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Coexpression cluster:C2157: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:4.75215118272197:0.0138620699668949:0.0487044819267463!GABPB1#2553;3:5.30076287713663:0.0101267882423427:0.0378414840331329!IRF1#3659;3:5.72787281517293:0.00809711479033333:0.0319887491143752!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0386710692547386!NR2C2#7182;2:16.3073054526204:0.00541182534464822:0.0245506744492101!RXRA#6256;2:10.0373085695666:0.0139170380592011:0.048871306878212
|tf_chipseq_enrich=CCNT2#905;3:4.75215118272197:0.0138620699668949:0.0487044819267463!GABPB1#2553;3:5.30076287713663:0.0101267882423427:0.0378414840331329!IRF1#3659;3:5.72787281517293:0.00809711479033333:0.0319887491143752!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0386710692547386!NR2C2#7182;2:16.3073054526204:0.00541182534464822:0.0245506744492101!RXRA#6256;2:10.0373085695666:0.0139170380592011:0.048871306878212
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}}
}}

Revision as of 15:20, 26 November 2012


Full id: C2157_Mallassezderived_Smooth_Alveolar_Bronchial_Keratocytes_Tracheal_mesothelioma



Phase1 CAGE Peaks

Hg19::chr11:6704513..6704578,-p1@MRPL17
Hg19::chr12:120720030..120720046,+p1@NME2P1
Hg19::chr16:67880820..67880844,+p1@NUTF2
Hg19::chr17:49243792..49243828,+p2@NME1-NME2
p2@NME2


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:0031967organelle envelope0.0286527553894789
GO:0031975envelope0.0286527553894789
GO:0006228UTP biosynthetic process0.0286527553894789
GO:0046051UTP metabolic process0.0286527553894789
GO:0004550nucleoside diphosphate kinase activity0.0286527553894789
GO:0046036CTP metabolic process0.0286527553894789
GO:0009209pyrimidine ribonucleoside triphosphate biosynthetic process0.0286527553894789
GO:0009208pyrimidine ribonucleoside triphosphate metabolic process0.0286527553894789
GO:0006241CTP biosynthetic process0.0286527553894789
GO:0006183GTP biosynthetic process0.0286527553894789
GO:0046039GTP metabolic process0.0286527553894789
GO:0009220pyrimidine ribonucleotide biosynthetic process0.0286527553894789
GO:0009218pyrimidine ribonucleotide metabolic process0.0286527553894789
GO:0009147pyrimidine nucleoside triphosphate metabolic process0.032089061554363
GO:0006221pyrimidine nucleotide biosynthetic process0.032089061554363
GO:0031090organelle membrane0.0353004691211007
GO:0006220pyrimidine nucleotide metabolic process0.0353004691211007
GO:0016776phosphotransferase activity, phosphate group as acceptor0.0353004691211007
GO:0005643nuclear pore0.0393385481596267
GO:0019205nucleobase, nucleoside, nucleotide kinase activity0.0393385481596267
GO:0046930pore complex0.0393385481596267
GO:0044249cellular biosynthetic process0.0393385481596267
GO:0044453nuclear membrane part0.0393385481596267
GO:0009206purine ribonucleoside triphosphate biosynthetic process0.0393385481596267
GO:0009145purine nucleoside triphosphate biosynthetic process0.0393385481596267
GO:0009201ribonucleoside triphosphate biosynthetic process0.0393385481596267
GO:0009142nucleoside triphosphate biosynthetic process0.0393385481596267
GO:0009205purine ribonucleoside triphosphate metabolic process0.0393385481596267
GO:0009144purine nucleoside triphosphate metabolic process0.0393385481596267
GO:0009199ribonucleoside triphosphate metabolic process0.0393385481596267
GO:0009152purine ribonucleotide biosynthetic process0.0393385481596267
GO:0009141nucleoside triphosphate metabolic process0.0393385481596267
GO:0031965nuclear membrane0.0393385481596267
GO:0009150purine ribonucleotide metabolic process0.0393385481596267
GO:0009260ribonucleotide biosynthetic process0.0393385481596267
GO:0006164purine nucleotide biosynthetic process0.0393385481596267
GO:0006163purine nucleotide metabolic process0.0393385481596267
GO:0009259ribonucleotide metabolic process0.0393385481596267
GO:0009058biosynthetic process0.0393385481596267
GO:0005635nuclear envelope0.0438641156314734



