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Coexpression cluster:C4384: Difference between revisions

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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 12:44, 17 September 2013


Full id: C4384_squamous_oral_serous_Corneal_Gingival_bronchioalveolar_Keratinocyte



Phase1 CAGE Peaks

Hg19::chr4:15920199..15920212,+p@chr4:15920199..15920212
+
Hg19::chr4:15920326..15920338,+p@chr4:15920326..15920338
+
Hg19::chr4:15920342..15920362,+p@chr4:15920342..15920362
+


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 cell5.02e-5142
endodermal cell8.26e-3858
epithelial cell3.65e-31253
respiratory epithelial cell5.30e-2913
epithelial cell of alimentary canal1.79e-2120
epithelial cell of tracheobronchial tree6.81e-189
epithelial cell of lower respiratory tract6.81e-189
gingival epithelial cell1.29e-113
duct epithelial cell4.27e-113
branched duct epithelial cell4.27e-113
tracheal epithelial cell4.27e-113
tracheoblast4.27e-113
bronchial epithelial cell1.06e-103
squamous epithelial cell4.43e-1063
embryonic cell6.13e-10250
stratified squamous epithelial cell1.32e-096
keratin accumulating cell1.32e-096
stratified epithelial cell1.32e-096
keratinizing barrier epithelial cell1.32e-096
epithelial fate stem cell1.32e-096
stratified epithelial stem cell1.32e-096
surface ectodermal cell1.32e-096
general ecto-epithelial cell1.02e-0814
corneal epithelial cell2.30e-082
keratinocyte4.36e-075
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure6.80e-15160
endoderm6.80e-15160
presumptive endoderm6.80e-15160
respiratory system1.44e-1474
tracheobronchial tree4.03e-1315
lower respiratory tract4.03e-1315
mouth mucosa3.07e-1213
gingival epithelium1.29e-113
lower respiratory tract epithelium1.06e-103
epithelium of bronchus1.06e-103
digestive system1.83e-10145
digestive tract1.83e-10145
primitive gut1.83e-10145
mucosa6.52e-1020
orifice5.82e-0936
respiratory tract9.18e-0954
oral opening1.05e-0822
mucosa of oral region2.49e-084
respiratory system mucosa2.49e-084
thoracic cavity element6.39e-0834
thoracic cavity6.39e-0834
mouth7.09e-0829
stomodeum7.09e-0829
trachea8.51e-087
respiratory airway8.51e-087
thoracic segment organ1.22e-0735
epithelial fold1.32e-0747
endo-epithelium1.65e-0782
epithelial bud6.60e-0737
surface structure8.97e-0799
Disease
Ontology termp-valuen
squamous cell carcinoma3.11e-1814
carcinoma2.01e-09106


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
MA0009.11.3275
MA0014.10.118426
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
MA0048.12.45333
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
MA0073.10.0185922
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
MA0103.10.628063
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
MA0119.14.04858
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
MA0140.12.07172
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.24.88709
MA0039.20.0526989
MA0138.21.04628
MA0002.21.20011
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
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0107199
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
GATA2#2624312.7449317335540.0004829527704283790.00438219847009292



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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