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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:40, 17 September 2013


Full id: C1217_Mammary_Keratinocyte_Mallassezderived_Bronchial_Tracheal_Gingival_Sebocyte



Phase1 CAGE Peaks

Hg19::chr16:2128918..2128926,+p20@TSC2
Hg19::chr17:48609903..48609947,+p8@EPN3
Hg19::chr17:48610042..48610069,+p4@EPN3
Hg19::chr17:48611912..48611919,+p7@EPN3
Hg19::chr17:48611940..48611947,+p5@EPN3
Hg19::chr17:48611955..48611976,+p2@EPN3
Hg19::chr8:145009825..145009834,-p@chr8:145009825..145009834
-


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

GO IDGO nameFDR corrected p-value
GO:0043547positive regulation of GTPase activity0.0197795403877896



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><br>

Cell Type
Ontology termp-valuen
respiratory epithelial cell2.56e-2013
endo-epithelial cell2.59e-1942
general ecto-epithelial cell6.89e-1914
epithelial cell of tracheobronchial tree7.27e-149
epithelial cell of lower respiratory tract7.27e-149
mammary gland epithelial cell8.09e-144
endodermal cell8.68e-1358
bronchial epithelial cell1.27e-113
epithelial cell1.94e-11253
duct epithelial cell2.62e-113
branched duct epithelial cell2.62e-113
tracheal epithelial cell2.62e-113
tracheoblast2.62e-113
gingival epithelial cell2.90e-113
epithelial cell of Malassez3.21e-113
epidermal cell8.25e-109
stratified squamous epithelial cell1.00e-096
keratin accumulating cell1.00e-096
stratified epithelial cell1.00e-096
keratinizing barrier epithelial cell1.00e-096
epithelial fate stem cell1.00e-096
stratified epithelial stem cell1.00e-096
surface ectodermal cell1.00e-096
ecto-epithelial cell3.16e-0834
sebum secreting cell4.51e-082
epithelial cell of sweat gland4.51e-082
epithelial cell of skin gland4.51e-082
acinar cell of sebaceous gland4.51e-082
epithelial cell of alimentary canal2.49e-0720
keratinocyte4.12e-075
Uber Anatomy
Ontology termp-valuen
mammary gland8.09e-144
mammary bud8.09e-144
mammary ridge8.09e-144
mammary placode8.09e-144
lower respiratory tract epithelium1.27e-113
epithelium of bronchus1.27e-113
gingival epithelium2.90e-113
tracheobronchial tree1.47e-1015
lower respiratory tract1.47e-1015
respiratory system2.48e-1074
mucosa2.03e-0920
respiratory tract5.71e-0954
mouth mucosa8.48e-0913
jaw skeleton1.66e-084
splanchnocranium1.66e-084
skin gland4.51e-082
epidermis gland4.51e-082
gland of integumental system4.51e-082
sebaceous gland4.51e-082
skin sebaceous gland4.51e-082
sweat gland4.51e-082
sweat gland placode4.51e-082
sebaceous gland placode4.51e-082
trachea4.95e-087
respiratory airway4.95e-087
surface structure1.13e-0799
ecto-epithelium1.48e-07104
endoderm-derived structure2.29e-07160
endoderm2.29e-07160
presumptive endoderm2.29e-07160
female organism3.02e-0741
bronchus4.21e-075
external ectoderm6.61e-078
primary subdivision of cranial skeletal system7.20e-075
organ8.26e-07503


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)
MA0003.11.69543
MA0004.10.502801
MA0006.10.341337
MA0007.12.10741
MA0009.10.973289
MA0014.10.187674
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.10.490116
MA0051.11.46692
MA0052.10.896548
MA0055.10.362619
MA0056.10
MA0057.11.22064
MA0058.11.04727
MA0059.10.404929
MA0060.10.224688
MA0061.11.71672
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.488375
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.17.08007
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.538456
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.9112
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.918548
MA0103.10.332048
MA0105.12.29445
MA0106.10.648997
MA0107.11.3795
MA0108.20.806528
MA0109.10
MA0111.11.14351
MA0113.10.665691
MA0114.10.741402
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.11.46178
MA0146.11.16205
MA0147.10.768766
MA0148.10.528066
MA0149.11.36656
MA0062.20.563664
MA0035.20.564239
MA0039.21.14159
MA0138.20.704862
MA0002.20.611548
MA0137.20.36398
MA0104.20.636673
MA0047.20.636643
MA0112.22.55032
MA0065.22.65697
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.685508
MA0155.14.54415
MA0156.10.959643
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.485816
MA0163.10.19677
MA0164.10.678332
MA0080.20.911393
MA0018.20.650405
MA0099.21.40221
MA0079.21.1389
MA0102.21.51913
MA0258.11.27333
MA0259.10.289405
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#1488217.91914295409380.005060297063777310.0235671065794354
CTCFL#14069038.462774725274730.003894874828871490.0189860831856481
EP300#203354.838529804445140.001132708190785470.00775730562212746
FOXA1#316957.915299820989610.0001074487077454390.00149584585286936
GATA1#262335.811560633057330.01119311600820290.041128587509436
MYC#460953.730201336863860.003821944222306690.0188710302871354



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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