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{{Coexpression_clusters
{
|full_id=C3414_Smooth_Alveolar_Mallassezderived_mucinous_Placental_Bronchial_hepatocellular
|

Latest revision as of 12:25, 17 September 2013


Full id: C3414_Smooth_Alveolar_Mallassezderived_mucinous_Placental_Bronchial_hepatocellular



Phase1 CAGE Peaks

Hg19::chr14:23504087..23504118,-p1@PSMB5
Hg19::chr14:24701539..24701583,-p1@NEDD8-MDP1
p1@NEDD8
Hg19::chr17:4699451..4699490,+p1@PSMB6


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

p.valueFDRnGenesnPathwayName
2.42990828311186e-060.00104406531902726245Proteasome (KEGG):03050
4.94817686742777e-060.00104406531902726264Proteasome Degradation (Wikipathways):WP183
1.66559167769667e-050.002635798829954982117Cell Cycle Checkpoints (Reactome):REACT_1538
4.88436109433595e-050.003435333969682952200DNA Replication (Reactome):REACT_383
0.0001213849637790880.007683668207216242315Cell Cycle, Mitotic (Reactome):REACT_152
3.28062162748213e-050.003435333969682952164Metabolism of RNA (Reactome):REACT_21257
4.94817686742777e-060.00104406531902726264Signaling by Wnt (Reactome):REACT_11045
2.63387331172458e-050.003334483612643322147Apoptosis (Reactome):REACT_578
4.59498110789263e-050.003435333969682952194HIV Infection (Reactome):REACT_6185
4.64259749243038e-050.003435333969682952195Metabolism of amino acids and derivatives (Reactome):REACT_13
0.000146494016037910.008430064741090642346{CDC2,351} (Static Module):NA



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:0004298threonine endopeptidase activity2.90963365692439e-05
GO:0005839proteasome core complex (sensu Eukaryota)2.90963365692439e-05
GO:0000502proteasome complex (sensu Eukaryota)6.0851107296576e-05
GO:0006511ubiquitin-dependent protein catabolic process0.000358939301823721
GO:0043632modification-dependent macromolecule catabolic process0.000358939301823721
GO:0019941modification-dependent protein catabolic process0.000358939301823721
GO:0051603proteolysis involved in cellular protein catabolic process0.000358939301823721
GO:0044257cellular protein catabolic process0.000358939301823721
GO:0030163protein catabolic process0.000474538006919738
GO:0043285biopolymer catabolic process0.000695007058246673
GO:0044265cellular macromolecule catabolic process0.000838715495874038
GO:0005829cytosol0.000906954100865701
GO:0009057macromolecule catabolic process0.00101380963655902
GO:0004175endopeptidase activity0.00147266438388624
GO:0044248cellular catabolic process0.00147266438388624
GO:0009056catabolic process0.00199753447215315
GO:0008233peptidase activity0.00303930587302639
GO:0006508proteolysis0.0032539008803968
GO:0043234protein complex0.0147781536685955
GO:0032991macromolecular complex0.0248985563881076
GO:0016787hydrolase activity0.0248985563881076
GO:0044444cytoplasmic part0.0323833408943997
GO:0044267cellular protein metabolic process0.0450366344531342
GO:0044260cellular macromolecule metabolic process0.0450366344531342
GO:0019538protein metabolic process0.0463788251414518
GO:0005634nucleus0.0476923425897552



