MCL coexpression mm9:67: Difference between revisions
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Latest revision as of 14:37, 17 September 2013
Phase1 CAGE Peaks
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
GO ID | GO name | FDR corrected p-value |
---|---|---|
GO:0005773 | vacuole | 7.96331827233826e-05 |
GO:0009605 | response to external stimulus | 9.634207924204e-05 |
GO:0005764 | lysosome | 0.000109926465810067 |
GO:0000323 | lytic vacuole | 0.000109926465810067 |
GO:0006954 | inflammatory response | 0.000402273609244876 |
GO:0009611 | response to wounding | 0.000415536642216724 |
GO:0042330 | taxis | 0.000472534034658768 |
GO:0006935 | chemotaxis | 0.000472534034658768 |
GO:0051017 | actin filament bundle formation | 0.00189735782855678 |
GO:0016020 | membrane | 0.00323703599937773 |
GO:0007626 | locomotory behavior | 0.014355133139629 |
GO:0044425 | membrane part | 0.014355133139629 |
GO:0031252 | leading edge | 0.019145004669026 |
GO:0001726 | ruffle | 0.0239854496757343 |
GO:0030036 | actin cytoskeleton organization and biogenesis | 0.0254344297798872 |
GO:0008092 | cytoskeletal protein binding | 0.0254344297798872 |
GO:0045087 | innate immune response | 0.0267628927679534 |
GO:0030029 | actin filament-based process | 0.0272351798690272 |
GO:0008154 | actin polymerization and/or depolymerization | 0.0272351798690272 |
GO:0007015 | actin filament organization | 0.0272351798690272 |
GO:0006955 | immune response | 0.032818333823859 |
GO:0006950 | response to stress | 0.0351299447563783 |
GO:0005886 | plasma membrane | 0.037118877286908 |
GO:0045576 | mast cell activation | 0.0411720031105915 |
GO:0006952 | defense response | 0.0421391917310396 |
GO:0007040 | lysosome organization and biogenesis | 0.0421391917310396 |
GO:0042221 | response to chemical stimulus | 0.0421391917310396 |
GO:0007610 | behavior | 0.0421391917310396 |
GO:0051270 | regulation of cell motility | 0.0421391917310396 |
GO:0032635 | interleukin-6 production | 0.0421391917310396 |
GO:0016021 | integral to membrane | 0.0421391917310396 |
GO:0007242 | intracellular signaling cascade | 0.0421391917310396 |
GO:0040012 | regulation of locomotion | 0.0421391917310396 |
GO:0031224 | intrinsic to membrane | 0.0421391917310396 |
GO:0004536 | deoxyribonuclease activity | 0.0421391917310396 |
GO:0051016 | barbed-end actin filament capping | 0.0421391917310396 |
GO:0005328 | neurotransmitter:sodium symporter activity | 0.0421391917310396 |
GO:0002376 | immune system process | 0.0421391917310396 |
GO:0030835 | negative regulation of actin filament depolymerization | 0.0421391917310396 |
GO:0007033 | vacuole organization and biogenesis | 0.0421391917310396 |
GO:0051693 | actin filament capping | 0.0421391917310396 |
GO:0005326 | neurotransmitter transporter activity | 0.0421391917310396 |
GO:0003779 | actin binding | 0.0421391917310396 |
GO:0030834 | regulation of actin filament depolymerization | 0.0421391917310396 |
GO:0030042 | actin filament depolymerization | 0.0421391917310396 |
GO:0045807 | positive regulation of endocytosis | 0.0421391917310396 |
GO:0006508 | proteolysis | 0.0421391917310396 |
GO:0044421 | extracellular region part | 0.0421391917310396 |
GO:0005884 | actin filament | 0.0421391917310396 |
GO:0033032 | regulation of myeloid cell apoptosis | 0.0421391917310396 |
