MCL coexpression mm9:1580: Difference between revisions
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{{MCL_coexpression_mm9| | 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sulfate proteoglycan biosynthetic process;0.00320495261052977;72136!GO:0030205;dermatan sulfate metabolic process;0.00320495261052977;72136!GO:0030208;dermatan sulfate biosynthetic process;0.00320495261052977;72136!GO:0050655;dermatan sulfate proteoglycan metabolic process;0.00320495261052977;72136!GO:0001537;N-acetylgalactosamine 4-O-sulfotransferase activity;0.00549360244756628;72136!GO:0030206;chondroitin sulfate biosynthetic process;0.00549360244756628;72136!GO:0030204;chondroitin sulfate metabolic process;0.00549360244756628;72136!GO:0050650;chondroitin sulfate proteoglycan biosynthetic process;0.00712055615693433;72136!GO:0050654;chondroitin sulfate proteoglycan metabolic process;0.00712055615693433;72136!GO:0006024;glycosaminoglycan biosynthetic process;0.00815537962692766;72136!GO:0006023;aminoglycan biosynthetic process;0.00815537962692766;72136!GO:0008417;fucosyltransferase activity;0.0117450554949872;73068!GO:0030166;proteoglycan biosynthetic process;0.0121668129786169;72136!GO:0005794;Golgi apparatus;0.0121668129786169;72136,73068!GO:0042632;cholesterol homeostasis;0.0121668129786169;70310!GO:0055088;lipid homeostasis;0.0121668129786169;70310!GO:0055092;sterol homeostasis;0.0121668129786169;70310!GO:0006029;proteoglycan metabolic process;0.0121668129786169;72136!GO:0006022;aminoglycan metabolic process;0.0121668129786169;72136!GO:0030203;glycosaminoglycan metabolic process;0.0121668129786169;72136!GO:0009059;macromolecule biosynthetic process;0.013359548991871;72136,73068!GO:0042593;glucose homeostasis;0.0154668522003998;70310!GO:0033500;carbohydrate homeostasis;0.0154668522003998;70310!GO:0044272;sulfur compound biosynthetic process;0.0154668522003998;72136!GO:0008146;sulfotransferase activity;0.022509751156262;72136!GO:0016782;transferase activity, transferring sulfur-containing groups;0.0250777257891718;72136!GO:0006790;sulfur metabolic process;0.0283964755883061;72136!GO:0009058;biosynthetic process;0.0311107170377084;72136,73068!GO:0006486;protein amino acid glycosylation;0.0325304211573446;73068!GO:0043413;biopolymer glycosylation;0.0325304211573446;73068!GO:0016051;carbohydrate biosynthetic process;0.0325304211573446;72136!GO:0009101;glycoprotein biosynthetic process;0.0334992009021274;73068!GO:0009100;glycoprotein metabolic process;0.0378689794229424;73068!|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0002048!3.82e-07!14;UBERON:0000117!3.82e-07!14;UBERON:0000171!3.82e-07!14;UBERON:0000170!3.82e-07!14;UBERON:0005597!3.82e-07!14;UBERON:0000118!3.82e-07!14|tfbs_overrepresentation_for_novel_motifs=0.557864,2.7192,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.310789,0.370407,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,1.41491,1.0421,0.489529,0.44579,0.727684,1.04384,1.32977,0.757752,1.38127,0.641282,0.456327,1.87618