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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:41, 17 September 2013


Full id: C1300_Tracheal_Bronchial_Small_Keratinocyte_Mammary_bronchial_Urothelial



Phase1 CAGE Peaks

Hg19::chr10:120261556..120261561,+p@chr10:120261556..120261561
+
Hg19::chr10:73679250..73679255,-p@chr10:73679250..73679255
-
Hg19::chr19:16845025..16845028,-p@chr19:16845025..16845028
-
Hg19::chr1:152475755..152475761,+p@chr1:152475755..152475761
+
Hg19::chr8:8377227..8377229,-p@chr8:8377227..8377229
-
Hg19::chr9:26747081..26747110,+p@chr9:26747081..26747110
+


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 cell2.01e-2842
respiratory epithelial cell7.47e-2613
epithelial cell4.46e-23253
endodermal cell2.28e-1958
epithelial cell of tracheobronchial tree1.17e-179
epithelial cell of lower respiratory tract1.17e-179
squamous epithelial cell3.12e-1563
bronchial epithelial cell2.51e-143
duct epithelial cell2.86e-143
branched duct epithelial cell2.86e-143
tracheal epithelial cell2.86e-143
tracheoblast2.86e-143
general ecto-epithelial cell7.61e-1414
epithelial cell of alimentary canal5.90e-1220
epidermal cell9.37e-129
stratified squamous epithelial cell1.03e-116
keratin accumulating cell1.03e-116
stratified epithelial cell1.03e-116
keratinizing barrier epithelial cell1.03e-116
epithelial fate stem cell1.03e-116
stratified epithelial stem cell1.03e-116
surface ectodermal cell1.03e-116
mammary gland epithelial cell1.67e-104
sebum secreting cell1.59e-092
epithelial cell of sweat gland1.59e-092
epithelial cell of skin gland1.59e-092
acinar cell of sebaceous gland1.59e-092
keratinocyte2.49e-085
Uber Anatomy
Ontology termp-valuen
mucosa of oral region4.13e-174
respiratory system mucosa4.13e-174
mouth mucosa1.05e-1413
lower respiratory tract epithelium2.51e-143
epithelium of bronchus2.51e-143
mucosa5.29e-1220
mammary gland1.67e-104
mammary bud1.67e-104
mammary ridge1.67e-104
mammary placode1.67e-104
surface structure1.88e-1099
tracheobronchial tree2.64e-1015
lower respiratory tract2.64e-1015
endoderm-derived structure3.47e-10160
endoderm3.47e-10160
presumptive endoderm3.47e-10160
skin gland1.59e-092
epidermis gland1.59e-092
gland of integumental system1.59e-092
sebaceous gland1.59e-092
skin sebaceous gland1.59e-092
sweat gland1.59e-092
sweat gland placode1.59e-092
sebaceous gland placode1.59e-092
respiratory system1.64e-0974
orifice2.39e-0936
bronchus9.32e-095
urothelium2.96e-085
epithelial bud9.79e-0837
epithelial fold4.15e-0747
transitional epithelium6.09e-076
skin epidermis6.41e-0715
outer epithelium6.41e-0715
enveloping layer of ectoderm6.41e-0715
neck7.03e-0710
Disease
Ontology termp-valuen
squamous cell carcinoma4.90e-2814
carcinoma2.99e-08106


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)
MA0003.10.00461978
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.0254709
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
MA0048.10.152639
MA0050.11.34656
MA0051.11.58921
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.450439
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00076337
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.32124
MA0089.10
MA0090.11.22966
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.11.68738
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
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.811435
MA0145.10.107156
MA0146.10.0213085
MA0147.10.327615
MA0148.10.584698
MA0149.13.68937
MA0062.20.23336
MA0035.20.621793
MA0039.20.0313803
MA0138.20.765223
MA0002.20.255126
MA0137.21.06611
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
MA0150.11.21643
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.318517
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.0270301
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.00183606
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
STAT3#677458.766220830961874.28672496720299e-050.000765824955268068



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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