MCL coexpression mm9:1966: Difference between revisions
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{{MCL_coexpression_mm9| | 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of fatty acid oxidation;0.00268449022078563;69183!GO:0045725;positive regulation of glycogen biosynthetic process;0.00268449022078563;69183!GO:0046321;positive regulation of fatty acid oxidation;0.00268449022078563;69183!GO:0005979;regulation of glycogen biosynthetic process;0.00268449022078563;69183!GO:0046326;positive regulation of glucose import;0.00429506668986796;69183!GO:0045923;positive regulation of fatty acid metabolic process;0.0053682450453898;69183!GO:0045913;positive regulation of carbohydrate metabolic process;0.0053682450453898;69183!GO:0043255;regulation of carbohydrate biosynthetic process;0.0053682450453898;69183!GO:0045834;positive regulation of lipid metabolic process;0.0053682450453898;69183!GO:0006109;regulation of carbohydrate metabolic process;0.0053682450453898;69183!GO:0046323;glucose import;0.0053682450453898;69183!GO:0046324;regulation of glucose import;0.0053682450453898;69183!GO:0019217;regulation of fatty acid metabolic process;0.00578102857893454;69183!GO:0009250;glucan biosynthetic process;0.00787234748550556;69183!GO:0005978;glycogen biosynthetic process;0.00787234748550556;69183!GO:0033692;cellular polysaccharide biosynthetic process;0.0112686815993754;69183!GO:0019216;regulation of lipid metabolic process;0.0112686815993754;69183!GO:0000271;polysaccharide biosynthetic process;0.0112686815993754;69183!GO:0019395;fatty acid oxidation;0.0112686815993754;69183!GO:0051260;protein homooligomerization;0.0112686815993754;69183!GO:0015758;glucose transport;0.0127924315383814;69183!GO:0008645;hexose transport;0.0127924315383814;69183!GO:0015749;monosaccharide transport;0.0127924315383814;69183!GO:0051259;protein oligomerization;0.0127924315383814;69183!GO:0006073;glucan metabolic process;0.0127924315383814;69183!GO:0005977;glycogen metabolic process;0.0127924315383814;69183!GO:0051050;positive regulation of transport;0.0131126695480243;69183!GO:0006112;energy reserve metabolic process;0.0133171017971613;69183!GO:0000187;activation of MAPK activity;0.0133171017971613;69183!GO:0043406;positive regulation of MAP kinase activity;0.0146591325437936;69183!GO:0031328;positive regulation of cellular biosynthetic process;0.0148774537991498;69183!GO:0005976;polysaccharide metabolic process;0.0152741876027265;69183!GO:0044264;cellular polysaccharide metabolic process;0.0152741876027265;69183!GO:0009891;positive regulation of biosynthetic process;0.0167147419428269;69183!GO:0043405;regulation of MAP kinase activity;0.0183781809141602;69183!GO:0008643;carbohydrate transport;0.0184622518725425;69183!GO:0043284;biopolymer biosynthetic process;0.0186169336431586;69183!GO:0015980;energy derivation by oxidation of organic compounds;0.0186169336431586;69183!GO:0016051;carbohydrate biosynthetic process;0.0217047770579539;69183!GO:0045860;positive regulation of protein kinase activity;0.0219497034466616;69183!GO:0051049;regulation of transport;0.0219497034466616;69183!GO:0033674;positive regulation of kinase activity;0.0221715039405213;69183!GO:0051347;positive regulation of transferase activity;0.0221715039405213;69183!GO:0005615;extracellular space;0.0259322755466698;69183,66695!GO:0000165;MAPKKK cascade;0.0278661181086713;69183!GO:0044421;extracellular region part;0.0278661181086713;69183,66695!GO:0006461;protein complex assembly;0.0283127897558507;69183!GO:0045859;regulation of protein kinase activity;0.0283127897558507;69183!GO:0043549;regulation of kinase activity;0.0283196743618672;69183!GO:0043085;positive regulation of catalytic activity;0.0283196743618672;69183!GO:0051338;regulation of transferase activity;0.0283196743618672;69183!GO:0031326;regulation of cellular biosynthetic process;0.0285948849026102;69183!GO:0009889;regulation of biosynthetic process;0.0312709881914443;69183!GO:0006631;fatty acid metabolic process;0.0316775990696353;69183!GO:0032787;monocarboxylic acid metabolic process;0.0413436845112987;69183!GO:0007243;protein kinase cascade;0.0417423164216104;69183!GO:0044262;cellular carbohydrate metabolic process;0.0464034268004006;69183!GO:0050790;regulation of catalytic activity;0.0490714453924019;69183!