MCL coexpression mm9:1196: Difference between revisions
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{{MCL_coexpression_mm9 | 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regulation of oxidoreductase activity;0.00366270264369207;12391!GO:0051001;negative regulation of nitric-oxide synthase activity;0.00366270264369207;12391!GO:0005159;insulin-like growth factor receptor binding;0.00366270264369207;16002!GO:0018445;prothoracicotrophic hormone activity;0.00366270264369207;16002!GO:0050999;regulation of nitric-oxide synthase activity;0.00366270264369207;12391!GO:0031579;lipid raft organization and biogenesis;0.00366270264369207;12391!GO:0051925;regulation of calcium ion transport via voltage-gated calcium channel;0.00366270264369207;12391!GO:0051341;regulation of oxidoreductase activity;0.00480716552389701;12391!GO:0043409;negative regulation of MAPKKK cascade;0.00712133649185093;12391!GO:0051924;regulation of calcium ion transport;0.00823950059692129;12391!GO:0016599;caveolar membrane;0.00823950059692129;12391!GO:0046716;muscle maintenance;0.00823950059692129;12391!GO:0005901;caveola;0.00823950059692129;12391!GO:0030315;T-tubule;0.00823950059692129;12391!GO:0007009;plasma membrane organization and biogenesis;0.0085444331595649;12391!GO:0043269;regulation of ion transport;0.00961196052071523;12391!GO:0042632;cholesterol homeostasis;0.0110661950770426;12391!GO:0055088;lipid homeostasis;0.0110661950770426;12391!GO:0055092;sterol homeostasis;0.0110661950770426;12391!GO:0043408;regulation of MAPKKK cascade;0.0110661950770426;12391!GO:0006641;triacylglycerol metabolic process;0.0110661950770426;12391!GO:0005184;neuropeptide hormone activity;0.0110661950770426;16002!GO:0006639;acylglycerol metabolic process;0.0123685928740176;12391!GO:0046486;glycerolipid metabolic process;0.0123685928740176;12391!GO:0006638;neutral lipid metabolic process;0.0123685928740176;12391!GO:0006662;glycerol ether metabolic process;0.0123685928740176;12391!GO:0042593;glucose homeostasis;0.0123685928740176;12391!GO:0042383;sarcolemma;0.0123685928740176;12391!GO:0033500;carbohydrate homeostasis;0.0123685928740176;12391!GO:0045121;lipid raft;0.0144084586727577;12391!GO:0006469;negative regulation of protein kinase activity;0.0144084586727577;12391!GO:0033673;negative regulation of kinase activity;0.0144084586727577;12391!GO:0051348;negative regulation of transferase activity;0.0147472431754467;12391!GO:0042391;regulation of membrane potential;0.0158184497285886;12391!GO:0043086;negative regulation of catalytic activity;0.0170620003455702;12391!GO:0048513;organ development;0.0170620003455702;12391,16002!GO:0048731;system development;0.0252956453033153;12391,16002!GO:0051049;regulation of transport;0.0282740943699344;12391!GO:0009968;negative regulation of signal transduction;0.0295120490852277;12391!GO:0048856;anatomical structure development;0.0318117007811852;12391,16002!GO:0006816;calcium ion transport;0.0321158751667335;12391!GO:0005179;hormone activity;0.0353633963699973;16002!GO:0000165;MAPKKK