GO:0002720 | positive regulation of cytokine production during immune response | 0.0421391917310396 |
GO:0033028 | myeloid cell apoptosis | 0.0421391917310396 |
GO:0032558 | adenyl deoxyribonucleotide binding | 0.0421391917310396 |
GO:0031143 | pseudopodium | 0.0421391917310396 |
GO:0045368 | positive regulation of interleukin-13 biosynthetic process | 0.0421391917310396 |
GO:0033025 | regulation of mast cell apoptosis | 0.0421391917310396 |
GO:0005368 | taurine transmembrane transporter activity | 0.0421391917310396 |
GO:0001761 | beta-alanine transmembrane transporter activity | 0.0421391917310396 |
GO:0006127 | glycerophosphate shuttle | 0.0421391917310396 |
GO:0007035 | vacuolar acidification | 0.0421391917310396 |
GO:0048549 | positive regulation of pinocytosis | 0.0421391917310396 |
GO:0015168 | glycerol transmembrane transporter activity | 0.0421391917310396 |
GO:0001762 | beta-alanine transport | 0.0421391917310396 |
GO:0015665 | alcohol transmembrane transporter activity | 0.0421391917310396 |
GO:0045362 | positive regulation of interleukin-1 biosynthetic process | 0.0421391917310396 |
GO:0019782 | ISG15 activating enzyme activity | 0.0421391917310396 |
GO:0030305 | heparanase activity | 0.0421391917310396 |
GO:0048548 | regulation of pinocytosis | 0.0421391917310396 |
GO:0004992 | platelet activating factor receptor activity | 0.0421391917310396 |
GO:0033024 | mast cell apoptosis | 0.0421391917310396 |
GO:0042222 | interleukin-1 biosynthetic process | 0.0421391917310396 |
GO:0032554 | purine deoxyribonucleotide binding | 0.0421391917310396 |
GO:0033033 | negative regulation of myeloid cell apoptosis | 0.0421391917310396 |
GO:0045360 | regulation of interleukin-1 biosynthetic process | 0.0421391917310396 |
GO:0004234 | macrophage elastase activity | 0.0421391917310396 |
GO:0015169 | glycerol-3-phosphate transmembrane transporter activity | 0.0421391917310396 |
GO:0004218 | cathepsin S activity | 0.0421391917310396 |
GO:0004213 | cathepsin B activity | 0.0421391917310396 |
GO:0015794 | glycerol-3-phosphate transport | 0.0421391917310396 |
GO:0032552 | deoxyribonucleotide binding | 0.0421391917310396 |
GO:0004557 | alpha-galactosidase activity | 0.0421391917310396 |
GO:0033026 | negative regulation of mast cell apoptosis | 0.0421391917310396 |
GO:0015734 | taurine transport | 0.0421391917310396 |
GO:0032733 | positive regulation of interleukin-10 production | 0.0421391917310396 |
GO:0033023 | mast cell homeostasis | 0.0421391917310396 |
GO:0015793 | glycerol transport | 0.0421391917310396 |
GO:0045366 | regulation of interleukin-13 biosynthetic process | 0.0421391917310396 |
GO:0015166 | polyol transmembrane transporter activity | 0.0421391917310396 |
GO:0002431 | Fc receptor mediated stimulatory signaling pathway | 0.0421391917310396 |
GO:0032765 | positive regulation of mast cell cytokine production | 0.0421391917310396 |
GO:0051015 | actin filament binding | 0.0435049872995941 |
GO:0008553 | hydrogen-exporting ATPase activity, phosphorylative mechanism | 0.0435049872995941 |
GO:0004197 | cysteine-type endopeptidase activity | 0.0465439713379019 |
GO:0048858 | cell projection morphogenesis | 0.0465439713379019 |
GO:0032990 | cell part morphogenesis | 0.0465439713379019 |
GO:0030030 | cell projection organization and biogenesis | 0.0465439713379019 |
GO:0010324 | membrane invagination | 0.0477253947078875 |
