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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:44, 17 September 2013


Full id: C1394_large_bronchioalveolar_prostate_nonsmall_papillary_small_Alveolar



Phase1 CAGE Peaks

Hg19::chr14:36989336..36989354,-p5@NKX2-1
Hg19::chr14:36989358..36989378,-p3@NKX2-1
Hg19::chr14:36989379..36989390,-p8@NKX2-1
Hg19::chr14:36989407..36989410,-p15@NKX2-1
Hg19::chr14:36989412..36989423,-p12@NKX2-1
Hg19::chr14:36989427..36989442,-p1@NKX2-1


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>disease_data<br>

Cell Type
Ontology termp-valuen
endo-epithelial cell6.89e-1142
endodermal cell4.57e-0858
respiratory epithelial cell1.33e-0713
Uber Anatomy
Ontology termp-valuen
respiratory tract5.17e-1654
respiratory primordium2.31e-1538
endoderm of foregut2.31e-1538
respiratory system2.69e-1474
endoderm-derived structure2.62e-12160
endoderm2.62e-12160
presumptive endoderm2.62e-12160
corpus striatum6.19e-114
striatum6.19e-114
ventral part of telencephalon6.19e-114
future corpus striatum6.19e-114
digestive system2.05e-10145
digestive tract2.05e-10145
primitive gut2.05e-10145
thyroid gland2.58e-105
pharyngeal pouch2.58e-105
thyroid diverticulum2.58e-105
pharyngeal pouch 22.58e-105
thyroid primordium2.58e-105
larynx3.91e-109
lung1.41e-0922
respiratory tube1.41e-0922
respiration organ1.41e-0922
pair of lungs1.41e-0922
lung primordium1.41e-0922
lung bud1.41e-0922
caudate-putamen7.87e-093
dorsal striatum7.87e-093
thoracic cavity element3.33e-0834
thoracic cavity3.33e-0834
thoracic segment organ6.69e-0835
epithelial bud1.79e-0737
subdivision of digestive tract2.59e-07118
segment of respiratory tract3.28e-0747
endo-epithelium3.47e-0782
organ system subdivision3.80e-07223
foregut5.81e-0787
throat6.60e-072
Disease
Ontology termp-valuen
carcinoma9.90e-12106
cell type cancer1.21e-08143
cancer2.42e-07235
disease of cellular proliferation5.14e-07239


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)
MA0003.11.37104
MA0004.10.558729
MA0006.10.391183
MA0007.11.33289
MA0009.11.03681
MA0014.12.03395
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.464411
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.12.04333
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.14.99286
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.130.7358
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.11.61871
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.02896
MA0103.10.381434
MA0105.12.61648
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.15.31039
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.232472
MA0147.10.327615
MA0148.12.43826
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.22.74691
MA0138.20.765223
MA0002.20.709311
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.21.12726
MA0065.21.7308
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.11.09123
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.14.25353
MA0163.16.52785
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.237.163
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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#1488662.71700033932811.6349770986689e-111.98783903618022e-09
CTCF#1066465.360256373075034.21437267579784e-050.000755094986940557
SUZ12#23512650.11578091106296.2866744827465e-116.97740697453307e-09



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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