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

Latest revision as of 12:37, 17 September 2013


Full id: C4016_gastrointestinal_anaplastic_maxillary_small_smallcell_argyrophil_Bronchial



Phase1 CAGE Peaks

Hg19::chr20:22565370..22565388,-p2@FOXA2
Hg19::chr20:22565612..22565627,-p@chr20:22565612..22565627
-
Hg19::chr20:22565646..22565665,-p@chr20:22565646..22565665
-


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
epithelial cell1.65e-15253
endodermal cell3.37e-1558
endo-epithelial cell1.80e-1142
respiratory epithelial cell1.86e-1013
epithelial cell of lung2.18e-0819
metabolising cell5.05e-0712
endopolyploid cell5.05e-0712
parenchymal cell5.05e-0712
polyploid cell5.05e-0712
hepatocyte5.05e-0712
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.50e-18160
endoderm1.50e-18160
presumptive endoderm1.50e-18160
digestive system4.02e-18145
digestive tract4.02e-18145
primitive gut4.02e-18145
subdivision of digestive tract2.05e-17118
endo-epithelium9.00e-1682
trunk region element1.12e-12101
foregut4.57e-1287
immaterial anatomical entity1.55e-11117
gut epithelium2.23e-0954
epithelium of foregut-midgut junction3.21e-0925
anatomical boundary3.21e-0925
hepatobiliary system3.21e-0925
foregut-midgut junction3.21e-0925
septum transversum3.21e-0925
respiratory tract4.98e-0954
epithelial bud8.42e-0937
lung1.30e-0822
respiratory tube1.30e-0822
respiration organ1.30e-0822
pair of lungs1.30e-0822
lung primordium1.30e-0822
lung bud1.30e-0822
thoracic cavity element1.88e-0834
thoracic cavity1.88e-0834
respiratory tract epithelium2.18e-0819
lung epithelium2.18e-0819
thoracic segment organ3.98e-0835
epithelial sac8.15e-0825
sac1.97e-0726
epithelial fold2.21e-0747
hepatic diverticulum2.26e-0722
liver primordium2.26e-0722
respiratory primordium2.97e-0738
endoderm of foregut2.97e-0738
subdivision of trunk3.00e-07112
respiratory system3.93e-0774
digestive tract diverticulum5.68e-0723
gastrointestinal system8.47e-0725
Disease
Ontology termp-valuen
carcinoma5.69e-17106
cell type cancer8.35e-14143
cancer4.18e-09235
disease of cellular proliferation1.10e-08239
respiratory system cancer2.78e-0816
gastrointestinal system cancer1.56e-0714
disease of anatomical entity4.83e-0739
lung cancer9.19e-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)
MA0003.10.401049
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.12.44638
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.06172
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
MA0073.10.211629
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.11.77664
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
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.707589
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.15986
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
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
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.23.14419
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
HDAC2#3066313.41562023662630.0004140761399857210.00391611862573293
SREBF1#6720347.00584944048839.62099323994382e-060.000254768487065541
SUZ12#23512233.41052060737530.00117826764536030.00799955110276175
ZNF263#1012738.221841637010680.001799043925565870.0109563443082497



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.