|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0000468!3.78e-11!333;UBERON:0003102!3.72e-07!22;UBERON:0000479!7.42e-07!349|tfbs_overrepresentation_for_novel_motifs=0.641384,0.128156,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.489964,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.928768,0.24402,0.570433,0.197567,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,0.535752,0.290745,0.711848,1.12823,0.471365,0.318879,0.503207,0.30022,1.16474,0.786577,0.434783,0.40068,0.478558,0.717547,0.185353,0.504971,0.325217,0.675898,0.938241,0.744678,0.49007,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.593145,1.32691,0.864765,2.29987,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,0.11855,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,1.09896,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,1.53136,1.25851,0.576517,0.7614,1.51002,0.476467,0.143825,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.293812,0.542121,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,0.589293|tfbs_overrepresentation_jaspar=MA0003.1;0.331308,MA0004.1;1.64673,MA0006.1;0.497533,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;0.276754,MA0017.1;0.528196,MA0019.1;0.964875,MA0024.1;1.11019,MA0025.1;1.39562,MA0027.1;2.81824,MA0028.1;0.509589,MA0029.1;1.08753,MA0030.1;1.09438,MA0031.1;1.05719,MA0038.1;0.846479,MA0040.1;2.62831,MA0041.1;0.604221,MA0042.1;0.589368,MA0043.1;1.25564,MA0046.1;1.1929,MA0048.1;0.266382,MA0050.1;0.731539,MA0051.1;0.856094,MA0052.1;1.17701,MA0055.1;0.125758,MA0056.1;0,MA0057.1;0.251896,MA0058.1;1.4226,MA0059.1;0.59559,MA0060.1;0.403071,MA0061.1;0.438628,MA0063.1;0,MA0066.1;0.834648,MA0067.1;1.50873,MA0068.1;0.713436,MA0069.1;1.17737,MA0070.1;1.16732,MA0071.1;0.73062,MA0072.1;1.15853,MA0073.1;0.00221226,MA0074.1;0.795862,MA0076.1;0.550092,MA0077.1;1.13603,MA0078.1;0.891476,MA0081.1;0.621611,MA0083.1;1.25482,MA0084.1;1.84013,MA0087.1;1.21037,MA0088.1;0.201215,MA0089.1;0,MA0090.1;0.650768,MA0091.1;0.703314,MA0092.1;0.651119,MA0093.1;1.29026,MA0095.1;0,MA0098.1;0,MA0100.1;0.783305,MA0101.1;0.605676,MA0103.1;0.540576,MA0105.1;0.313353,MA0106.1;0.899777,MA0107.1;0.533522,MA0108.2;0.989014,MA0109.1;0,MA0111.1;0.666525,MA0113.1;0.869608,MA0114.1;0.43587,MA0115.1;1.25852,MA0116.1;0.497293,MA0117.1;1.22527,MA0119.1;2.50824,MA0122.1;1.24573,MA0124.1;1.45461,MA0125.1;1.37907,MA0130.1;0,MA0131.1;0.960068,MA0132.1;0,MA0133.1;0,MA0135.1;1.29308,MA0136.1;0.817395,MA0139.1;0.957842,MA0140.1;0.78318,MA0141.1;0.563066,MA0142.1;1.04199,MA0143.1;0.887119,MA0144.1;0.439506,MA0145.1;1.14526,MA0146.1;0.0944145,MA0147.1;1.15069,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.319836,MA0035.2;0.788288,MA0039.2;0.0959929,MA0138.2;0.951653,MA0002.2;0.368961,MA0137.2;0.559766,MA0104.2;1.0034,MA0047.2;0.845655,MA0112.2;0.211985,MA0065.2;0.212467,MA0150.1;0.67206,MA0151.1;0,MA0152.1;0.84577,MA0153.1;1.31015,MA0154.1;0.263609,MA0155.1;1.21457,MA0156.1;0.549102,MA0157.1;1.0083,MA0158.1;0,MA0159.1;0.465802,MA0160.1;0.71003,MA0161.1;0,MA0162.1;0.10667,MA0163.1;0.0996272,MA0164.1;0.817786,MA0080.2;0.534538,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;0.000201415,MA0102.2;1.8929,MA0258.1;0.419871,MA0259.1;0.441366,MA0442.1;0}} | ||
