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MCL coexpression mm9:1750: Difference between revisions

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{{MCL_coexpression_mm9
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4-beta-glucuronosyltransferase activity;0.0161051764061131;14043!GO:0050508;glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity;0.0161051764061131;14043!GO:0008475;procollagen-lysine 5-dioxygenase activity;0.0161051764061131;26433!GO:0015012;heparan sulfate proteoglycan biosynthetic process;0.0225423057380206;14043!GO:0030201;heparan sulfate proteoglycan metabolic process;0.0225423057380206;14043!GO:0043410;positive regulation of MAPKKK cascade;0.0241498236359184;66208!GO:0030166;proteoglycan biosynthetic process;0.0268022710415322;14043!GO:0043408;regulation of MAPKKK cascade;0.0268022710415322;66208!GO:0031418;L-ascorbic acid binding;0.0268022710415322;26433!GO:0006029;proteoglycan metabolic process;0.0268022710415322;14043!GO:0015020;glucuronosyltransferase activity;0.0268022710415322;14043!GO:0005783;endoplasmic reticulum;0.0268022710415322;26433,14043!GO:0016706;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors;0.0268022710415322;26433!GO:0001707;mesoderm formation;0.0268022710415322;14043!GO:0048332;mesoderm morphogenesis;0.0268022710415322;14043!GO:0001704;formation of primary germ layer;0.0268022710415322;14043!GO:0044272;sulfur compound biosynthetic process;0.0268022710415322;14043!GO:0008375;acetylglucosaminyltransferase activity;0.0268022710415322;14043!GO:0007498;mesoderm development;0.0414298065478486;14043!GO:0051213;dioxygenase activity;0.0414706873941803;26433!GO:0016702;oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen;0.0414706873941803;26433!GO:0006790;sulfur metabolic process;0.0414706873941803;14043!GO:0016701;oxidoreductase activity, acting on single donors with incorporation of molecular oxygen;0.0414706873941803;26433!GO:0007369;gastrulation;0.0414706873941803;14043!GO:0009967;positive regulation of signal transduction;0.0417313724965586;66208!GO:0048729;tissue morphogenesis;0.0462742073363588;14043!GO:0016051;carbohydrate biosynthetic process;0.0469265999411267;14043!GO:0008194;UDP-glycosyltransferase 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|gostat_on_MCL_coexpression=GO:0050509;N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity;0.0161051764061131;14043!GO:0050508;glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity;0.0161051764061131;14043!GO:0008475;procollagen-lysine 5-dioxygenase activity;0.0161051764061131;26433!GO:0015012;heparan sulfate proteoglycan biosynthetic process;0.0225423057380206;14043!GO:0030201;heparan sulfate proteoglycan metabolic process;0.0225423057380206;14043!GO:0043410;positive regulation of MAPKKK cascade;0.0241498236359184;66208!GO:0030166;proteoglycan biosynthetic process;0.0268022710415322;14043!GO:0043408;regulation of MAPKKK cascade;0.0268022710415322;66208!GO:0031418;L-ascorbic acid binding;0.0268022710415322;26433!GO:0006029;proteoglycan metabolic process;0.0268022710415322;14043!GO:0015020;glucuronosyltransferase activity;0.0268022710415322;14043!GO:0005783;endoplasmic reticulum;0.0268022710415322;26433,14043!GO:0016706;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors;0.0268022710415322;26433!GO:0001707;mesoderm formation;0.0268022710415322;14043!GO:0048332;mesoderm morphogenesis;0.0268022710415322;14043!GO:0001704;formation of primary germ layer;0.0268022710415322;14043!GO:0044272;sulfur compound biosynthetic process;0.0268022710415322;14043!GO:0008375;acetylglucosaminyltransferase activity;0.0268022710415322;14043!GO:0007498;mesoderm development;0.0414298065478486;14043!GO:0051213;dioxygenase activity;0.0414706873941803;26433!GO:0016702;oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen;0.0414706873941803;26433!GO:0006790;sulfur metabolic process;0.0414706873941803;14043!GO:0016701;oxidoreductase activity, acting on single donors with incorporation of molecular oxygen;0.0414706873941803;26433!GO:0007369;gastrulation;0.0414706873941803;14043!GO:0009967;positive regulation of signal transduction;0.0417313724965586;66208!GO:0048729;tissue morphogenesis;0.0462742073363588;14043!GO:0016051;carbohydrate biosynthetic process;0.0469265999411267;14043!GO:0008194;UDP-glycosyltransferase activity;0.0492412841194071;14043!
|ontology_enrichment_celltype=CL:0000055!1.15e-08!49;CL:0000333!1.93e-07!10;CL:0000095!1.93e-07!10;CL:0000243!1.93e-07!10;CL:0000123!1.93e-07!10;CL:0000125!1.93e-07!10;CL:0000030!1.93e-07!10;CL:0000339!1.93e-07!10;CL:0002453!9.18e-07!8
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004121!7.73e-07!95;UBERON:0000924!7.73e-07!95;UBERON:0006601!7.73e-07!95
|tfbs_overrepresentation_for_novel_motifs=0.557864,3.40233,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.310789,0.746305,0.668936,0.702872,0.812978,0.728641,0.424775,0,0.930881,0.397593,0.283802,0.185796,0.489529,0.44579,0.727684,0.404661,1.32977,0.757752,0.274609,0.641282,0.456327,0.227599,0.626183,1.03545,0.395107,0.253145,0.425309,0.454919,0.384813,0.699032,0.360612,0.328675,0.401916,0.631725,0.419293,0.426986,0.84962,0.591277,0.847828,0.658142,0.746467,0.459555,0.912738,0.786094,0.627649,1.18062,1.19842,0.73621,0.469329,0.689304,0.731291,0.734051,2.31619,0.796017,0.865544,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,0.46305,1.23259,1.31774,1.27178,0.253065,0.835925,0.997094,0.494135,0.830212,0.948899,0.794502,0.293164,1.1148,1.99513,0.0882907,0.645625,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.3366,0.297538,1.05152,0.848095,0.20438,0.384901,1.03517,1.16282,0.913356,0.91226,1.52669,0.97421,0.653843,0.499439,0.491483,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,2.24107,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,1.85301,0.230371,1.33841,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,1.75672,0.997706,0.701187,0.0513167
}}

