MCL coexpression mm9:35: Difference between revisions
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Latest revision as of 14:33, 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:0030016 | myofibril | 4.00661982209194e-17 |
| GO:0043292 | contractile fiber | 4.00661982209194e-17 |
| GO:0030017 | sarcomere | 9.10776078501327e-17 |
| GO:0044449 | contractile fiber part | 1.41829398911132e-16 |
| GO:0031674 | I band | 3.26452523337004e-12 |
| GO:0005856 | cytoskeleton | 1.67134528778977e-11 |
| GO:0030018 | Z disc | 4.03759866066056e-11 |
| GO:0005737 | cytoplasm | 4.00108188857103e-08 |
| GO:0016528 | sarcoplasm | 6.17005003355759e-08 |
| GO:0043228 | non-membrane-bound organelle | 7.69639482687148e-07 |
| GO:0043232 | intracellular non-membrane-bound organelle | 7.69639482687148e-07 |
| GO:0016529 | sarcoplasmic reticulum | 8.14770608828913e-07 |
| GO:0007517 | muscle development | 1.28885467200404e-06 |
| GO:0044444 | cytoplasmic part | 1.28885467200404e-06 |
| GO:0030239 | myofibril assembly | 1.44368928789299e-06 |
| GO:0055002 | striated muscle cell development | 1.44368928789299e-06 |
| GO:0055001 | muscle cell development | 2.02689876071578e-06 |
| GO:0008092 | cytoskeletal protein binding | 3.64282392414532e-06 |
| GO:0003779 | actin binding | 5.08156073270842e-06 |
| GO:0031032 | actomyosin structure organization and biogenesis | 6.52510394938986e-06 |
| GO:0048628 | myoblast maturation | 1.07555152863837e-05 |
| GO:0007519 | skeletal muscle development | 1.15464707563275e-05 |
| GO:0048627 | myoblast development | 1.26384663037468e-05 |
| GO:0042383 | sarcolemma | 4.37273091328514e-05 |
| GO:0051146 | striated muscle cell differentiation | 5.04441297801224e-05 |
| GO:0014706 | striated muscle development | 6.62666942390881e-05 |
| GO:0045445 | myoblast differentiation | 0.000142650820186643 |
| GO:0006936 | muscle contraction | 0.000678114668893953 |
| GO:0003012 | muscle system process | 0.000678114668893953 |
| GO:0005200 | structural constituent of cytoskeleton | 0.00091509663385354 |
| GO:0045214 | sarcomere organization | 0.00100563940070711 |
| GO:0016459 | myosin complex | 0.00119062776238504 |
| GO:0015629 | actin cytoskeleton | 0.00133137548372836 |
| GO:0044430 | cytoskeletal part | 0.00156751975638065 |
| GO:0016010 | dystrophin-associated glycoprotein complex | 0.00161653645134736 |
| GO:0042692 | muscle cell differentiation | 0.00171888865353774 |
| GO:0048741 | skeletal muscle fiber development | 0.00175672862862005 |
| GO:0048747 | muscle fiber development | 0.00175672862862005 |
| GO:0005859 | muscle myosin complex | 0.0023432206423252 |
| GO:0043687 | post-translational protein modification | 0.0023432206423252 |
| GO:0048469 | cell maturation | 0.003255906102858 |
| GO:0016460 | myosin II complex | 0.00336042176678738 |
| GO:0043412 | biopolymer modification | 0.00488534414496261 |
