MCL coexpression mm9:1583: Difference between revisions
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{{MCL_coexpression_mm9| | 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protein catabolic process;0.0150817990477646;192193!GO:0007620;copulation;0.0150817990477646;18436!GO:0004571;mannosyl-oligosaccharide 1,2-alpha-mannosidase activity;0.0150817990477646;192193!GO:0006515;misfolded or incompletely synthesized protein catabolic process;0.0150817990477646;192193!GO:0015924;mannosyl-oligosaccharide mannosidase activity;0.0150817990477646;192193!GO:0043161;proteasomal ubiquitin-dependent protein catabolic process;0.0201052086526011;192193!GO:0007618;mating;0.0201052086526011;18436!GO:0015923;mannosidase activity;0.0201052086526011;192193!GO:0006940;regulation of smooth muscle contraction;0.0219703145114774;18436!GO:0030176;integral to endoplasmic reticulum membrane;0.023495730629226;192193!GO:0031227;intrinsic to endoplasmic reticulum membrane;0.024766379441129;192193!GO:0006939;smooth muscle contraction;0.0258339695861031;18436!GO:0006986;response to unfolded protein;0.0258339695861031;192193!GO:0051789;response to protein stimulus;0.0258339695861031;192193!GO:0006937;regulation of muscle contraction;0.0258339695861031;18436!GO:0016502;nucleotide receptor activity;0.0258339695861031;18436!GO:0001614;purinergic nucleotide receptor activity;0.0258339695861031;18436!GO:0031301;integral to organelle membrane;0.0339790161096225;192193!GO:0031300;intrinsic to organelle membrane;0.035503201710864;192193!GO:0005789;endoplasmic reticulum membrane;0.0392493008543478;192193!GO:0048609;reproductive process in a multicellular organism;0.0392493008543478;18436!GO:0032504;multicellular organism reproduction;0.0392493008543478;18436!GO:0042175;nuclear envelope-endoplasmic reticulum network;0.0392493008543478;192193!GO:0044432;endoplasmic reticulum part;0.0396565940540057;192193!GO:0003012;muscle system process;0.0396565940540057;18436!GO:0006936;muscle contraction;0.0396565940540057;18436!GO:0004553;hydrolase activity, hydrolyzing O-glycosyl compounds;0.0400787904412177;192193!GO:0016798;hydrolase activity, acting on glycosyl bonds;0.0454545468189168;192193!GO:0045211;postsynaptic membrane;0.0454545468189168;18436!GO:0006511;ubiquitin-dependent protein catabolic process;0.0454545468189168;192193!GO:0044456;synapse part;0.0454545468189168;18436!GO:0043632;modification-dependent macromolecule catabolic process;0.0454545468189168;192193!GO:0019941;modification-dependent protein catabolic process;0.0454545468189168;192193!GO:0051603;proteolysis involved in cellular protein catabolic process;0.0454545468189168;192193!GO:0044257;cellular protein catabolic process;0.0454545468189168;192193!