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Coexpression cluster:C2487: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2487_Alveolar_Mesenchymal_Renal_Placental_Bronchial_acute_Tracheal
|id=C2487
}}

Latest revision as of 12:06, 17 September 2013


Full id: C2487_Alveolar_Mesenchymal_Renal_Placental_Bronchial_acute_Tracheal



Phase1 CAGE Peaks

Hg19::chr19:39421556..39421632,+p1@MRPS12
Hg19::chr19:39971470..39971498,+p1@TIMM50
Hg19::chr1:26496382..26496457,+p1@ZNF593
Hg19::chr21:46359907..46359962,+p1@FAM207A


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:0044429mitochondrial part0.0469200548296613
GO:0005744mitochondrial inner membrane presequence translocase complex0.0469200548296613
GO:0043021ribonucleoprotein binding0.0469200548296613
GO:0007006mitochondrial membrane organization and biogenesis0.0469200548296613
GO:0031974membrane-enclosed lumen0.0469200548296613
GO:0043233organelle lumen0.0469200548296613
GO:0005739mitochondrion0.0469200548296613



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
trunk5.71e-16199
unilaminar epithelium2.15e-13148
mesenchyme4.17e-13160
entire embryonic mesenchyme4.17e-13160
organism subdivision4.18e-13264
epithelial vesicle2.22e-1278
trunk mesenchyme3.80e-11122
epithelial tube1.32e-10117
multilaminar epithelium2.55e-1083
somite1.61e-0971
presomitic mesoderm1.61e-0971
presumptive segmental plate1.61e-0971
dermomyotome1.61e-0971
trunk paraxial mesoderm1.61e-0971
paraxial mesoderm4.47e-0972
presumptive paraxial mesoderm4.47e-0972
dense mesenchyme tissue6.85e-0973
trunk region element8.31e-09101
subdivision of trunk4.05e-08112
nephron epithelium5.97e-0815
renal tubule5.97e-0815
nephron tubule5.97e-0815
nephron5.97e-0815
uriniferous tubule5.97e-0815
nephrogenic mesenchyme5.97e-0815
skeletal muscle tissue1.41e-0762
striated muscle tissue1.41e-0762
myotome1.41e-0762
cortex1.77e-0715
cell layer2.11e-07309
cortex of kidney3.37e-0712
renal parenchyma3.37e-0712
urinary system structure3.71e-0747
epithelium4.42e-07306
parenchyma4.49e-0715
excretory tube7.86e-0716
kidney epithelium7.86e-0716
renal system8.60e-0748
Disease
Ontology termp-valuen
cancer2.14e-18235
disease of cellular proliferation2.49e-18239
cell type cancer1.84e-10143
organ system cancer1.92e-08137
hematologic cancer7.55e-0851
immune system cancer7.55e-0851
carcinoma9.38e-08106


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)
MA0003.13.49532
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.11.86845
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.13.41834
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
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.11.80156
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
MA0073.10.214613
MA0074.10.819248
MA0076.12.5647
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.11.15856
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
MA0139.10.912459
MA0140.10.779643
MA0141.11.46638
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.11.08195
MA0146.10.481
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.23.45291
MA0035.20.778873
MA0039.20.777367
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.180766
MA0156.11.37856
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.10.756582
MA0161.10
MA0162.10.640035
MA0163.10.918944
MA0164.10.90014
MA0080.20.535868
MA0018.22.02192
MA0099.20.7872
MA0079.20.0626799
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
CCNT2#90534.752151182721970.01386206996689490.0487241518955519
CEBPB#105135.978360719368610.007153832484726970.029727414589281
CHD2#110637.758017125587640.003351522464536340.0172965189837284
CTCF#1066445.360256373075030.001211145381643620.0081738812609679
E2F6#187645.017155731697390.00157802193473060.00997017742536775
ELF1#199744.258097958807540.003041525565781240.0160902587663168
ESRRA#21011120.9600785340310.008241662461779040.032484846807025
ETS1#211349.728760922202340.0001115955317418140.00154574611930813
FOS#235336.74846648167080.005032452776317940.023465681556651
GABPB1#255335.300762877136630.01012678824234270.0378618041541502
HEY1#2346244.040111043105710.00375304636917980.0186091444595152
HMGN3#932436.133910792512940.006640696683324720.0282965206409527
IRF1#365947.63716375356390.0002938853996185490.00307515251485439
JUNB#3726215.30531632991060.006126947148475620.0271002978671711
JUND#372735.245997956403270.01043432751748420.038691664533944
MAX#414946.452555509007120.0005767613195645490.0048546401881046
MEF2C#4208220.6556772463120.003402570579445040.0173575474403683
MXI1#460149.96157162875930.0001015224754950450.00142378216976326
MYC#460945.22228187160940.001344309395272740.00887810351162826
NANOG#79923214.62238924050630.006698757715363760.028490452721733
NR2C2#7182216.30730545262040.005411825344648220.0245549407928454
PAX5#507946.669565531177830.0005052774169483260.00443898621708161
REST#597837.237521537096020.004104697304192610.0195793780202134
SIN3A#2594245.408884726815140.001168172384885160.00796414620438807
SP1#666745.69838137814090.0009482606065333980.00684229580528821
SP2#6668319.61514787038350.0002171004269245340.00248615696135651
SRF#6722310.34788369662590.001439893778401260.00923830116245542
TAF1#687243.343046285745290.008005664898701650.0322284869273215
TAF7#687938.574802053692940.00250055433515240.0140338220328326
TBP#690843.706770687096390.005296377814784350.0244269552924823
USF1#739146.361499277207960.0006105011399140830.00507927416167346
YY1#752844.911170749853860.00171871838055440.0106877778473785
ZBTB7A#5134147.35190930787590.000342223540015990.00346567286878018
ZNF143#7702310.12565741417090.001534861610688180.00976601753129422



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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