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{{Coexpression_clusters
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|full_id=C3629_clear_serous_papillotubular_testicular_signet_breast_esophagus
|id=C3629
}}

Latest revision as of 12:30, 17 September 2013


Full id: C3629_clear_serous_papillotubular_testicular_signet_breast_esophagus



Phase1 CAGE Peaks

Hg19::chr17:37894179..37894202,+p3@GRB7
Hg19::chr17:37894206..37894222,+p2@GRB7
Hg19::chr17:37894570..37894614,+p1@GRB7


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 cell1.42e-40253
endodermal cell6.14e-2058
endo-epithelial cell1.39e-1842
epithelial cell of alimentary canal1.99e-0920
kidney tubule cell1.98e-0810
nephron tubule epithelial cell1.98e-0810
kidney cell2.83e-0717
kidney epithelial cell2.83e-0717
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure4.77e-25160
endoderm4.77e-25160
presumptive endoderm4.77e-25160
digestive system1.77e-21145
digestive tract1.77e-21145
primitive gut1.77e-21145
subdivision of digestive tract1.86e-20118
trunk region element6.41e-18101
immaterial anatomical entity9.54e-15117
foregut9.87e-1587
respiratory system1.95e-1374
organ2.97e-13503
anatomical space4.11e-1395
renal system6.73e-1348
urinary system structure2.27e-1247
organ part2.97e-12218
endo-epithelium2.42e-1182
subdivision of trunk3.68e-11112
respiratory tract7.29e-1154
respiratory primordium3.80e-1038
endoderm of foregut3.80e-1038
organ system subdivision1.10e-09223
multi-tissue structure1.36e-09342
organism subdivision3.00e-09264
epithelial bud7.15e-0937
nephron tubule epithelium1.98e-0810
primordium2.00e-08160
reproductive structure3.16e-0859
reproductive system3.16e-0859
kidney3.40e-0826
kidney mesenchyme3.40e-0826
upper urinary tract3.40e-0826
kidney rudiment3.40e-0826
kidney field3.40e-0826
segment of respiratory tract5.97e-0847
abdomen element7.19e-0854
abdominal segment element7.19e-0854
thoracic cavity element8.86e-0834
thoracic cavity8.86e-0834
reproductive organ1.02e-0748
internal genitalia1.26e-0725
cavitated compound organ1.37e-0731
epithelial fold1.38e-0747
orifice1.40e-0736
thoracic segment organ2.55e-0735
organ segment2.98e-0798
lung4.37e-0722
respiratory tube4.37e-0722
respiration organ4.37e-0722
pair of lungs4.37e-0722
lung primordium4.37e-0722
lung bud4.37e-0722
anatomical cluster4.77e-07373
embryo5.27e-07592
multi-cellular organism6.72e-07656
anatomical cavity8.55e-0761
excretory tube9.50e-0716
kidney epithelium9.50e-0716
Disease
Ontology termp-valuen
carcinoma3.67e-34106
cell type cancer2.99e-24143
adenocarcinoma9.56e-1225
cancer2.31e-09235
squamous cell carcinoma4.89e-0914
disease of cellular proliferation1.49e-08239


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)
MA0003.10.708947
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.11.59304
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
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
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.12.5782
MA0105.13.21605
MA0106.10.986396
MA0107.11.36919
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
MA0145.10.752137
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
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
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.12.48891
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.26.90173
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
GATA3#2625327.2365163572064.94721007899563e-050.000850644836088615
HNF4A#3172215.42152690863580.005444210486686610.0246740105458715



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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