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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 12:25, 17 September 2013


Full id: C3405_squamous_Urothelial_Mallassezderived_Sebocyte_Gingival_Small_Prostate



Phase1 CAGE Peaks

Hg19::chr14:21510433..21510440,+p4@RNASE7
Hg19::chr14:21510460..21510479,+p2@RNASE7
Hg19::chr14:21510487..21510506,+p3@RNASE7


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 cell2.70e-3542
endodermal cell1.04e-2558
epithelial cell1.03e-20253
epithelial cell of alimentary canal1.67e-2020
respiratory epithelial cell3.68e-2013
general ecto-epithelial cell3.50e-1914
acinar cell3.05e-145
transitional epithelial cell9.14e-134
urothelial cell9.14e-134
protein secreting cell8.38e-126
squamous epithelial cell3.53e-1163
epithelial cell of tracheobronchial tree2.52e-109
epithelial cell of lower respiratory tract2.52e-109
gingival epithelial cell6.14e-103
epithelial cell of Malassez1.03e-093
ecto-epithelial cell1.14e-0934
duct epithelial cell7.33e-093
branched duct epithelial cell7.33e-093
tracheal epithelial cell7.33e-093
tracheoblast7.33e-093
acinar cell of salivary gland1.02e-083
bronchial epithelial cell1.13e-083
chorionic membrane mesenchymal stem cell1.26e-083
epidermal cell3.96e-089
stratified squamous epithelial cell6.56e-086
keratin accumulating cell6.56e-086
stratified epithelial cell6.56e-086
keratinizing barrier epithelial cell6.56e-086
epithelial fate stem cell6.56e-086
stratified epithelial stem cell6.56e-086
surface ectodermal cell6.56e-086
glandular epithelial cell9.90e-089
mammary gland epithelial cell2.00e-074
sebum secreting cell3.20e-072
epithelial cell of sweat gland3.20e-072
epithelial cell of skin gland3.20e-072
acinar cell of sebaceous gland3.20e-072
embryonic cell4.96e-07250
Uber Anatomy
Ontology termp-valuen
respiratory system8.71e-2074
oral opening3.72e-1822
orifice8.44e-1836
endoderm-derived structure6.03e-17160
endoderm6.03e-17160
presumptive endoderm6.03e-17160
surface structure5.55e-1699
urothelium2.94e-155
mouth2.96e-1529
stomodeum2.96e-1529
mucosa1.17e-1420
anterior region of body5.22e-1462
craniocervical region5.22e-1462
head5.29e-1356
mouth mucosa8.67e-1313
transitional epithelium1.22e-126
respiratory tract8.81e-1254
mucosa of oral region4.11e-114
respiratory system mucosa4.11e-114
pharynx1.48e-1011
subdivision of head2.22e-1049
gingival epithelium6.14e-103
digestive system1.40e-09145
digestive tract1.40e-09145
primitive gut1.40e-09145
neck7.06e-0910
chordate pharynx9.66e-0910
pharyngeal region of foregut9.66e-0910
lower respiratory tract epithelium1.13e-083
epithelium of bronchus1.13e-083
tongue1.19e-083
gustatory system1.19e-083
future tongue1.19e-083
acellular anatomical structure1.26e-083
egg chorion1.26e-083
pharyngeal arch system1.97e-0818
respiratory system epithelium9.10e-0828
segment of respiratory tract9.84e-0847
mammary gland2.00e-074
mammary bud2.00e-074
mammary ridge2.00e-074
mammary placode2.00e-074
jaw skeleton2.32e-074
splanchnocranium2.32e-074
skin gland3.20e-072
epidermis gland3.20e-072
gland of integumental system3.20e-072
sebaceous gland3.20e-072
skin sebaceous gland3.20e-072
sweat gland3.20e-072
sweat gland placode3.20e-072
sebaceous gland placode3.20e-072
subdivision of digestive tract9.73e-07118
organ component layer9.97e-0766
Disease
Ontology termp-valuen
squamous cell carcinoma1.18e-2114


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
MA0009.14.74507
MA0014.10.118426
MA0017.11.64148
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
MA0048.10.341392
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
MA0073.11.36698
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
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.11.52002
MA0105.10.31555
MA0106.12.25834
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
MA0115.11.57693
MA0116.11.3784
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
MA0144.11.31729
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
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
MA0154.10.312019
MA0155.11.31345
MA0156.11.60572
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.12.32251
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0373086
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
GATA1#2623313.56030814380040.0004009615963782630.00387239025006005



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.