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Coexpression cluster:C2487: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2487_Alveolar_Mesenchymal_Renal_Placental_Bronchial_acute_Tracheal
|full_id=C2487_Alveolar_Mesenchymal_Renal_Placental_Bronchial_acute_Tracheal
|gostat_on_coexpression_clusters=GO:0044429!mitochondrial part!0.0469200548296613!92609;6183$GO:0005744!mitochondrial inner membrane presequence translocase complex!0.0469200548296613!92609$GO:0043021!ribonucleoprotein binding!0.0469200548296613!92609$GO:0007006!mitochondrial membrane organization and biogenesis!0.0469200548296613!92609$GO:0031974!membrane-enclosed lumen!0.0469200548296613!92609;6183$GO:0043233!organelle lumen!0.0469200548296613!92609;6183$GO:0005739!mitochondrion!0.0469200548296613!92609;6183
|gostat_on_coexpression_clusters=GO:0044429!mitochondrial part!0.0469200548296613!92609;6183$GO:0005744!mitochondrial inner membrane presequence translocase complex!0.0469200548296613!92609$GO:0043021!ribonucleoprotein binding!0.0469200548296613!92609$GO:0007006!mitochondrial membrane organization and biogenesis!0.0469200548296613!92609$GO:0031974!membrane-enclosed lumen!0.0469200548296613!92609;6183$GO:0043233!organelle lumen!0.0469200548296613!92609;6183$GO:0005739!mitochondrion!0.0469200548296613!92609;6183

Revision as of 15:13, 12 September 2012


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
mesenchyme1.99e-16238
entire embryonic mesenchyme1.99e-16238
trunk6.84e-15216
trunk mesenchyme8.45e-13143
unilaminar epithelium1.38e-11138
multilaminar epithelium9.60e-1182
epithelial tube1.59e-10118
dermomyotome6.49e-1070
somite8.58e-0983
paraxial mesoderm8.58e-0983
presomitic mesoderm8.58e-0983
presumptive segmental plate8.58e-0983
trunk paraxial mesoderm8.58e-0983
presumptive paraxial mesoderm8.58e-0983
subdivision of trunk1.18e-08113
trunk region element6.32e-08107
skeletal muscle tissue8.06e-0861
striated muscle tissue8.06e-0861
myotome8.06e-0861
cell layer9.97e-08312
nephron epithelium1.45e-0716
nephron1.45e-0716
uriniferous tubule1.45e-0716
metanephric mesenchyme1.45e-0716
nephrogenic mesenchyme1.45e-0716
epithelium2.09e-07309
cortex2.24e-0716
primordium4.56e-07168
muscle tissue6.96e-0763
musculature6.96e-0763
musculature of body6.96e-0763
multi-tissue structure8.07e-07347
Disease
Ontology termp-valuen
cancer2.76e-18235
disease of cellular proliferation3.71e-18239
cell type cancer1.70e-10143
organ system cancer2.17e-08137
hematologic cancer7.57e-0851
immune system cancer7.57e-0851
carcinoma9.84e-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)

{{{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
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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