Latest revision as of 17:26, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr1:193141969..193142005,-p1@Nenf
Mm9::chr2:93662694..93662738,-p1@Ext2
Mm9::chr5:137463258..137463284,+p2@Plod3
Mm9::chr6:128305815..128305842,-p2@Tulp3
Mm9::chr6:128305844..128305874,-p1@Tulp3


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:0050509N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity0.0161051764061131
GO:0050508glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity0.0161051764061131
GO:0008475procollagen-lysine 5-dioxygenase activity0.0161051764061131
GO:0015012heparan sulfate proteoglycan biosynthetic process0.0225423057380206
GO:0030201heparan sulfate proteoglycan metabolic process0.0225423057380206
GO:0043410positive regulation of MAPKKK cascade0.0241498236359184
GO:0030166proteoglycan biosynthetic process0.0268022710415322
GO:0043408regulation of MAPKKK cascade0.0268022710415322
GO:0031418L-ascorbic acid binding0.0268022710415322
GO:0006029proteoglycan metabolic process0.0268022710415322
GO:0015020glucuronosyltransferase activity0.0268022710415322
GO:0005783endoplasmic reticulum0.0268022710415322
GO:0016706oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors0.0268022710415322
GO:0001707mesoderm formation0.0268022710415322
GO:0048332mesoderm morphogenesis0.0268022710415322
GO:0001704formation of primary germ layer0.0268022710415322
GO:0044272sulfur compound biosynthetic process0.0268022710415322
GO:0008375acetylglucosaminyltransferase activity0.0268022710415322
GO:0007498mesoderm development0.0414298065478486
GO:0051213dioxygenase activity0.0414706873941803
GO:0016702oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen0.0414706873941803
GO:0006790sulfur metabolic process0.0414706873941803
GO:0016701oxidoreductase activity, acting on single donors with incorporation of molecular oxygen0.0414706873941803
GO:0007369gastrulation0.0414706873941803
GO:0009967positive regulation of signal transduction0.0417313724965586
GO:0048729tissue morphogenesis0.0462742073363588
GO:0016051carbohydrate biosynthetic process0.0469265999411267
GO:0008194UDP-glycosyltransferase activity0.0492412841194071



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>cell_data<br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure7.73e-0795
ectoderm7.73e-0795
presumptive ectoderm7.73e-0795


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)
MA0003.11.79223
MA0004.10.603793
MA0006.10.419915
MA0007.10.587678
MA0009.11.06266
MA0014.10.418772
MA0017.10.449113
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.10.43138
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
MA0057.10.562607
MA0058.10.50032
MA0059.10.513699
MA0060.10.881183
MA0061.10.364227
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.10.197245
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.10.310158
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.453686
MA0089.10
MA0090.11.39153
MA0091.10.617887
MA0092.10.567278
MA0093.10.440484
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.10.460936
MA0105.10.248108
MA0106.10.809991
MA0107.10.454197
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.10.780358
MA0114.10.361633
MA0115.11.16466
MA0116.11.89177
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
MA0139.11.45902
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.10.157686
MA0146.10.822925
MA0147.10.986917
MA0148.10.621195
MA0149.120.7523
MA0062.20.254018
MA0035.20.700704
MA0039.21.8247
MA0138.23.31401
MA0002.20.809945
MA0137.20.479301
MA0104.21.52809
MA0047.20.75686
MA0112.22.12679
MA0065.20.477991
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.11.74374
MA0155.12.24718
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.10.898893
MA0163.10.230013
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.21.19329
MA0102.21.79669
MA0258.10.346619
MA0259.10.960816
MA0442.10
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