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{{Coexpression_clusters
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|full_id=C2586_Alveolar_acute_Renal_Mesenchymal_Bronchial_Trabecular_Corneal
|gostat_on_coexpression_clusters=GO:0005819!spindle!0.0375988370513273!991$GO:0007067!mitosis!0.0375988370513273!991$GO:0000087!M phase of mitotic cell cycle!0.0375988370513273!991$GO:0051301!cell division!0.0375988370513273!991$GO:0006511!ubiquitin-dependent protein catabolic process!0.0375988370513273!991$GO:0043632!modification-dependent macromolecule catabolic process!0.0375988370513273!991$GO:0019941!modification-dependent protein catabolic process!0.0375988370513273!991$GO:0051603!proteolysis involved in cellular protein catabolic process!0.0375988370513273!991$GO:0044257!cellular protein catabolic process!0.0375988370513273!991$GO:0000279!M phase!0.0375988370513273!991$GO:0000278!mitotic cell cycle!0.0375988370513273!991$GO:0030163!protein catabolic process!0.0375988370513273!991$GO:0022403!cell cycle phase!0.0375988370513273!991$GO:0043285!biopolymer catabolic process!0.0427774430153552!991$GO:0015630!microtubule cytoskeleton!0.0427774430153552!991$GO:0044265!cellular macromolecule catabolic process!0.0427774430153552!991$GO:0006512!ubiquitin cycle!0.0427774430153552!991$GO:0022402!cell cycle process!0.0435730353789808!991$GO:0009057!macromolecule catabolic process!0.0435730353789808!991
|id=C2586
|ontology_enrichment_celltype=CL:0000548!9.69e-24!679;CL:0000004!9.69e-24!679;CL:0000255!9.69e-24!679;CL:0000066!1.53e-23!254;CL:0000012!2.68e-23!682;CL:0002321!3.70e-17!248;CL:0000220!1.41e-16!246;CL:0000003!2.89e-12!722;CL:0000144!1.89e-11!625;CL:0000055!1.52e-10!180;CL:0000063!8.09e-10!578;CL:0000076!1.31e-09!62;CL:0000222!5.13e-08!119;CL:0002371!2.21e-07!591;CL:0000213!9.17e-07!57;CL:0000215!9.17e-07!57
|ontology_enrichment_disease=DOID:162!1.58e-31!235;DOID:14566!3.14e-30!239;DOID:0050686!7.05e-16!137;DOID:2531!1.01e-14!51;DOID:0060083!1.01e-14!51;DOID:0050687!1.64e-14!143;DOID:1240!2.45e-12!39;DOID:305!1.59e-11!106;DOID:8692!1.34e-09!31
|ontology_enrichment_uberon=UBERON:0003104!1.45e-07!238;UBERON:0009142!1.45e-07!238;UBERON:0000487!5.53e-07!22;UBERON:0000072!6.93e-07!46
}}

Latest revision as of 12:08, 17 September 2013


Full id: C2586_Alveolar_acute_Renal_Mesenchymal_Bronchial_Trabecular_Corneal



Phase1 CAGE Peaks

Hg19::chr1:43824577..43824636,+p2@CDC20
Hg19::chr1:43824639..43824659,+p1@CDC20
Hg19::chr1:43824669..43824680,+p3@CDC20
Hg19::chr9:89626496..89626506,+p1@CDC20P1


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:0005819spindle0.0375988370513273
GO:0007067mitosis0.0375988370513273
GO:0000087M phase of mitotic cell cycle0.0375988370513273
GO:0051301cell division0.0375988370513273
GO:0006511ubiquitin-dependent protein catabolic process0.0375988370513273
GO:0043632modification-dependent macromolecule catabolic process0.0375988370513273
GO:0019941modification-dependent protein catabolic process0.0375988370513273
GO:0051603proteolysis involved in cellular protein catabolic process0.0375988370513273
GO:0044257cellular protein catabolic process0.0375988370513273
GO:0000279M phase0.0375988370513273
GO:0000278mitotic cell cycle0.0375988370513273
GO:0030163protein catabolic process0.0375988370513273
GO:0022403cell cycle phase0.0375988370513273
GO:0043285biopolymer catabolic process0.0427774430153552
GO:0015630microtubule cytoskeleton0.0427774430153552
GO:0044265cellular macromolecule catabolic process0.0427774430153552
GO:0006512ubiquitin cycle0.0427774430153552
GO:0022402cell cycle process0.0435730353789808
GO:0009057macromolecule catabolic process0.0435730353789808



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 cell4.80e-24253
animal cell1.39e-23679
eukaryotic cell1.39e-23679
embryonic cell3.99e-17250
native cell1.77e-12722
squamous epithelial cell2.49e-0963
mesodermal cell2.91e-08121
lining cell2.50e-0758
barrier cell2.50e-0758
epithelial cell of nephron2.67e-0715
kidney cell4.32e-0717
kidney epithelial cell4.32e-0717
Uber Anatomy
Ontology termp-valuen
nephron epithelium2.67e-0715
renal tubule2.67e-0715
nephron tubule2.67e-0715
nephron2.67e-0715
uriniferous tubule2.67e-0715
nephrogenic mesenchyme2.67e-0715
simple squamous epithelium3.44e-0722
segment of respiratory tract9.97e-0747
Disease
Ontology termp-valuen
cancer5.60e-32235
disease of cellular proliferation9.52e-31239
organ system cancer6.37e-16137
cell type cancer9.55e-15143
hematologic cancer1.47e-1451
immune system cancer1.47e-1451
leukemia4.77e-1239
carcinoma7.84e-12106
myeloid leukemia3.00e-0931


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)
MA0003.10.443649
MA0004.10.71247
MA0006.10.532262
MA0007.11.65296
MA0009.11.20602
MA0014.10.896009
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.11.35734
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.13.69367
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.100363
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.14.77747
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.11.9583
MA0101.12.29123
MA0103.10.521546
MA0105.10.232357
MA0106.12.01886
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.16.90001
MA0146.12.31379
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.22.51225
MA0035.20.778873
MA0039.23.66694
MA0138.20.928035
MA0002.20.379056
MA0137.21.37305
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.918944
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.22.72671
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
BRCA1#672315.13817298241780.0004682184421431190.00430232851301999
CHD2#110637.758017125587640.003351522464536340.017300793528752
E2F4#187439.501045236463330.001850751034728270.0109296345669203
EP300#203335.08045629466740.01144298405398240.0418993027246035
ETS1#211337.296570691651750.00400857377511390.0192068374775942
FOS#235336.74846648167080.005032452776317940.0234709210693462
GABPB1#255335.300762877136630.01012678824234270.037864515152586
HDAC2#3066310.06171517746970.00156372754474740.00992489462448336
IRF1#365935.727872815172930.008097114790333330.0320117565048121
IRF3#3661335.23646415861723.79279212646878e-050.000720078925461322
MAX#414934.839416631755340.01315737137836840.0466301099251896
MXI1#460137.471178721569470.003741314738550960.018635912146684
NFYA#4800313.81918552487290.0006132411806734510.00508828916090844
NFYB#4801312.56984494015230.000811456397697350.00619002956096075
PAX5#507935.002174148383370.01196533174786410.0435038218421297
POU2F2#545236.829593043306890.004860473775203740.0227643849772861
SP2#6668319.61514787038350.0002171004269245340.00248642959618065
TAF7#687938.574802053692940.00250055433515240.0140360848225831
ZBTB33#10009323.74854377248590.0001229451908818380.00165574117221255



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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