Latest revision as of 17:47, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr11:43287783..43287842,+ | p1@C1qtnf2 |
| Mm9::chr13:49639848..49639902,+ | p1@Aspn |
| Mm9::chr13:49639994..49640005,+ | p2@Aspn |
| Mm9::chr17:8020154..8020175,- | p1@Fndc1 |
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:0046320 | regulation of fatty acid oxidation | 0.00268449022078563 |
| GO:0045725 | positive regulation of glycogen biosynthetic process | 0.00268449022078563 |
| GO:0046321 | positive regulation of fatty acid oxidation | 0.00268449022078563 |
| GO:0005979 | regulation of glycogen biosynthetic process | 0.00268449022078563 |
| GO:0046326 | positive regulation of glucose import | 0.00429506668986796 |
| GO:0045923 | positive regulation of fatty acid metabolic process | 0.0053682450453898 |
| GO:0045913 | positive regulation of carbohydrate metabolic process | 0.0053682450453898 |
| GO:0043255 | regulation of carbohydrate biosynthetic process | 0.0053682450453898 |
| GO:0045834 | positive regulation of lipid metabolic process | 0.0053682450453898 |
| GO:0006109 | regulation of carbohydrate metabolic process | 0.0053682450453898 |
| GO:0046323 | glucose import | 0.0053682450453898 |
| GO:0046324 | regulation of glucose import | 0.0053682450453898 |
| GO:0019217 | regulation of fatty acid metabolic process | 0.00578102857893454 |
| GO:0009250 | glucan biosynthetic process | 0.00787234748550556 |
| GO:0005978 | glycogen biosynthetic process | 0.00787234748550556 |
| GO:0033692 | cellular polysaccharide biosynthetic process | 0.0112686815993754 |
| GO:0019216 | regulation of lipid metabolic process | 0.0112686815993754 |
| GO:0000271 | polysaccharide biosynthetic process | 0.0112686815993754 |
| GO:0019395 | fatty acid oxidation | 0.0112686815993754 |
| GO:0051260 | protein homooligomerization | 0.0112686815993754 |
| GO:0015758 | glucose transport | 0.0127924315383814 |
| GO:0008645 | hexose transport | 0.0127924315383814 |
| GO:0015749 | monosaccharide transport | 0.0127924315383814 |
| GO:0051259 | protein oligomerization | 0.0127924315383814 |
| GO:0006073 | glucan metabolic process | 0.0127924315383814 |
| GO:0005977 | glycogen metabolic process | 0.0127924315383814 |
| GO:0051050 | positive regulation of transport | 0.0131126695480243 |
| GO:0006112 | energy reserve metabolic process | 0.0133171017971613 |
| GO:0000187 | activation of MAPK activity | 0.0133171017971613 |
| GO:0043406 | positive regulation of MAP kinase activity | 0.0146591325437936 |
| GO:0031328 | positive regulation of cellular biosynthetic process | 0.0148774537991498 |
| GO:0005976 | polysaccharide metabolic process | 0.0152741876027265 |
| GO:0044264 | cellular polysaccharide metabolic process | 0.0152741876027265 |
| GO:0009891 | positive regulation of biosynthetic process | 0.0167147419428269 |
| GO:0043405 | regulation of MAP kinase activity | 0.0183781809141602 |
| GO:0008643 | carbohydrate transport | 0.0184622518725425 |
| GO:0043284 | biopolymer biosynthetic process | 0.0186169336431586 |
| GO:0015980 | energy derivation by oxidation of organic compounds | 0.0186169336431586 |
| GO:0016051 | carbohydrate biosynthetic process | 0.0217047770579539 |
| GO:0045860 | positive regulation of protein kinase activity | 0.0219497034466616 |
| GO:0051049 | regulation of transport | 0.0219497034466616 |
| GO:0033674 | positive regulation of kinase activity | 0.0221715039405213 |
| GO:0051347 | positive regulation of transferase activity | 0.0221715039405213 |
| GO:0005615 | extracellular space | 0.0259322755466698 |
| GO:0000165 | MAPKKK cascade | 0.0278661181086713 |
| GO:0044421 | extracellular region part | 0.0278661181086713 |
| GO:0006461 | protein complex assembly | 0.0283127897558507 |
| GO:0045859 | regulation of protein kinase activity | 0.0283127897558507 |