,0.626183,1.03545,0.395107,0.704734,0.425309,0.20704,0.384813,0.699032,0.360612,0.328675,0.401916,0.631725,0.134724,0.426986,0.0637209,0.591277,0.847828,0.658142,0.115788,0.459555,0.912738,1.84811,0.220111,1.18062,1.19842,0.73621,0.469329,1.64777,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,0.152094,1.23259,0.257421,1.27178,0.253065,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.293164,1.1148,0.574099,0.297068,0.227755,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.3366,0.297538,1.05152,0.848095,0.20438,0.384901,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,1.23125,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,0.0998646,0.607321,0.932233,0.380707,1.23809,0.879184,1.7936,0.834976,5.1756,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,3.28302,2.18247,0.569503,0.408309,0.651755,0.133815,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,1.14345|tfbs_overrepresentation_jaspar=MA0003.1;1.36559,MA0004.1;1.46913,MA0006.1;0.419915,MA0007.1;0.587678,MA0009.1;1.06266,MA0014.1;3.30772,MA0017.1;0.449113,MA0019.1;0.874061,MA0024.1;1.01759,MA0025.1;1.30092,MA0027.1;2.72141,MA0028.1;1.10192,MA0029.1;0.995171,MA0030.1;1.00195,MA0031.1;0.965177,MA0038.1;0.757669,MA0040.1;1.07552,MA0041.1;0.522007,MA0042.1;0.507715,MA0043.1;1.1618,MA0046.1;1.09955,MA0048.1;0.205696,MA0050.1;0.645342,MA0051.1;0.767098,MA0052.1;1.08379,MA0055.1;0.602741,MA0056.1;0,MA0057.1;0.562607,MA0058.1;2.16203,MA0059.1;1.27866,MA0060.1;0.330907,MA0061.1;0.364227,MA0063.1;0,MA0066.1;0.746072,MA0067.1;1.41352,MA0068.1;1.08757,MA0069.1;1.08414,MA0070.1;1.07418,MA0071.1;0.644448,MA0072.1;1.06547,MA0073.1;0.0481612,MA0074.1;0.708108,MA0076.1;1.1853,MA0077.1;1.04318,MA0078.1;0.801834,MA0081.1;0.53877,MA0083.1;1.16099,MA0084.1;1.74401,MA0087.1;1.11687,MA0088.1;3.51516,MA0089.1;0,MA0090.1;0.566938,MA0091.1;0.617887,MA0092.1;0.567278,MA0093.1;1.12162,MA0095.1;0,MA0098.1;0,MA0100.1;0.695835,MA0101.1;0.523409,MA0103.1;0.460936,MA0105.1;0.248108,MA0106.1;0.809991,MA0107.1;0.454197,MA0108.2;0.897859,MA0109.1;0,MA0111.1;0.582193,MA0113.1;0.780358,MA0114.1;0.949408,MA0115.1;1.16466,MA0116.1;0.419688,MA0117.1;1.13165,MA0119.1;0.524046,MA0122.1;1.15196,MA0124.1;1.35963,MA0125.1;1.28445,MA0130.1;0,MA0131.1;0.869325,MA0132.1;0,MA0133.1;0,MA0135.1;1.19898,MA0136.1;0.729175,MA0139.1;0.295945,MA0140.1;0.695713,MA0141.1;0.482463,MA0142.1;0.950155,MA0143.1;0.797553,MA0144.1;0.365053,MA0145.1;0.476962,MA0146.1;0.822925,MA0147.1;1.75115,MA0148.1;0.621195,MA0149.1;0.529387,MA0062.2;0.254018,MA0035.2;0.700704,MA0039.2;6.99635,MA0138.2;0.861035,MA0002.2;0.299191,MA0137.2;0.479301,MA0104.2;1.52809,MA0047.2;0.75686,MA0112.2;4.45936,MA0065.2;0.477991,MA0150.1;0.587557,MA0151.1;0,MA0152.1;0.756973,MA0153.1;1.21594,MA0154.1;1.11105,MA0155.1;0.173445,MA0156.1;0.469089,MA0157.1;0.91689,MA0158.1;0,MA0159.1;1.78974,MA0160.1;0.624415,MA0161.1;0,MA0162.1;0.898893,MA0163.1;0.855539,MA0164.1;0.729558,MA0080.2;0.455167,MA0018.2;0.739807,MA0099.2;0.854449,MA0079.2;3.01303,MA0102.2;1.79669,MA0258.1;0.91616,MA0259.1;0.366802,MA0442.1;0}} | ||