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 cell7.92e-39250
animal cell9.47e-31679
eukaryotic cell9.47e-31679
mesodermal cell1.83e-29121
epithelial cell2.84e-26253
contractile cell1.30e-1959
electrically responsive cell4.34e-1961
electrically active cell4.34e-1961
muscle precursor cell9.80e-1958
myoblast9.80e-1958
multi-potent skeletal muscle stem cell9.80e-1958
non-terminally differentiated cell1.80e-18106
muscle cell2.90e-1855
native cell2.79e-16722
smooth muscle cell9.74e-1643
smooth muscle myoblast9.74e-1643
somatic cell4.91e-14588
vascular associated smooth muscle cell9.59e-1432
lining cell2.23e-1058
barrier cell2.23e-1058
squamous epithelial cell1.85e-0963
meso-epithelial cell5.25e-0945
endothelial cell1.38e-0836
epithelial cell of nephron3.19e-0815
ectodermal cell1.39e-0772
kidney cortical cell3.52e-0712
renal cortical epithelial cell3.52e-0712
blood vessel endothelial cell3.97e-0718
embryonic blood vessel endothelial progenitor cell3.97e-0718
endothelial cell of vascular tree6.24e-0724
Uber Anatomy
Ontology termp-valuen
epithelial vesicle1.30e-2378
unilaminar epithelium2.31e-22148
multilaminar epithelium7.90e-2183
somite6.67e-2071
presomitic mesoderm6.67e-2071
presumptive segmental plate6.67e-2071
dermomyotome6.67e-2071
trunk paraxial mesoderm6.67e-2071
vasculature1.05e-1978
vascular system1.05e-1978
dense mesenchyme tissue2.43e-1973
paraxial mesoderm3.78e-1972
presumptive paraxial mesoderm3.78e-1972
mesenchyme4.08e-19160
entire embryonic mesenchyme4.08e-19160
epithelial tube5.74e-19117
trunk1.36e-18199
organism subdivision6.47e-18264
trunk mesenchyme3.93e-17122
skeletal muscle tissue6.52e-1762
striated muscle tissue6.52e-1762
myotome6.52e-1762
splanchnic layer of lateral plate mesoderm6.79e-1783
vessel1.29e-1668
epithelial tube open at both ends3.40e-1659
blood vessel3.40e-1659
blood vasculature3.40e-1659
vascular cord3.40e-1659
muscle tissue1.55e-1564
musculature1.55e-1564
musculature of body1.55e-1564
artery1.42e-1442
arterial blood vessel1.42e-1442
arterial system1.42e-1442
cell layer4.77e-13309
cardiovascular system2.05e-12109
epithelium2.47e-12306
circulatory system1.33e-11112
systemic artery3.10e-1033
systemic arterial system3.10e-1033
multi-tissue structure2.61e-09342
nephron epithelium3.19e-0815
renal tubule3.19e-0815
nephron tubule3.19e-0815
nephron3.19e-0815
uriniferous tubule3.19e-0815
nephrogenic mesenchyme3.19e-0815
parenchyma7.29e-0815
anatomical cluster1.22e-07373
excretory tube3.42e-0716
kidney epithelium3.42e-0716
cortex of kidney3.52e-0712
renal parenchyma3.52e-0712
blood vessel endothelium3.97e-0718
endothelium3.97e-0718
cardiovascular system endothelium3.97e-0718
simple squamous epithelium4.35e-0722
urinary system structure7.48e-0747
larynx8.48e-079


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#90534.752151182721970.01386206996689490.0487044819267463
GABPB1#255335.300762877136630.01012678824234270.0378414840331329
IRF1#365935.727872815172930.008097114790333330.0319887491143752
JUND#372735.245997956403270.01043432751748420.0386710692547386
NR2C2#7182216.30730545262040.005411825344648220.0245506744492101
RXRA#6256210.03730856956660.01391703805920110.048871306878212



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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