| GO:0007010 | cytoskeleton organization and biogenesis | 0.00519393644581443 |
| GO:0055003 | cardiac myofibril assembly | 0.00523451550623999 |
| GO:0021700 | developmental maturation | 0.00763132833473368 |
| GO:0006464 | protein modification process | 0.0077257626668082 |
| GO:0044424 | intracellular part | 0.00879705307883244 |
| GO:0005622 | intracellular | 0.00889307951997942 |
| GO:0005515 | protein binding | 0.0110107071285535 |
| GO:0016012 | sarcoglycan complex | 0.0110107071285535 |
| GO:0005523 | tropomyosin binding | 0.0110107071285535 |
| GO:0055013 | cardiac muscle cell development | 0.0110107071285535 |
| GO:0005605 | basal lamina | 0.0115382950186431 |
| GO:0006512 | ubiquitin cycle | 0.0138501128585861 |
| GO:0016011 | dystroglycan complex | 0.0142684521679624 |
| GO:0003956 | NAD(P)+-protein-arginine ADP-ribosyltransferase activity | 0.0142684521679624 |
| GO:0006941 | striated muscle contraction | 0.0148712602109169 |
| GO:0004437 | inositol or phosphatidylinositol phosphatase activity | 0.0161620949147884 |
| GO:0007507 | heart development | 0.016360038812081 |
| GO:0008307 | structural constituent of muscle | 0.0176967808077369 |
| GO:0045121 | lipid raft | 0.0209343432321864 |
| GO:0046716 | muscle maintenance | 0.0209343432321864 |
| GO:0042577 | lipid phosphatase activity | 0.02528367075441 |
| GO:0005626 | insoluble fraction | 0.0303170489822444 |
| GO:0032982 | myosin filament | 0.0408330852134899 |
| GO:0005863 | striated muscle thick filament | 0.0408330852134899 |
| GO:0048513 | organ development | 0.0443365530896437 |
| GO:0030036 | actin cytoskeleton organization and biogenesis | 0.048234907779194 |
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 |
|---|---|---|
| primary circulatory organ | 1.02e-13 | 18 |
| heart | 1.02e-13 | 18 |
| primitive heart tube | 1.02e-13 | 18 |
| primary heart field | 1.02e-13 | 18 |
| anterior lateral plate mesoderm | 1.02e-13 | 18 |
| heart tube | 1.02e-13 | 18 |
| heart primordium | 1.02e-13 | 18 |
| cardiac mesoderm | 1.02e-13 | 18 |
| cardiogenic plate | 1.02e-13 | 18 |
| heart rudiment | 1.02e-13 | 18 |
| cardiovascular system | 9.07e-11 | 23 |
| circulatory system | 9.07e-11 | 23 |
| hindlimb bud | 6.83e-07 | 5 |
| stylopod | 6.83e-07 | 5 |
| lower limb segment | 6.83e-07 | 5 |
| multi-limb segment region | 6.83e-07 | 5 |
| pelvic appendage | 6.83e-07 | 5 |
| limb segment | 6.83e-07 | 5 |
| paired limb/fin segment | 6.83e-07 | 5 |
| pelvic appendage bud | 6.83e-07 | 5 |
| subdivision of organism along appendicular axis | 6.83e-07 | 5 |
| leg | 6.83e-07 | 5 |
| hindlimb | 6.83e-07 | 5 |
| hindlimb stylopod | 6.83e-07 | 5 |
| posterior region of body | 6.83e-07 | 5 |
| pelvic complex | 6.83e-07 | 5 |
| hindlimb/pelvic fin field | 6.83e-07 | 5 |
| splanchnic layer of lateral plate mesoderm | 6.84e-07 | 33 |
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 | 0.000425055 |
| MA0004.1 | 0.0996753 |