Latest revision as of 17:09, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr11:69660112..69660161,+ | p1@Plscr3 |
| Mm9::chr14:21514178..21514207,+ | p1@Fut11 |
| Mm9::chr2:118752232..118752290,+ | p1@Chst14 |
| Mm9::chr2:118752291..118752311,+ | p2@Chst14 |
| Mm9::chr2:118752312..118752344,+ | p3@Chst14 |
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:0050651 | dermatan sulfate proteoglycan biosynthetic process | 0.00320495261052977 |
| GO:0030205 | dermatan sulfate metabolic process | 0.00320495261052977 |
| GO:0030208 | dermatan sulfate biosynthetic process | 0.00320495261052977 |
| GO:0050655 | dermatan sulfate proteoglycan metabolic process | 0.00320495261052977 |
| GO:0001537 | N-acetylgalactosamine 4-O-sulfotransferase activity | 0.00549360244756628 |
| GO:0030206 | chondroitin sulfate biosynthetic process | 0.00549360244756628 |
| GO:0030204 | chondroitin sulfate metabolic process | 0.00549360244756628 |
| GO:0050650 | chondroitin sulfate proteoglycan biosynthetic process | 0.00712055615693433 |
| GO:0050654 | chondroitin sulfate proteoglycan metabolic process | 0.00712055615693433 |
| GO:0006024 | glycosaminoglycan biosynthetic process | 0.00815537962692766 |
| GO:0006023 | aminoglycan biosynthetic process | 0.00815537962692766 |
| GO:0008417 | fucosyltransferase activity | 0.0117450554949872 |
| GO:0030166 | proteoglycan biosynthetic process | 0.0121668129786169 |
| GO:0005794 | Golgi apparatus | 0.0121668129786169 |
| GO:0042632 | cholesterol homeostasis | 0.0121668129786169 |
| GO:0055088 | lipid homeostasis | 0.0121668129786169 |
| GO:0055092 | sterol homeostasis | 0.0121668129786169 |
| GO:0006029 | proteoglycan metabolic process | 0.0121668129786169 |
| GO:0006022 | aminoglycan metabolic process | 0.0121668129786169 |
| GO:0030203 | glycosaminoglycan metabolic process | 0.0121668129786169 |
| GO:0009059 | macromolecule biosynthetic process | 0.013359548991871 |
| GO:0042593 | glucose homeostasis | 0.0154668522003998 |
| GO:0033500 | carbohydrate homeostasis | 0.0154668522003998 |
| GO:0044272 | sulfur compound biosynthetic process | 0.0154668522003998 |
| GO:0008146 | sulfotransferase activity | 0.022509751156262 |
| GO:0016782 | transferase activity, transferring sulfur-containing groups | 0.0250777257891718 |
| GO:0006790 | sulfur metabolic process | 0.0283964755883061 |
| GO:0009058 | biosynthetic process | 0.0311107170377084 |
| GO:0006486 | protein amino acid glycosylation | 0.0325304211573446 |
| GO:0043413 | biopolymer glycosylation | 0.0325304211573446 |
| GO:0016051 | carbohydrate biosynthetic process | 0.0325304211573446 |
| GO:0009101 | glycoprotein biosynthetic process | 0.0334992009021274 |
| GO:0009100 | glycoprotein metabolic process | 0.0378689794229424 |
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 |
|---|---|---|
| lung | 3.82e-07 | 14 |
| respiratory tube | 3.82e-07 | 14 |
| respiration organ | 3.82e-07 | 14 |