GO:0006897 | endocytosis | 0.0477253947078875 |
Relative expression of the co-expression cluster over median <br>Analyst:
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><br>uberon_data<br><br>
Ontology term | p-value | n |
---|---|---|
musculoskeletal system | 3.07e-11 | 32 |
bone element | 2.30e-09 | 22 |
skeletal element | 2.30e-09 | 22 |
skeletal system | 2.30e-09 | 22 |
bone marrow | 5.38e-08 | 16 |
mesoderm | 1.95e-07 | 120 |
mesoderm-derived structure | 1.95e-07 | 120 |
presumptive mesoderm | 1.95e-07 | 120 |
TFBS overrepresentation<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 | 9.66791e-12 |
MA0004.1 | 0.0464651 |
MA0006.1 | 0.0113542 |
MA0007.1 | 0.0356628 |
MA0009.1 | 0.293788 |
MA0014.1 | 1.59596e-14 |
MA0017.1 | 0.146079 |
MA0019.1 | 0.0767969 |
MA0024.1 | 0.107011 |
MA0025.1 | 0.790403 |
MA0027.1 | 1.12503 |
MA0028.1 | 0.00172006 |
MA0029.1 | 1.11734 |
MA0030.1 | 0.00593677 |
MA0031.1 | 0.296074 |
MA0038.1 | 0.276388 |
MA0040.1 | 0.0120431 |
MA0041.1 | 0.00960702 |
MA0042.1 | 0.0278265 |
MA0043.1 | 0.102564 |
MA0046.1 | 0.0691407 |
MA0048.1 | 0.0279375 |
MA0050.1 | 2.54601 |
MA0051.1 | 0.811588 |
MA0052.1 | 0.0619544 |
MA0055.1 | 0.0944252 |
MA0056.1 | 0 |
MA0057.1 | 5.3342e-05 |
MA0058.1 | 0.109576 |
MA0059.1 | 0.0886833 |
MA0060.1 | 0.000387795 |
MA0061.1 | 0.0212385 |
MA0063.1 | 0 |
MA0066.1 | 0.374052 |
MA0067.1 | 0.319269 |
MA0068.1 | 0.0881698 |
MA0069.1 | 0.553909 |
MA0070.1 | 0.0578172 |
MA0071.1 | 0.216125 |
MA0072.1 | 0.298289 |
MA0073.1 | 0.0939254 |
MA0074.1 | 0.103844 |
MA0076.1 | 0.00242162 |
MA0077.1 | 0.263669 |
MA0078.1 | 0.558399 |
MA0081.1 | 0.481013 |
MA0083.1 | 0.250638 |
MA0084.1 | 0.279239 |
MA0087.1 | 0.07763 |
MA0088.1 | 0.000149663 |
MA0089.1 | 0 |
MA0090.1 | 0.373821 |
MA0091.1 | 0.159871 |
MA0092.1 | 0.793224 |
MA0093.1 | 0.0105609 |
MA0095.1 | 0 |
MA0098.1 | 0 |
MA0100.1 | 0.241564 |
MA0101.1 | 0.156061 |
MA0103.1 | 0.0533503 |
MA0105.1 | 8.65801e-05 |
MA0106.1 | 0.0396019 |
MA0107.1 | 0.0463522 |
MA0108.2 | 0.0388567 |
MA0109.1 | 0 |
MA0111.1 | 0.23087 |
MA0113.1 | 0.482881 |
MA0114.1 | 0.143857 |
MA0115.1 | 0.255211 |
MA0116.1 | 0.00575929 |
MA0117.1 | 0.215672 |
MA0119.1 | 1.17717 |
MA0122.1 | 0.734881 |
MA0124.1 | 0.262421 |
MA0125.1 | 0.192286 |
MA0130.1 | 0 |
MA0131.1 | 0.00792994 |
MA0132.1 | 0 |
MA0133.1 | 0 |
MA0135.1 | 0.126426 |
MA0136.1 | 1.57483 |
MA0139.1 | 0.0358142 |
MA0140.1 | 0.153718 |
MA0141.1 | 0.326875 |
MA0142.1 | 0.440606 |
MA0143.1 | 0.542903 |
MA0144.1 | 0.035078 |
MA0145.1 | 0.053696 |
MA0146.1 | 5.86871e-05 |
MA0147.1 | 0.00137136 |
MA0148.1 | 0.248001 |
MA0149.1 | 0.0113734 |
MA0062.2 | 0.00652246 |
MA0035.2 | 0.16203 |
MA0039.2 | 1.14203e-05 |
MA0138.2 | 1.04982 |
MA0002.2 | 0.749899 |
MA0137.2 | 0.233558 |
MA0104.2 | 0.000907563 |
MA0047.2 | 0.274512 |
MA0112.2 | 0.112856 |
MA0065.2 | 0.0158761 |
MA0150.1 | 0.598332 |
MA0151.1 | 0 |
MA0152.1 | 0.983212 |
MA0153.1 | 0.138279 |
MA0154.1 | 0.0170635 |
MA0155.1 | 0.000283395 |
MA0156.1 | 1.01936 |
MA0157.1 | 0.550307 |
MA0158.1 | 0 |
MA0159.1 | 0.0656532 |
MA0160.1 | 0.362058 |
MA0161.1 | 0 |
MA0162.1 | 7.4881e-08 |
MA0163.1 | 0.000152045 |
MA0164.1 | 0.326918 |
MA0080.2 | 2.58114 |
MA0018.2 | 0.0810773 |
MA0099.2 | 1.61392 |
MA0079.2 | 4.82164e-17 |
MA0102.2 | 0.315889 |
MA0258.1 | 0.475416 |
MA0259.1 | 0.000845687 |
MA0442.1 | 0 |