cascade;0.0353633963699973;12391!GO:0007275;multicellular organismal development;0.035923362439894;12391,16002!GO:0045859;regulation of protein kinase activity;0.035923362439894;12391!GO:0043549;regulation of kinase activity;0.035923362439894;12391!GO:0015674;di-, tri-valent inorganic cation transport;0.035923362439894;12391!GO:0051338;regulation of transferase activity;0.035923362439894;12391!GO:0055082;cellular chemical homeostasis;0.0372851529850379;12391!GO:0006873;cellular ion homeostasis;0.0372851529850379;12391!GO:0008083;growth factor activity;0.0373021045432671;16002!GO:0007517;muscle development;0.0389795489121627;12391!GO:0050801;ion homeostasis;0.0389795489121627;12391!GO:0010324;membrane invagination;0.0389795489121627;12391!GO:0006897;endocytosis;0.0389795489121627;12391!GO:0048878;chemical homeostasis;0.0471827861399006;12391!GO:0019725;cellular homeostasis;0.0471827861399006;12391!GO:0032502;developmental process;0.0473012205455537;12391,16002!GO:0007243;protein kinase cascade;0.0473012205455537;12391!GO:0016044;membrane organization and 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| ||
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| |||
| | |||
}} | |||
Latest revision as of 16:32, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr3:137728133..137728161,+ | p@chr3:137728133..137728161 + |
| Mm9::chr6:112409709..112409743,+ | p1@Cav3 |
| Mm9::chr6:112409745..112409752,+ | p5@Cav3 |
| Mm9::chr7:149846882..149846893,- | p12@Igf2 |
| Mm9::chr7:149846894..149846945,- | p3@Igf2 |
| Mm9::chr7:149846948..149846963,- | p9@Igf2 |
| Mm9::chr7:149847093..149847111,- | p7@Igf2 |
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:0051354 | negative regulation of oxidoreductase activity | 0.00366270264369207 |
| GO:0051001 | negative regulation of nitric-oxide synthase activity | 0.00366270264369207 |
| GO:0005159 | insulin-like growth factor receptor binding | 0.00366270264369207 |
| GO:0018445 | prothoracicotrophic hormone activity | 0.00366270264369207 |
| GO:0050999 | regulation of nitric-oxide synthase activity | 0.00366270264369207 |
| GO:0031579 | lipid raft organization and biogenesis | 0.00366270264369207 |
| GO:0051925 | regulation of calcium ion transport via voltage-gated calcium channel | 0.00366270264369207 |
| GO:0051341 | regulation of oxidoreductase activity | 0.00480716552389701 |
| GO:0043409 | negative regulation of MAPKKK cascade | 0.00712133649185093 |
| GO:0051924 | regulation of calcium ion transport | 0.00823950059692129 |
| GO:0016599 | caveolar membrane | 0.00823950059692129 |
| GO:0046716 | muscle maintenance | 0.00823950059692129 |
| GO:0005901 | caveola | 0.00823950059692129 |
| GO:0030315 | T-tubule | 0.00823950059692129 |
| GO:0007009 | plasma membrane organization and biogenesis | 0.0085444331595649 |
| GO:0043269 | regulation of ion transport | 0.00961196052071523 |
| GO:0042632 | cholesterol homeostasis | 0.0110661950770426 |
| GO:0055088 | lipid homeostasis | 0.0110661950770426 |
| GO:0055092 | sterol homeostasis | 0.0110661950770426 |
