Coexpression cluster:C1002: Difference between revisions
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Latest revision as of 11:35, 17 September 2013
Full id: C1002_Mesenchymal_Whole_Smooth_Renal_osteosarcoma_Fibroblast_Reticulocytes
Phase1 CAGE Peaks
Hg19::chr11:66367106..66367110,+ | p4@CCS |
Hg19::chr12:49717819..49717823,+ | p@chr12:49717819..49717823 + |
Hg19::chr17:5284799..5284803,+ | p@chr17:5284799..5284803 + |
Hg19::chr1:149897719..149897733,- | p@chr1:149897719..149897733 - |
Hg19::chr1:156223236..156223240,- | p4@SMG5 |
Hg19::chr1:45471462..45471466,- | p2@HECTD3 |
Hg19::chr20:44586221..44586225,- | p@chr20:44586221..44586225 - |
Hg19::chr20:44983518..44983521,- | p@chr20:44983518..44983521 - |
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 ID | GO name | FDR corrected p-value |
---|---|---|
GO:0015680 | intracellular copper ion transport | 0.0112151183327446 |
GO:0051721 | protein phosphatase 2A binding | 0.0129779004996243 |
GO:0051353 | positive regulation of oxidoreductase activity | 0.0129779004996243 |
GO:0035303 | regulation of dephosphorylation | 0.0129779004996243 |
GO:0004785 | copper, zinc superoxide dismutase activity | 0.0129779004996243 |
GO:0016721 | oxidoreductase activity, acting on superoxide radicals as acceptor | 0.0129779004996243 |
GO:0004784 | superoxide dismutase activity | 0.0129779004996243 |
GO:0030071 | regulation of mitotic metaphase/anaphase transition | 0.0129779004996243 |
GO:0007091 | mitotic metaphase/anaphase transition | 0.0129779004996243 |
GO:0051341 | regulation of oxidoreductase activity | 0.0129779004996243 |
GO:0005375 | copper ion transmembrane transporter activity | 0.0129779004996243 |
GO:0019903 | protein phosphatase binding | 0.0129779004996243 |
GO:0005680 | anaphase-promoting complex | 0.0129779004996243 |
GO:0006825 | copper ion transport | 0.0129779004996243 |
GO:0006801 | superoxide metabolic process | 0.0129779004996243 |
GO:0000184 | mRNA catabolic process, nonsense-mediated decay | 0.0129779004996243 |
GO:0000152 | nuclear ubiquitin ligase complex | 0.0129779004996243 |
GO:0006406 | mRNA export from nucleus | 0.0129779004996243 |
GO:0019902 | phosphatase binding | 0.0129779004996243 |
GO:0046907 | intracellular transport | 0.0134110274761918 |
GO:0006402 | mRNA catabolic process | 0.0146159308186139 |
GO:0046915 | transition metal ion transmembrane transporter activity | 0.0146159308186139 |
GO:0006405 | RNA export from nucleus | 0.0146159308186139 |
GO:0051649 | establishment of cellular localization | 0.0162125008845377 |
GO:0051641 | cellular localization | 0.0163590933226291 |
GO:0051168 | nuclear export | 0.0184004411671435 |
GO:0006800 | oxygen and reactive oxygen species metabolic process | 0.0184004411671435 |
GO:0006401 | RNA catabolic process | 0.0184004411671435 |
GO:0015082 | di-, tri-valent inorganic cation transmembrane transporter activity | 0.020850759210351 |
GO:0005634 | nucleus | 0.0234028841151839 |
GO:0007088 | regulation of mitosis | 0.0234028841151839 |
GO:0051174 | regulation of phosphorus metabolic process | 0.0234028841151839 |
GO:0019220 | regulation of phosphate metabolic process | 0.0234028841151839 |
GO:0051028 | mRNA transport | 0.0257257353024162 |
GO:0000151 | ubiquitin ligase complex | 0.0257257353024162 |
GO:0065007 | biological regulation | 0.0257257353024162 |
GO:0050658 | RNA transport | 0.0257257353024162 |
GO:0051236 | establishment of RNA localization | 0.0257257353024162 |
GO:0050657 | nucleic acid transport | 0.0257257353024162 |
GO:0006403 | RNA localization | 0.0257257353024162 |
GO:0000041 | transition metal ion transport | 0.027686652566795 |
GO:0015931 | nucleobase, nucleoside, nucleotide and nucleic acid transport | 0.027686652566795 |
GO:0005507 | copper ion binding | 0.0304114713492289 |
GO:0006913 | nucleocytoplasmic transport | 0.0387019507964772 |
GO:0051169 | nuclear transport | 0.0387019507964772 |
GO:0004842 | ubiquitin-protein ligase activity | 0.0394187598909581 |
GO:0008639 | small protein conjugating enzyme activity | 0.0394187598909581 |
