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{{Coexpression_clusters
{
|full_id=C1917_clear_epididymis_serous_uterus_kidney_B_ductus
 

Latest revision as of 11:54, 17 September 2013


Full id: C1917_clear_epididymis_serous_uterus_kidney_B_ductus



Phase1 CAGE Peaks

Hg19::chr3:112127710..112127713,-p@chr3:112127710..112127713
-
Hg19::chr3:112128019..112128034,-p1@ENST00000486726
Hg19::chr3:112128117..112128134,-p2@ENST00000486726
Hg19::chr5:138905822..138905827,+p10@UBE2D2
Hg19::chr7:76911466..76911478,+p4@CCDC146


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:0004842ubiquitin-protein ligase activity0.033249604249251
GO:0008639small protein conjugating enzyme activity0.033249604249251
GO:0019787small conjugating protein ligase activity0.033249604249251
GO:0006511ubiquitin-dependent protein catabolic process0.033249604249251
GO:0043632modification-dependent macromolecule catabolic process0.033249604249251
GO:0019941modification-dependent protein catabolic process0.033249604249251
GO:0051603proteolysis involved in cellular protein catabolic process0.033249604249251
GO:0044257cellular protein catabolic process0.033249604249251
GO:0016881acid-amino acid ligase activity0.033249604249251
GO:0030163protein catabolic process0.0337550710210548
GO:0016879ligase activity, forming carbon-nitrogen bonds0.0337550710210548
GO:0051246regulation of protein metabolic process0.0349518608084486
GO:0043285biopolymer catabolic process0.0349518608084486
GO:0044265cellular macromolecule catabolic process0.0366301660190745
GO:0006512ubiquitin cycle0.0366301660190745
GO:0009057macromolecule catabolic process0.0380901919227599
GO:0016874ligase activity0.0380901919227599
GO:0044248cellular catabolic process0.0449814880228161



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>

Uber Anatomy
Ontology termp-valuen
urinary system structure1.13e-2447
renal system4.20e-2448
nephron tubule epithelium1.71e-2310
excretory tube1.14e-1916
kidney epithelium1.14e-1916
kidney1.79e-1926
kidney mesenchyme1.79e-1926
upper urinary tract1.79e-1926
kidney rudiment1.79e-1926
kidney field1.79e-1926
cavitated compound organ4.28e-1631
nephron epithelium1.70e-1515
renal tubule1.70e-1515
nephron tubule1.70e-1515
nephron1.70e-1515
uriniferous tubule1.70e-1515
nephrogenic mesenchyme1.70e-1515
male genital duct4.59e-103
internal male genitalia4.59e-103
renal cortex tubule7.15e-103
region of nephron tubule7.15e-103
proximal tubule7.15e-103
acellular anatomical structure2.21e-093
egg chorion2.21e-093
reproductive structure2.64e-0959
reproductive system2.64e-0959
cortex of kidney4.75e-0912
renal parenchyma4.75e-0912
chorion1.13e-087
abdomen element1.30e-0854
abdominal segment element1.30e-0854
epididymis2.89e-081
epithelium of female gonad3.32e-081
vas deferens4.35e-081
spermatic cord4.35e-081
uterus or analog4.66e-081
duct of male reproductive system9.42e-084
abdominal segment of trunk1.32e-0760
abdomen1.32e-0760
reproductive organ1.37e-0748
male organism2.87e-0722
male reproductive system2.87e-0722
cortex2.96e-0715
parenchyma2.96e-0715
Disease
Ontology termp-valuen
ovary epithelial cancer3.32e-081


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)
MA0003.10.00991994
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.11.55893
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.692739
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.00220137
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.11.36977
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.973423
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.12.57792
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.442008
MA0146.10.6031
MA0147.10.386018
MA0148.10.653474
MA0149.12.7505
MA0062.20.284987
MA0035.20.691506
MA0039.20.0118463
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.839774
MA0065.20.880827
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.12.71958
MA0154.10.172764
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.23.83292e-05
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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

No analysis results for this cluster

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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