|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0000949!3.26e-14!72;UBERON:0001264!3.51e-12!12;UBERON:0002370!1.01e-11!23;UBERON:0000974!1.01e-11!23;UBERON:0004807!1.01e-11!23;UBERON:0005058!1.01e-11!23;UBERON:0003351!1.01e-11!23;UBERON:0009113!1.01e-11!23;UBERON:0003295!1.01e-11!23;UBERON:0009722!1.01e-11!23;UBERON:0005562!1.01e-11!23;UBERON:0007690!1.01e-11!23;UBERON:0006562!5.22e-11!24;UBERON:0003408!5.22e-11!24;UBERON:0001557!5.22e-11!24;UBERON:0001042!5.22e-11!24;UBERON:0008814!5.22e-11!24;UBERON:0009145!5.22e-11!24;UBERON:0004177!2.17e-10!29;UBERON:0005057!2.17e-10!29;UBERON:0000077!7.48e-10!35;UBERON:0000072!3.34e-09!27;UBERON:0002075!8.22e-09!19;UBERON:0002530!6.17e-08!65;UBERON:0003929!1.39e-07!55;UBERON:0002368!8.86e-07!60|tfbs_overrepresentation_for_novel_motifs=0.557864,1.52338,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.310789,0.115752,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.775038,0.545768,0.489529,0.44579,0.727684,1.04384,0.537749,0.757752,0.754069,0.641282,0.456327,0.645258,0.626183,1.03545,0.395107,0.704734,0.425309,0.0566307,0.384813,0.699032,0.360612,0.328675,0.401916,0.631725,0.419293,0.426986,0.4934,0.591277,0.847828,0.658142,0.746467,0.459555,0.912738,0.786094,0.627649,1.18062,1.19842,0.73621,0.469329,0.689304,0.731291,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,0.152094,1.23259,0.257421,0.245132,0.253065,0.835925,0.997094,0.494135,0.830212,0.948899,0.794502,0.293164,1.1148,0.272382,0.0882907,0.227755,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.3366,0.297538,1.05152,0.848095,0.20438,0.384901,1.03517,2.61649,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,0.491483,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,0.328405,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.651755,0.133815,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,3.33644|tfbs_overrepresentation_jaspar=MA0003.1;3.33169,MA0004.1;0.603793,MA0006.1;0.419915,MA0007.1;0.587678,MA0009.1;1.06266,MA0014.1;0.736185,MA0017.1;2.9605,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;0.192781,MA0058.1;0.50032,MA0059.1;0.513699,MA0060.1;1.58413,MA0061.1;0.955135,MA0063.1;0,MA0066.1;0.746072,MA0067.1;1.41352,MA0068.1;0.197245,MA0069.1;1.08414,MA0070.1;1.07418,MA0071.1;0.644448,MA0072.1;1.06547,MA0073.1;0.0176764,MA0074.1;0.708108,MA0076.1;0.470037,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;0.148348,MA0089.1;0,MA0090.1;0.566938,MA0091.1;0.617887,MA0092.1;0.567278,MA0093.1;0.440484,MA0095.1;0,MA0098.1;0,MA0100.1;0.695835,MA0101.1;0.523409,MA0103.1;0.460936,MA0105.1;1.28296,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;1.69206,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;1.21195,MA0142.1;0.950155,MA0143.1;0.797553,MA0144.1;0.365053,MA0145.1;0.476962,MA0146.1;1.74263,MA0147.1;0.378658,MA0148.1;0.621195,MA0149.1;0.529387,MA0062.2;0.254018,MA0035.2;0.700704,MA0039.2;1.42062,MA0138.2;0.861035,MA0002.2;0.299191,MA0137.2;0.479301,MA0104.2;0.315156,MA0047.2;0.75686,MA0112.2;2.12679,MA0065.2;0.929207,MA0150.1;0.587557,MA0151.1;0,MA0152.1;0.756973,MA0153.1;1.21594,MA0154.1;0.587595,MA0155.1;0.99229,MA0156.1;0.469089,MA0157.1;0.91689,MA0158.1;0,MA0159.1;1.01146,MA0160.1;0.624415,MA0161.1;0,MA0162.1;0.0699535,MA0163.1;0.0644585,MA0164.1;0.729558,MA0080.2;0.455167,MA0018.2;0.739807,MA0099.2;0.854449,MA0079.2;0.130118,MA0102.2;1.79669,MA0258.1;0.346619,MA0259.1;0.366802,MA0442.1;0}} | ||
