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MCL coexpression mm9:1583: Difference between revisions

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|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
|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_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
}}
}}

Revision as of 13:33, 23 January 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 IDGO nameFDR corrected p-value
GO:0007320insemination0.0150817990477646
GO:0030433ER-associated protein catabolic process0.0150817990477646
GO:0007620copulation0.0150817990477646
GO:0004571mannosyl-oligosaccharide 1,2-alpha-mannosidase activity0.0150817990477646
GO:0006515misfolded or incompletely synthesized protein catabolic process0.0150817990477646
GO:0015924mannosyl-oligosaccharide mannosidase activity0.0150817990477646
GO:0043161proteasomal ubiquitin-dependent protein catabolic process0.0201052086526011
GO:0007618mating0.0201052086526011
GO:0015923mannosidase activity0.0201052086526011
GO:0006940regulation of smooth muscle contraction0.0219703145114774
GO:0030176integral to endoplasmic reticulum membrane0.023495730629226
GO:0031227intrinsic to endoplasmic reticulum membrane0.024766379441129
GO:0006939smooth muscle contraction0.0258339695861031
GO:0006986response to unfolded protein0.0258339695861031
GO:0051789response to protein stimulus0.0258339695861031
GO:0006937regulation of muscle contraction0.0258339695861031
GO:0016502nucleotide receptor activity0.0258339695861031
GO:0001614purinergic nucleotide receptor activity0.0258339695861031
GO:0031301integral to organelle membrane0.0339790161096225
GO:0031300intrinsic to organelle membrane0.035503201710864
GO:0005789endoplasmic reticulum membrane0.0392493008543478
GO:0048609reproductive process in a multicellular organism0.0392493008543478
GO:0032504multicellular organism reproduction0.0392493008543478
GO:0042175nuclear envelope-endoplasmic reticulum network0.0392493008543478
GO:0044432endoplasmic reticulum part0.0396565940540057
GO:0003012muscle system process0.0396565940540057
GO:0006936muscle contraction0.0396565940540057
GO:0004553hydrolase activity, hydrolyzing O-glycosyl compounds0.0400787904412177
GO:0016798hydrolase activity, acting on glycosyl bonds0.0454545468189168
GO:0045211postsynaptic membrane0.0454545468189168
GO:0006511ubiquitin-dependent protein catabolic process0.0454545468189168
GO:0044456synapse part0.0454545468189168
GO:0043632modification-dependent macromolecule catabolic process0.0454545468189168
GO:0019941modification-dependent protein catabolic process0.0454545468189168
GO:0051603proteolysis involved in cellular protein catabolic process0.0454545468189168
GO:0044257cellular protein catabolic process0.0454545468189168



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>


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)
MA0003.13.33169
MA0004.10.603793
MA0006.10.419915
MA0007.10.587678
MA0009.11.06266
MA0014.10.736185
MA0017.12.9605
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.11.10192
MA0029.10.995171
MA0030.11.00195
MA0031.10.965177
MA0038.10.757669
MA0040.11.07552
MA0041.10.522007
MA0042.10.507715
MA0043.11.1618
MA0046.11.09955
MA0048.10.205696
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.602741
MA0056.10
MA0057.10.192781
MA0058.10.50032
MA0059.10.513699
MA0060.11.58413
MA0061.10.955135
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.10.197245
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.10.0176764
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.148348
MA0089.10
MA0090.10.566938
MA0091.10.617887
MA0092.10.567278
MA0093.10.440484
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.10.460936
MA0105.11.28296
MA0106.10.809991
MA0107.10.454197
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.10.780358
MA0114.11.69206
MA0115.11.16466
MA0116.10.419688
MA0117.11.13165
MA0119.10.524046
MA0122.11.15196
MA0124.11.35963
MA0125.11.28445
MA0130.10
MA0131.10.869325
MA0132.10
MA0133.10
MA0135.11.19898
MA0136.10.729175
MA0139.10.295945
MA0140.10.695713
MA0141.11.21195
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.10.476962
MA0146.11.74263
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.20.254018
MA0035.20.700704
MA0039.21.42062
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.20.315156
MA0047.20.75686
MA0112.22.12679
MA0065.20.929207
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.587595
MA0155.10.99229
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.11.01146
MA0160.10.624415
MA0161.10
MA0162.10.0699535
MA0163.10.0644585
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.20.130118
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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