.14.23774
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.777367
MA0138.20.928035
MA0002.21.75253
MA0137.20.558189
MA0104.20.392359
MA0047.21.99204
MA0112.20.187982
MA0065.20.199162
MA0150.11.53138
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.533581
MA0156.10.560797
MA0157.12.23474
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.539587
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.869502
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
CTBP2#1488231.35850016966410.001492676882047230.00953828199242111
SUZ12#23512225.05789045553150.002325256716520610.0131853342500107



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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