| GO:0043408 | regulation of MAPKKK cascade | 0.0110661950770426 |
| GO:0006641 | triacylglycerol metabolic process | 0.0110661950770426 |
| GO:0005184 | neuropeptide hormone activity | 0.0110661950770426 |
| GO:0006639 | acylglycerol metabolic process | 0.0123685928740176 |
| GO:0046486 | glycerolipid metabolic process | 0.0123685928740176 |
| GO:0006638 | neutral lipid metabolic process | 0.0123685928740176 |
| GO:0006662 | glycerol ether metabolic process | 0.0123685928740176 |
| GO:0042593 | glucose homeostasis | 0.0123685928740176 |
| GO:0042383 | sarcolemma | 0.0123685928740176 |
| GO:0033500 | carbohydrate homeostasis | 0.0123685928740176 |
| GO:0045121 | lipid raft | 0.0144084586727577 |
| GO:0006469 | negative regulation of protein kinase activity | 0.0144084586727577 |
| GO:0033673 | negative regulation of kinase activity | 0.0144084586727577 |
| GO:0051348 | negative regulation of transferase activity | 0.0147472431754467 |
| GO:0042391 | regulation of membrane potential | 0.0158184497285886 |
| GO:0043086 | negative regulation of catalytic activity | 0.0170620003455702 |
| GO:0048513 | organ development | 0.0170620003455702 |
| GO:0048731 | system development | 0.0252956453033153 |
| GO:0051049 | regulation of transport | 0.0282740943699344 |
| GO:0009968 | negative regulation of signal transduction | 0.0295120490852277 |
| GO:0048856 | anatomical structure development | 0.0318117007811852 |
| GO:0006816 | calcium ion transport | 0.0321158751667335 |
| GO:0005179 | hormone activity | 0.0353633963699973 |
| GO:0000165 | MAPKKK cascade | 0.0353633963699973 |
| GO:0007275 | multicellular organismal development | 0.035923362439894 |
| GO:0045859 | regulation of protein kinase activity | 0.035923362439894 |
| GO:0043549 | regulation of kinase activity | 0.035923362439894 |
| GO:0015674 | di-, tri-valent inorganic cation transport | 0.035923362439894 |
| GO:0051338 | regulation of transferase activity | 0.035923362439894 |
| GO:0055082 | cellular chemical homeostasis | 0.0372851529850379 |
| GO:0006873 | cellular ion homeostasis | 0.0372851529850379 |
| GO:0008083 | growth factor activity | 0.0373021045432671 |
| GO:0007517 | muscle development | 0.0389795489121627 |
| GO:0050801 | ion homeostasis | 0.0389795489121627 |
| GO:0010324 | membrane invagination | 0.0389795489121627 |
| GO:0006897 | endocytosis | 0.0389795489121627 |
| GO:0048878 | chemical homeostasis | 0.0471827861399006 |
| GO:0019725 | cellular homeostasis | 0.0471827861399006 |
| GO:0032502 | developmental process | 0.0473012205455537 |
| GO:0007243 | protein kinase cascade | 0.0473012205455537 |
| GO:0016044 | membrane organization and biogenesis | 0.0494671991631394 |
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 |
|---|---|---|
| multi-cellular organism | 3.78e-09 | 333 |
| primary circulatory organ | 1.98e-07 | 18 |
| heart | 1.98e-07 | 18 |
| primitive heart tube | 1.98e-07 | 18 |
| primary heart field | 1.98e-07 | 18 |
| anterior lateral plate mesoderm | 1.98e-07 | 18 |
| heart tube | 1.98e-07 | 18 |
| heart primordium | 1.98e-07 | 18 |
