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Coexpression cluster:C3414

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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 cell8.07e-32248
mesodermal cell6.24e-27119
non-terminally differentiated cell6.35e-26180
contractile cell1.41e-2159
electrically responsive cell1.80e-2060
electrically active cell1.80e-2060
muscle precursor cell9.22e-2057
myoblast9.22e-2057
multi-potent skeletal muscle stem cell9.22e-2057
muscle cell3.75e-1954
animal cell4.09e-19679
eukaryotic cell4.09e-19679
smooth muscle cell1.26e-1742
smooth muscle myoblast1.26e-1742
epithelial cell3.60e-16254
vascular associated smooth muscle cell1.48e-1432
somatic cell5.60e-12591
endothelial cell4.05e-0935
meso-epithelial cell5.14e-0944
native cell1.12e-08722
lining cell3.64e-0857
barrier cell3.64e-0857
endothelial cell of vascular tree6.78e-0824
epithelial cell of nephron1.14e-0716
blood vessel endothelial cell1.39e-0718
embryonic blood vessel endothelial progenitor cell1.39e-0718
fibroblast8.93e-0775
Uber Anatomy
Ontology termp-valuen
trunk mesenchyme4.32e-25143
somite2.93e-2483
paraxial mesoderm2.93e-2483
presomitic mesoderm2.93e-2483
presumptive segmental plate2.93e-2483
trunk paraxial mesoderm2.93e-2483
presumptive paraxial mesoderm2.93e-2483
epithelial tube1.85e-23118
multilaminar epithelium4.27e-2282
dermomyotome5.58e-2270
unilaminar epithelium2.97e-21138
cell layer4.03e-20312
vasculature7.33e-2079
vascular system7.33e-2079
epithelium1.00e-19309
skeletal muscle tissue1.24e-1961
striated muscle tissue1.24e-1961
myotome1.24e-1961
trunk1.73e-19216
mesenchyme2.48e-18238
entire embryonic mesenchyme2.48e-18238
muscle tissue4.99e-1863
musculature4.99e-1863
musculature of body4.99e-1863
splanchnic layer of lateral plate mesoderm9.22e-1884
multi-tissue structure1.15e-17347
vessel6.06e-1769
blood vessel3.43e-1660
epithelial tube open at both ends3.43e-1660
blood vasculature3.43e-1660
vascular cord3.43e-1660
organism subdivision2.13e-15365
artery3.66e-1542
arterial blood vessel3.66e-1542
arterial system3.66e-1542
anatomical cluster1.10e-14286
circulatory system1.76e-13113
cardiovascular system4.33e-13110
tube9.19e-12194
anatomical conduit1.56e-11241
systemic artery5.97e-1133
systemic arterial system5.97e-1133
multi-cellular organism3.99e-10659
nephron epithelium1.14e-0716
nephron1.14e-0716
uriniferous tubule1.14e-0716
metanephric mesenchyme1.14e-0716
nephrogenic mesenchyme1.14e-0716
simple squamous epithelium1.32e-0722
endothelium1.39e-0718
blood vessel endothelium1.39e-0718
cardiovascular system endothelium1.39e-0718
organ part1.41e-07219
subdivision of trunk2.26e-07113
compound organ2.51e-0769
squamous epithelium3.50e-0725
embryo4.30e-07612
excretory tube5.88e-0717
mesonephric epithelium5.88e-0717
mesonephric tubule5.88e-0717
nephric duct5.88e-0717
kidney epithelium5.88e-0717
renal duct5.88e-0717
mesonephric duct5.88e-0717
pronephric duct5.88e-0717
anatomical system5.92e-07625
anatomical group7.31e-07626


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)

{{{tfbs_overrepresentation_jaspar}}}



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.