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
embryonic cell2.89e-31250
mesodermal cell2.65e-27121
contractile cell5.30e-2159
animal cell6.41e-21679
eukaryotic cell6.41e-21679
electrically responsive cell4.59e-2061
electrically active cell4.59e-2061
muscle precursor cell1.49e-1958
myoblast1.49e-1958
multi-potent skeletal muscle stem cell1.49e-1958
muscle cell3.45e-1955
non-terminally differentiated cell6.00e-18106
smooth muscle cell2.36e-1743
smooth muscle myoblast2.36e-1743
epithelial cell2.65e-15253
vascular associated smooth muscle cell2.61e-1432
somatic cell5.94e-13588
meso-epithelial cell2.69e-1045
endothelial cell3.34e-1036
native cell4.18e-10722
lining cell1.30e-0858
barrier cell1.30e-0858
endothelial cell of vascular tree2.42e-0824
blood vessel endothelial cell4.71e-0818
embryonic blood vessel endothelial progenitor cell4.71e-0818
epithelial cell of nephron1.31e-0715
Uber Anatomy
Ontology termp-valuen
epithelial vesicle5.16e-2578
unilaminar epithelium2.76e-23148
epithelial tube7.42e-23117
multilaminar epithelium1.66e-2183
somite2.71e-2171
presomitic mesoderm2.71e-2171
presumptive segmental plate2.71e-2171
dermomyotome2.71e-2171
trunk paraxial mesoderm2.71e-2171
dense mesenchyme tissue4.12e-2173
paraxial mesoderm4.78e-2172
presumptive paraxial mesoderm4.78e-2172
vasculature4.58e-2078
vascular system4.58e-2078
cell layer8.11e-20309
mesenchyme1.03e-19160
entire embryonic mesenchyme1.03e-19160
epithelium1.95e-19306
skeletal muscle tissue3.35e-1962
striated muscle tissue3.35e-1962
myotome3.35e-1962
trunk mesenchyme3.05e-18122
splanchnic layer of lateral plate mesoderm4.75e-1883
muscle tissue9.40e-1864
musculature9.40e-1864
musculature of body9.40e-1864
vessel2.33e-1768
epithelial tube open at both ends1.10e-1659
blood vessel1.10e-1659
blood vasculature1.10e-1659
vascular cord1.10e-1659
trunk2.78e-16199
organism subdivision5.40e-16264
multi-tissue structure7.55e-16342
artery2.69e-1542
arterial blood vessel2.69e-1542
arterial system2.69e-1542
anatomical cluster2.51e-14373
cardiovascular system3.03e-13109
circulatory system3.38e-13112
tube5.42e-11192
systemic artery1.21e-1033
systemic arterial system1.21e-1033
anatomical conduit2.85e-10240
multi-cellular organism1.49e-08656
simple squamous epithelium3.66e-0822
blood vessel endothelium4.71e-0818
endothelium4.71e-0818
cardiovascular system endothelium4.71e-0818
squamous epithelium7.82e-0825
nephron epithelium1.31e-0715
renal tubule1.31e-0715
nephron tubule1.31e-0715
nephron1.31e-0715
uriniferous tubule1.31e-0715
nephrogenic mesenchyme1.31e-0715
subdivision of trunk7.12e-07112
excretory tube7.67e-0716
kidney epithelium7.67e-0716


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
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
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.84332
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.15.1975
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.11.66081
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
MA0145.10.273764
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.20.0526989
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
MA0154.10.838867
MA0155.10.711948
MA0156.11.60572
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.11.2663
MA0164.11.01792
MA0080.21.55139
MA0018.20.987913
MA0099.20.902716
MA0079.23.14419
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
ATF3#467214.97544968400580.005768294540793880.0259480085086778
ELF1#199734.258097958807540.01295179875054610.0460970866176487
MAFK#7975218.06715542521990.003983674744936810.0191076975606896
MYC#460935.22228187160940.007020843755740150.0293769992390123
NFKB1#479035.488063424193840.006049381815655430.0269076400104445
NR2C2#7182221.74307393682720.002762207975496010.0151370678325547
RFX5#5993312.04791082719510.0005717246050312580.0048368040522365
SIX5#147912317.0867153554590.0002004060546325010.00239339141678259
YY1#752834.911170749853860.008441455341808260.0328557058265238
ZNF263#1012738.221841637010680.001799043925565870.0109124374806699



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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