| pair of lungs | 3.82e-07 | 14 |
| lung primordium | 3.82e-07 | 14 |
| lung bud | 3.82e-07 | 14 |
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 | 1.36559 |
| MA0004.1 | 1.46913 |
| MA0006.1 | 0.419915 |
| MA0007.1 | 0.587678 |
| MA0009.1 | 1.06266 |
| MA0014.1 | 3.30772 |
| MA0017.1 | 0.449113 |
| MA0019.1 | 0.874061 |
| MA0024.1 | 1.01759 |
| MA0025.1 | 1.30092 |
| MA0027.1 | 2.72141 |
| MA0028.1 | 1.10192 |
| MA0029.1 | 0.995171 |
| MA0030.1 | 1.00195 |
| MA0031.1 | 0.965177 |
| MA0038.1 | 0.757669 |
| MA0040.1 | 1.07552 |
| MA0041.1 | 0.522007 |
| MA0042.1 | 0.507715 |
| MA0043.1 | 1.1618 |
| MA0046.1 | 1.09955 |
| MA0048.1 | 0.205696 |
| MA0050.1 | 0.645342 |
| MA0051.1 | 0.767098 |
| MA0052.1 | 1.08379 |
| MA0055.1 | 0.602741 |
| MA0056.1 | 0 |
| MA0057.1 | 0.562607 |
| MA0058.1 | 2.16203 |
| MA0059.1 | 1.27866 |
| MA0060.1 | 0.330907 |
| MA0061.1 | 0.364227 |
| MA0063.1 | 0 |
| MA0066.1 | 0.746072 |
| MA0067.1 | 1.41352 |
| MA0068.1 | 1.08757 |
| MA0069.1 | 1.08414 |
| MA0070.1 | 1.07418 |
| MA0071.1 | 0.644448 |
| MA0072.1 | 1.06547 |
| MA0073.1 | 0.0481612 |
| MA0074.1 | 0.708108 |
| MA0076.1 | 1.1853 |
| MA0077.1 | 1.04318 |
| MA0078.1 | 0.801834 |
| MA0081.1 | 0.53877 |
| MA0083.1 | 1.16099 |
| MA0084.1 | 1.74401 |
| MA0087.1 | 1.11687 |
| MA0088.1 | 3.51516 |
| MA0089.1 | 0 |
| MA0090.1 | 0.566938 |
| MA0091.1 | 0.617887 |
| MA0092.1 | 0.567278 |
| MA0093.1 | 1.12162 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.695835 |
| MA0101.1 | 0.523409 |
| MA0103.1 | 0.460936 |
| MA0105.1 | 0.248108 |
| MA0106.1 | 0.809991 |
| MA0107.1 | 0.454197 |
| MA0108.2 | 0.897859 |
| MA0109.1 | 0 |
| MA0111.1 | 0.582193 |
| MA0113.1 | 0.780358 |
| MA0114.1 | 0.949408 |
| MA0115.1 | 1.16466 |
| MA0116.1 | 0.419688 |
| MA0117.1 | 1.13165 |
| MA0119.1 | 0.524046 |
| MA0122.1 | 1.15196 |
| MA0124.1 | 1.35963 |
| MA0125.1 | 1.28445 |
| MA0130.1 | 0 |
| MA0131.1 | 0.869325 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.19898 |
| MA0136.1 | 0.729175 |
| MA0139.1 | 0.295945 |
| MA0140.1 | 0.695713 |
| MA0141.1 | 0.482463 |
| MA0142.1 | 0.950155 |
| MA0143.1 | 0.797553 |
| MA0144.1 | 0.365053 |
| MA0145.1 | 0.476962 |
| MA0146.1 | 0.822925 |
| MA0147.1 | 1.75115 |
| MA0148.1 | 0.621195 |
| MA0149.1 | 0.529387 |
| MA0062.2 | 0.254018 |
| MA0035.2 | 0.700704 |
| MA0039.2 | 6.99635 |
| MA0138.2 | 0.861035 |
| MA0002.2 | 0.299191 |
| MA0137.2 | 0.479301 |
| MA0104.2 | 1.52809 |
| MA0047.2 | 0.75686 |
| MA0112.2 | 4.45936 |
| MA0065.2 | 0.477991 |
| MA0150.1 | 0.587557 |
| MA0151.1 | 0 |
| MA0152.1 | 0.756973 |
| MA0153.1 | 1.21594 |
| MA0154.1 | 1.11105 |
| MA0155.1 | 0.173445 |
| MA0156.1 | 0.469089 |
| MA0157.1 | 0.91689 |
| MA0158.1 | 0 |
| MA0159.1 | 1.78974 |
| MA0160.1 | 0.624415 |
| MA0161.1 | 0 |
| MA0162.1 | 0.898893 |
| MA0163.1 | 0.855539 |
| MA0164.1 | 0.729558 |
| MA0080.2 | 0.455167 |
| MA0018.2 | 0.739807 |
| MA0099.2 | 0.854449 |
| MA0079.2 | 3.01303 |
| MA0102.2 | 1.79669 |
| MA0258.1 | 0.91616 |
| MA0259.1 | 0.366802 |
| MA0442.1 | 0 |