Latest revision as of 17:10, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr11:72823222..72823239,+ | p5@P2rx1 |
| Mm9::chr6:108778502..108778511,+ | p6@Edem1 |
| Mm9::chr6:108778599..108778610,+ | p4@Edem1 |
| Mm9::chr6:108794661..108794664,+ | p@chr6:108794661..108794664 + |
| Mm9::chr7:134422075..134422089,+ | p@chr7:134422075..134422089 + |
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:0007320 | insemination | 0.0150817990477646 |
| GO:0030433 | ER-associated protein catabolic process | 0.0150817990477646 |
| GO:0007620 | copulation | 0.0150817990477646 |
| GO:0004571 | mannosyl-oligosaccharide 1,2-alpha-mannosidase activity | 0.0150817990477646 |
| GO:0006515 | misfolded or incompletely synthesized protein catabolic process | 0.0150817990477646 |
| GO:0015924 | mannosyl-oligosaccharide mannosidase activity | 0.0150817990477646 |
| GO:0043161 | proteasomal ubiquitin-dependent protein catabolic process | 0.0201052086526011 |
| GO:0007618 | mating | 0.0201052086526011 |
| GO:0015923 | mannosidase activity | 0.0201052086526011 |
| GO:0006940 | regulation of smooth muscle contraction | 0.0219703145114774 |
| GO:0030176 | integral to endoplasmic reticulum membrane | 0.023495730629226 |
| GO:0031227 | intrinsic to endoplasmic reticulum membrane | 0.024766379441129 |
| GO:0006939 | smooth muscle contraction | 0.0258339695861031 |
| GO:0006986 | response to unfolded protein | 0.0258339695861031 |
| GO:0051789 | response to protein stimulus | 0.0258339695861031 |
| GO:0006937 | regulation of muscle contraction | 0.0258339695861031 |
| GO:0016502 | nucleotide receptor activity | 0.0258339695861031 |
| GO:0001614 | purinergic nucleotide receptor activity | 0.0258339695861031 |
| GO:0031301 | integral to organelle membrane | 0.0339790161096225 |
| GO:0031300 | intrinsic to organelle membrane | 0.035503201710864 |
| GO:0005789 | endoplasmic reticulum membrane | 0.0392493008543478 |
| GO:0048609 | reproductive process in a multicellular organism | 0.0392493008543478 |
| GO:0032504 | multicellular organism reproduction | 0.0392493008543478 |
| GO:0042175 | nuclear envelope-endoplasmic reticulum network | 0.0392493008543478 |
| GO:0044432 | endoplasmic reticulum part | 0.0396565940540057 |
| GO:0003012 | muscle system process | 0.0396565940540057 |
| GO:0006936 | muscle contraction | 0.0396565940540057 |
| GO:0004553 | hydrolase activity, hydrolyzing O-glycosyl compounds | 0.0400787904412177 |
| GO:0016798 | hydrolase activity, acting on glycosyl bonds | 0.0454545468189168 |
| GO:0045211 | postsynaptic membrane | 0.0454545468189168 |
| GO:0006511 | ubiquitin-dependent protein catabolic process | 0.0454545468189168 |
| GO:0044456 | synapse part | 0.0454545468189168 |
| GO:0043632 | modification-dependent macromolecule catabolic process | 0.0454545468189168 |
| GO:0019941 | modification-dependent protein catabolic process | 0.0454545468189168 |
| GO:0051603 | proteolysis involved in cellular protein catabolic process | 0.0454545468189168 |
| GO:0044257 | cellular protein catabolic process | 0.0454545468189168 |