| GO:0043549 | regulation of kinase activity | 0.0283196743618672 |
| GO:0043085 | positive regulation of catalytic activity | 0.0283196743618672 |
| GO:0051338 | regulation of transferase activity | 0.0283196743618672 |
| GO:0031326 | regulation of cellular biosynthetic process | 0.0285948849026102 |
| GO:0009889 | regulation of biosynthetic process | 0.0312709881914443 |
| GO:0006631 | fatty acid metabolic process | 0.0316775990696353 |
| GO:0032787 | monocarboxylic acid metabolic process | 0.0413436845112987 |
| GO:0007243 | protein kinase cascade | 0.0417423164216104 |
| GO:0044262 | cellular carbohydrate metabolic process | 0.0464034268004006 |
| GO:0050790 | regulation of catalytic activity | 0.0490714453924019 |
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-11 | 333 |
| surface structure | 3.72e-07 | 22 |
| tissue | 7.42e-07 | 349 |
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 | 0.331308 |
| MA0004.1 | 1.64673 |
| MA0006.1 | 0.497533 |
| MA0007.1 | 0.672186 |
| MA0009.1 | 1.15569 |
| MA0014.1 | 0.276754 |
| MA0017.1 | 0.528196 |
| MA0019.1 | 0.964875 |
| MA0024.1 | 1.11019 |
| MA0025.1 | 1.39562 |
| MA0027.1 | 2.81824 |
| MA0028.1 | 0.509589 |
| MA0029.1 | 1.08753 |
| MA0030.1 | 1.09438 |
| MA0031.1 | 1.05719 |
| MA0038.1 | 0.846479 |
| MA0040.1 | 2.62831 |
| MA0041.1 | 0.604221 |
| MA0042.1 | 0.589368 |
| MA0043.1 | 1.25564 |
| MA0046.1 | 1.1929 |
| MA0048.1 | 0.266382 |
| MA0050.1 | 0.731539 |
| MA0051.1 | 0.856094 |
| MA0052.1 | 1.17701 |
| MA0055.1 | 0.125758 |
| MA0056.1 | 0 |
| MA0057.1 | 0.251896 |
| MA0058.1 | 1.4226 |
| MA0059.1 | 0.59559 |
| MA0060.1 | 0.403071 |
| MA0061.1 | 0.438628 |
| MA0063.1 | 0 |
| MA0066.1 | 0.834648 |
| MA0067.1 | 1.50873 |
| MA0068.1 | 0.713436 |
| MA0069.1 | 1.17737 |
| MA0070.1 | 1.16732 |
| MA0071.1 | 0.73062 |
| MA0072.1 | 1.15853 |
| MA0073.1 | 0.00221226 |
| MA0074.1 | 0.795862 |
| MA0076.1 | 0.550092 |
| MA0077.1 | 1.13603 |
| MA0078.1 | 0.891476 |
| MA0081.1 | 0.621611 |
| MA0083.1 | 1.25482 |
| MA0084.1 | 1.84013 |
| MA0087.1 | 1.21037 |
| MA0088.1 | 0.201215 |
| MA0089.1 | 0 |
| MA0090.1 | 0.650768 |
| MA0091.1 | 0.703314 |
| MA0092.1 | 0.651119 |
| MA0093.1 | 1.29026 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.783305 |
| MA0101.1 | 0.605676 |
| MA0103.1 | 0.540576 |
| MA0105.1 | 0.313353 |
| MA0106.1 | 0.899777 |
| MA0107.1 | 0.533522 |
| MA0108.2 | 0.989014 |
| MA0109.1 | 0 |
| MA0111.1 | 0.666525 |
| MA0113.1 | 0.869608 |
| MA0114.1 | 0.43587 |
| MA0115.1 | 1.25852 |
| MA0116.1 | 0.497293 |
| MA0117.1 | 1.22527 |
| MA0119.1 | 2.50824 |
| MA0122.1 | 1.24573 |
| MA0124.1 | 1.45461 |
| MA0125.1 | 1.37907 |
| MA0130.1 | 0 |
| MA0131.1 | 0.960068 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.29308 |
| MA0136.1 | 0.817395 |
| MA0139.1 | 0.957842 |
| MA0140.1 | 0.78318 |
| MA0141.1 | 0.563066 |
| MA0142.1 | 1.04199 |
| MA0143.1 | 0.887119 |
| MA0144.1 | 0.439506 |
| MA0145.1 | 1.14526 |
| MA0146.1 | 0.0944145 |
| MA0147.1 | 1.15069 |
| MA0148.1 | 0.706718 |
| MA0149.1 | 0.611881 |
| MA0062.2 | 0.319836 |
| MA0035.2 | 0.788288 |
| MA0039.2 | 0.0959929 |
| MA0138.2 | 0.951653 |
| MA0002.2 | 0.368961 |
| MA0137.2 | 0.559766 |
| MA0104.2 | 1.0034 |
| MA0047.2 | 0.845655 |
| MA0112.2 | 0.211985 |
| MA0065.2 | 0.212467 |
| MA0150.1 | 0.67206 |
| MA0151.1 | 0 |
| MA0152.1 | 0.84577 |
| MA0153.1 | 1.31015 |
| MA0154.1 | 0.263609 |
| MA0155.1 | 1.21457 |
| MA0156.1 | 0.549102 |
| MA0157.1 | 1.0083 |
| MA0158.1 | 0 |
| MA0159.1 | 0.465802 |
| MA0160.1 | 0.71003 |
| MA0161.1 | 0 |
| MA0162.1 | 0.10667 |
| MA0163.1 | 0.0996272 |
| MA0164.1 | 0.817786 |
| MA0080.2 | 0.534538 |
| MA0018.2 | 0.828253 |
| MA0099.2 | 0.944966 |
| MA0079.2 | 0.000201415 |
| MA0102.2 | 1.8929 |
| MA0258.1 | 0.419871 |
| MA0259.1 | 0.441366 |
| MA0442.1 | 0 |