GO:0043231 | intracellular membrane-bound organelle | 0.0454542410847666 |
GO:0043227 | membrane-bound organelle | 0.0454542410847666 |
GO:0005515 | protein binding | 0.0472949942100303 |
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>
Ontology term | p-value | n |
---|---|---|
native cell | 3.06e-11 | 722 |
contractile cell | 4.95e-08 | 59 |
animal cell | 1.01e-07 | 679 |
eukaryotic cell | 1.01e-07 | 679 |
muscle precursor cell | 3.31e-07 | 58 |
myoblast | 3.31e-07 | 58 |
multi-potent skeletal muscle stem cell | 3.31e-07 | 58 |
somatic cell | 3.43e-07 | 588 |
non-terminally differentiated cell | 4.27e-07 | 106 |
Ontology term | p-value | n |
---|---|---|
unilaminar epithelium | 4.78e-10 | 148 |
cardiovascular system | 3.27e-09 | 109 |
circulatory system | 2.02e-08 | 112 |
multilaminar epithelium | 2.24e-08 | 83 |
organism subdivision | 1.14e-07 | 264 |
blood | 1.81e-07 | 15 |
haemolymphatic fluid | 1.81e-07 | 15 |
organism substance | 1.81e-07 | 15 |
epithelial vesicle | 4.67e-07 | 78 |
somite | 5.61e-07 | 71 |
presomitic mesoderm | 5.61e-07 | 71 |
presumptive segmental plate | 5.61e-07 | 71 |
dermomyotome | 5.61e-07 | 71 |
trunk paraxial mesoderm | 5.61e-07 | 71 |
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) |
---|---|
MA0003.1 | 0.06829 |
MA0004.1 | 0.455723 |
MA0006.1 | 0.300178 |
MA0007.1 | 1.1148 |
MA0009.1 | 2.12026 |
MA0014.1 | 0.134069 |
MA0017.1 | 0.337901 |
MA0019.1 | 0.602411 |
MA0024.1 | 0.813542 |
MA0025.1 | 1.05265 |
MA0027.1 | 2.5321 |
MA0028.1 | 0.315574 |
MA0029.1 | 0.832916 |
MA0030.1 | 0.821423 |
MA0031.1 | 0.756713 |
MA0038.1 | 0.557409 |
MA0040.1 | 0.838784 |
MA0041.1 | 0.474018 |
MA0042.1 | 0.442535 |
MA0043.1 | 0.919032 |
MA0046.1 | 0.90778 |
MA0048.1 | 0.0955945 |
MA0050.1 | 0.443405 |
MA0051.1 | 0.553205 |
MA0052.1 | 0.842664 |
MA0055.1 | 0.118169 |
MA0056.1 | 0 |
MA0057.1 | 0.305162 |
MA0058.1 | 0.362328 |
MA0059.1 | 0.948176 |
MA0060.1 | 0.190336 |
MA0061.1 | 0.961853 |
MA0063.1 | 0 |
MA0066.1 | 0.557833 |
MA0067.1 | 1.23721 |
MA0068.1 | 1.33409 |
MA0069.1 | 0.903908 |
MA0070.1 | 0.892666 |
MA0071.1 | 0.518907 |
MA0072.1 | 0.888148 |
MA0073.1 | 0.0344109 |
MA0074.1 | 1.36092 |
MA0076.1 | 0.377799 |
MA0077.1 | 0.880402 |
MA0078.1 | 0.652193 |
MA0081.1 | 0.948525 |
MA0083.1 | 0.926258 |
MA0084.1 | 1.42483 |
MA0087.1 | 0.885691 |
MA0088.1 | 0.441522 |
MA0089.1 | 0 |
MA0090.1 | 0.391903 |
MA0091.1 | 0.458301 |
MA0092.1 | 0.421159 |
MA0093.1 | 0.303084 |
MA0095.1 | 0 |
MA0098.1 | 0 |
MA0100.1 | 0.571227 |
MA0101.1 | 0.30624 |
MA0103.1 | 0.792149 |
MA0105.1 | 0.586268 |
MA0106.1 | 0.59853 |
MA0107.1 | 0.236528 |
MA0108.2 | 0.753643 |
MA0109.1 | 0 |
MA0111.1 | 1.04489 |
MA0113.1 | 0.614917 |
MA0114.1 | 0.231781 |
MA0115.1 | 1.1606 |
MA0116.1 | 1.25157 |
MA0117.1 | 0.956472 |
MA0119.1 | 0.345493 |
MA0122.1 | 0.982472 |
MA0124.1 | 1.11898 |
MA0125.1 | 1.0347 |
MA0130.1 | 0 |
MA0131.1 | 0.670358 |
MA0132.1 | 0 |
MA0133.1 | 0 |
MA0135.1 | 0.949204 |
MA0136.1 | 0.564434 |
MA0139.1 | 0.155155 |
MA0140.1 | 0.516266 |
MA0141.1 | 0.944441 |
MA0142.1 | 0.724856 |
MA0143.1 | 0.615094 |
MA0144.1 | 0.218541 |
MA0145.1 | 1.7555 |
MA0146.1 | 0.418694 |
MA0147.1 | 0.243042 |
MA0148.1 | 0.480298 |
MA0149.1 | 0.506665 |
MA0062.2 | 0.161302 |
MA0035.2 | 0.515566 |
MA0039.2 | 0.164269 |
MA0138.2 | 0.653421 |
MA0002.2 | 0.179788 |
MA0137.2 | 0.321796 |
MA0104.2 | 0.189646 |
MA0047.2 | 0.586412 |
MA0112.2 | 0.79629 |
MA0065.2 | 0.226158 |
MA0150.1 | 0.386144 |
MA0151.1 | 0 |
MA0152.1 | 0.52279 |
MA0153.1 | 1.01778 |
MA0154.1 | 0.577214 |
MA0155.1 | 0.764865 |
MA0156.1 | 0.323987 |
MA0157.1 | 0.697424 |
MA0158.1 | 0 |
MA0159.1 | 0.682702 |
MA0160.1 | 0.495355 |
MA0161.1 | 0 |
MA0162.1 | 0.0163939 |
MA0163.1 | 0.0517199 |
MA0164.1 | 0.627336 |
MA0080.2 | 0.303167 |
MA0018.2 | 0.599912 |
MA0099.2 | 0.523145 |
MA0079.2 | 0.00818581 |
MA0102.2 | 1.46209 |
MA0258.1 | 1.13653 |
MA0259.1 | 0.699589 |
MA0442.1 | 0 |
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
No analysis results for this cluster
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.