| MA0006.1 | 0.00191199 |
| MA0007.1 | 0.0486148 |
| MA0009.1 | 0.0346889 |
| MA0014.1 | 1.94913e-05 |
| MA0017.1 | 0.128287 |
| MA0019.1 | 0.102811 |
| MA0024.1 | 0.169952 |
| MA0025.1 | 0.0409346 |
| MA0027.1 | 0.858646 |
| MA0028.1 | 9.569e-06 |
| MA0029.1 | 0.655341 |
| MA0030.1 | 0.358222 |
| MA0031.1 | 0.265081 |
| MA0038.1 | 0.132583 |
| MA0040.1 | 0.273616 |
| MA0041.1 | 0.00024072 |
| MA0042.1 | 0.127211 |
| MA0043.1 | 0.037433 |
| MA0046.1 | 0.0049427 |
| MA0048.1 | 2.2554 |
| MA0050.1 | 0.00886885 |
| MA0051.1 | 1.1486 |
| MA0052.1 | 46.9815 |
| MA0055.1 | 5.12275 |
| MA0056.1 | 0 |
| MA0057.1 | 0.00859277 |
| MA0058.1 | 0.0793647 |
| MA0059.1 | 0.144422 |
| MA0060.1 | 2.1834e-05 |
| MA0061.1 | 0.31592 |
| MA0063.1 | 0 |
| MA0066.1 | 0.232756 |
| MA0067.1 | 1.03257 |
| MA0068.1 | 0.0212413 |
| MA0069.1 | 0.177198 |
| MA0070.1 | 1.30856 |
| MA0071.1 | 0.199244 |
| MA0072.1 | 0.253523 |
| MA0073.1 | 1.19753e-05 |
| MA0074.1 | 0.452212 |
| MA0076.1 | 5.3129e-07 |
| MA0077.1 | 0.00931059 |
| MA0078.1 | 0.0363398 |
| MA0081.1 | 0.0724839 |
| MA0083.1 | 6.89356 |
| MA0084.1 | 0.119278 |
| MA0087.1 | 0.128 |
| MA0088.1 | 0.0290677 |
| MA0089.1 | 0 |
| MA0090.1 | 2.08994 |
| MA0091.1 | 0.701145 |
| MA0092.1 | 0.368216 |
| MA0093.1 | 0.0410399 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.393855 |
| MA0101.1 | 0.133475 |
| MA0103.1 | 0.391146 |
| MA0105.1 | 0.0992255 |
| MA0106.1 | 0.176422 |
| MA0107.1 | 0.231177 |
| MA0108.2 | 7.54286 |
| MA0109.1 | 0 |
| MA0111.1 | 0.367812 |
| MA0113.1 | 0.253279 |
| MA0114.1 | 0.205579 |
| MA0115.1 | 0.18606 |
| MA0116.1 | 0.512909 |
| MA0117.1 | 0.402239 |
| MA0119.1 | 0.725369 |
| MA0122.1 | 1.48896 |
| MA0124.1 | 0.0132857 |
| MA0125.1 | 0.103814 |
| MA0130.1 | 0 |
| MA0131.1 | 0.0556763 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 0.00259775 |
| MA0136.1 | 0.00153999 |
| MA0139.1 | 0.0025877 |
| MA0140.1 | 0.0160019 |
| MA0141.1 | 2.68531 |
| MA0142.1 | 0.146925 |
| MA0143.1 | 0.0984585 |
| MA0144.1 | 0.512782 |
| MA0145.1 | 0.84116 |
| MA0146.1 | 1.01034 |
| MA0147.1 | 0.0124697 |
| MA0148.1 | 0.0970238 |
| MA0149.1 | 8.08986e-08 |
| MA0062.2 | 1.12891e-08 |
| MA0035.2 | 0.0834347 |
| MA0039.2 | 4.10994e-07 |
| MA0138.2 | 1.5449 |
| MA0002.2 | 0.036625 |
| MA0137.2 | 0.020895 |
| MA0104.2 | 0.000170612 |
| MA0047.2 | 0.0301737 |
| MA0112.2 | 1.06099 |
| MA0065.2 | 0.786152 |
| MA0150.1 | 2.93806 |
| MA0151.1 | 0 |
| MA0152.1 | 0.0858719 |
| MA0153.1 | 0.0612728 |
| MA0154.1 | 2.97178 |
| MA0155.1 | 0.322747 |
| MA0156.1 | 1.47311e-05 |
| MA0157.1 | 0.364627 |
| MA0158.1 | 0 |
| MA0159.1 | 1.9771 |
| MA0160.1 | 3.73764 |
| MA0161.1 | 0 |
| MA0162.1 | 2.81714e-10 |
| MA0163.1 | 0.000465538 |
| MA0164.1 | 0.698934 |
| MA0080.2 | 1.68543e-05 |
| MA0018.2 | 0.102279 |
| MA0099.2 | 1.25271 |
| MA0079.2 | 2.16419e-09 |
| MA0102.2 | 0.144504 |
| MA0258.1 | 1.70296 |
| MA0259.1 | 0.0320327 |
| MA0442.1 | 0 |