| cardiac mesoderm | 1.98e-07 | 18 |
| cardiogenic plate | 1.98e-07 | 18 |
| heart rudiment | 1.98e-07 | 18 |
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 | 0.188259 |
| MA0004.1 | 0.481116 |
| MA0006.1 | 0.837454 |
| MA0007.1 | 0.465969 |
| MA0009.1 | 0.92425 |
| MA0014.1 | 0.222567 |
| MA0017.1 | 0.337808 |
| MA0019.1 | 0.740036 |
| MA0024.1 | 0.880057 |
| MA0025.1 | 1.15921 |
| MA0027.1 | 2.57545 |
| MA0028.1 | 0.321735 |
| MA0029.1 | 0.858105 |
| MA0030.1 | 0.864739 |
| MA0031.1 | 0.828781 |
| MA0038.1 | 0.62758 |
| MA0040.1 | 0.936879 |
| MA0041.1 | 0.404721 |
| MA0042.1 | 0.391504 |
| MA0043.1 | 1.02178 |
| MA0046.1 | 0.960497 |
| MA0048.1 | 0.128106 |
| MA0050.1 | 0.520357 |
| MA0051.1 | 0.636645 |
| MA0052.1 | 0.945011 |
| MA0055.1 | 0.648475 |
| MA0056.1 | 0 |
| MA0057.1 | 0.376102 |
| MA0058.1 | 0.384683 |
| MA0059.1 | 0.397033 |
| MA0060.1 | 0.232592 |
| MA0061.1 | 1.33382 |
| MA0063.1 | 0 |
| MA0066.1 | 2.54082 |
| MA0067.1 | 1.27078 |
| MA0068.1 | 0.385183 |
| MA0069.1 | 0.945354 |
| MA0070.1 | 0.93557 |
| MA0071.1 | 0.519509 |
| MA0072.1 | 0.927016 |
| MA0073.1 | 0.00223012 |
| MA0074.1 | 0.580087 |
| MA0076.1 | 0.356883 |
| MA0077.1 | 0.905143 |
| MA0078.1 | 1.60783 |
| MA0081.1 | 0.420276 |
| MA0083.1 | 5.41262 |
| MA0084.1 | 1.59945 |
| MA0087.1 | 0.977537 |
| MA0088.1 | 0.0841779 |
| MA0089.1 | 0 |
| MA0090.1 | 1.1347 |
| MA0091.1 | 0.494398 |
| MA0092.1 | 0.446857 |
| MA0093.1 | 0.329976 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.568369 |
| MA0101.1 | 1.0468 |
| MA0103.1 | 0.348572 |
| MA0105.1 | 0.9471 |
| MA0106.1 | 0.677988 |
| MA0107.1 | 0.342432 |
| MA0108.2 | 0.763162 |
| MA0109.1 | 0 |
| MA0111.1 | 0.460823 |
| MA0113.1 | 0.649407 |
| MA0114.1 | 0.719313 |
| MA0115.1 | 1.0246 |
| MA0116.1 | 0.311187 |
| MA0117.1 | 0.992087 |
| MA0119.1 | 1.04809 |
| MA0122.1 | 1.01209 |
| MA0124.1 | 1.21735 |
| MA0125.1 | 1.14291 |
| MA0130.1 | 0 |
| MA0131.1 | 0.735438 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.05845 |
| MA0136.1 | 0.600242 |
| MA0139.1 | 0.202522 |
| MA0140.1 | 0.568252 |
| MA0141.1 | 2.58258 |
| MA0142.1 | 0.814115 |
| MA0143.1 | 0.665982 |
| MA0144.1 | 2.05933 |
| MA0145.1 | 0.0910975 |
| MA0146.1 | 1.57153 |
| MA0147.1 | 0.274511 |
| MA0148.1 | 0.49752 |
| MA0149.1 | 0.411562 |
| MA0062.2 | 0.167299 |
| MA0035.2 | 0.573016 |
| MA0039.2 | 0.367001 |
| MA0138.2 | 0.727395 |
| MA0002.2 | 0.205289 |
| MA0137.2 | 1.70505 |
| MA0104.2 | 0.218974 |
| MA0047.2 | 0.626803 |
| MA0112.2 | 1.5617 |
| MA0065.2 | 0.0914071 |
| MA0150.1 | 0.465855 |
| MA0151.1 | 0 |
| MA0152.1 | 1.5176 |
| MA0153.1 | 1.07519 |
| MA0154.1 | 0.792589 |
| MA0155.1 | 0.687925 |
| MA0156.1 | 0.356017 |
| MA0157.1 | 0.781683 |
| MA0158.1 | 0 |
| MA0159.1 | 0.776527 |
| MA0160.1 | 0.50056 |
| MA0161.1 | 0 |
| MA0162.1 | 0.127623 |
| MA0163.1 | 0.519779 |
| MA0164.1 | 1.46244 |
| MA0080.2 | 0.343316 |
| MA0018.2 | 0.610433 |
| MA0099.2 | 0.721008 |
| MA0079.2 | 0.000323799 |
| MA0102.2 | 1.65195 |
| MA0258.1 | 0.688848 |
| MA0259.1 | 1.34223 |
| MA0442.1 | 0 |