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 |
|---|---|---|
| endocrine system | 3.26e-14 | 72 |
| pancreas | 3.51e-12 | 12 |
| thymus | 1.01e-11 | 23 |
| neck | 1.01e-11 | 23 |
| respiratory system epithelium | 1.01e-11 | 23 |
| hemolymphoid system gland | 1.01e-11 | 23 |
| pharyngeal epithelium | 1.01e-11 | 23 |
| thymic region | 1.01e-11 | 23 |
| pharyngeal gland | 1.01e-11 | 23 |
| entire pharyngeal arch endoderm | 1.01e-11 | 23 |
| thymus primordium | 1.01e-11 | 23 |
| early pharyngeal endoderm | 1.01e-11 | 23 |
| pharynx | 5.22e-11 | 24 |
| gland of gut | 5.22e-11 | 24 |
| upper respiratory tract | 5.22e-11 | 24 |
| chordate pharynx | 5.22e-11 | 24 |
| pharyngeal arch system | 5.22e-11 | 24 |
| pharyngeal region of foregut | 5.22e-11 | 24 |
| hemopoietic organ | 2.17e-10 | 29 |
| immune organ | 2.17e-10 | 29 |
| mixed endoderm/mesoderm-derived structure | 7.48e-10 | 35 |
| segment of respiratory tract | 3.34e-09 | 27 |
| viscus | 8.22e-09 | 19 |
| gland | 6.17e-08 | 65 |
| gut epithelium | 1.39e-07 | 55 |
| endocrine gland | 8.86e-07 | 60 |
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 | 3.33169 |
| MA0004.1 | 0.603793 |
| MA0006.1 | 0.419915 |
| MA0007.1 | 0.587678 |
| MA0009.1 | 1.06266 |
| MA0014.1 | 0.736185 |
| MA0017.1 | 2.9605 |
| 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 | 0.192781 |
| MA0058.1 | 0.50032 |
| MA0059.1 | 0.513699 |
| MA0060.1 | 1.58413 |
| MA0061.1 | 0.955135 |
| MA0063.1 | 0 |
| MA0066.1 | 0.746072 |
| MA0067.1 | 1.41352 |
| MA0068.1 | 0.197245 |
| MA0069.1 | 1.08414 |
| MA0070.1 | 1.07418 |
| MA0071.1 | 0.644448 |
| MA0072.1 | 1.06547 |
| MA0073.1 | 0.0176764 |
| MA0074.1 | 0.708108 |
| MA0076.1 | 0.470037 |
| 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 | 0.148348 |
| MA0089.1 | 0 |
| MA0090.1 | 0.566938 |
| MA0091.1 | 0.617887 |
| MA0092.1 | 0.567278 |
| MA0093.1 | 0.440484 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.695835 |
| MA0101.1 | 0.523409 |
| MA0103.1 | 0.460936 |
| MA0105.1 | 1.28296 |
| 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 | 1.69206 |
| 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 | 1.21195 |
| MA0142.1 | 0.950155 |
| MA0143.1 | 0.797553 |
| MA0144.1 | 0.365053 |
| MA0145.1 | 0.476962 |
| MA0146.1 | 1.74263 |
| MA0147.1 | 0.378658 |
| MA0148.1 | 0.621195 |
| MA0149.1 | 0.529387 |
| MA0062.2 | 0.254018 |
| MA0035.2 | 0.700704 |
| MA0039.2 | 1.42062 |
| MA0138.2 | 0.861035 |
| MA0002.2 | 0.299191 |
| MA0137.2 | 0.479301 |
| MA0104.2 | 0.315156 |
| MA0047.2 | 0.75686 |
| MA0112.2 | 2.12679 |
| MA0065.2 | 0.929207 |
| MA0150.1 | 0.587557 |
| MA0151.1 | 0 |
| MA0152.1 | 0.756973 |
| MA0153.1 | 1.21594 |
| MA0154.1 | 0.587595 |
| MA0155.1 | 0.99229 |
| MA0156.1 | 0.469089 |
| MA0157.1 | 0.91689 |
| MA0158.1 | 0 |
| MA0159.1 | 1.01146 |
| MA0160.1 | 0.624415 |
| MA0161.1 | 0 |
| MA0162.1 | 0.0699535 |
| MA0163.1 | 0.0644585 |
| MA0164.1 | 0.729558 |
| MA0080.2 | 0.455167 |
| MA0018.2 | 0.739807 |
| MA0099.2 | 0.854449 |
| MA0079.2 | 0.130118 |
| MA0102.2 | 1.79669 |
| MA0258.1 | 0.346619 |
| MA0259.1 | 0.366802 |
| MA0442.1 | 0 |
