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MCL coexpression mm9:1747: Difference between revisions

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{{MCL_coexpression_mm9
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GTPase regulator activity;0.00509899699284794;226751,69632!GO:0030695;GTPase regulator activity;0.00821737696392652;226751,69632!GO:0007097;nuclear migration;0.00821737696392652;226751!GO:0040023;establishment of nucleus localization;0.00986004192010371;226751!GO:0051647;nucleus localization;0.00986004192010371;226751!GO:0051656;establishment of organelle localization;0.027715412429569;226751!GO:0007242;intracellular signaling cascade;0.027715412429569;226751,69632!GO:0051640;organelle localization;0.027715412429569;226751!GO:0019992;diacylglycerol binding;0.0403401200135352;226751!GO:0005089;Rho guanyl-nucleotide exchange factor activity;0.0403401200135352;69632!GO:0035023;regulation of Rho protein signal transduction;0.0403401200135352;69632!GO:0005088;Ras guanyl-nucleotide exchange factor activity;0.0403401200135352;69632!GO:0000226;microtubule cytoskeleton organization and biogenesis;0.0403871732472332;226751!GO:0007266;Rho protein signal 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|gostat_on_MCL_coexpression=GO:0005083;small GTPase regulator activity;0.00509899699284794;226751,69632!GO:0030695;GTPase regulator activity;0.00821737696392652;226751,69632!GO:0007097;nuclear migration;0.00821737696392652;226751!GO:0040023;establishment of nucleus localization;0.00986004192010371;226751!GO:0051647;nucleus localization;0.00986004192010371;226751!GO:0051656;establishment of organelle localization;0.027715412429569;226751!GO:0007242;intracellular signaling cascade;0.027715412429569;226751,69632!GO:0051640;organelle localization;0.027715412429569;226751!GO:0019992;diacylglycerol binding;0.0403401200135352;226751!GO:0005089;Rho guanyl-nucleotide exchange factor activity;0.0403401200135352;69632!GO:0035023;regulation of Rho protein signal transduction;0.0403401200135352;69632!GO:0005088;Ras guanyl-nucleotide exchange factor activity;0.0403401200135352;69632!GO:0000226;microtubule cytoskeleton organization and biogenesis;0.0403871732472332;226751!GO:0007266;Rho protein signal transduction;0.0468573864306494;69632!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004111!1.60e-16!122;UBERON:0000025!1.73e-15!114;UBERON:0010314!1.86e-11!92;UBERON:0000468!2.27e-10!333;UBERON:0000073!5.30e-10!54;UBERON:0002346!4.27e-09!64;UBERON:0003075!4.27e-09!64;UBERON:0007284!4.27e-09!64;UBERON:0001049!5.03e-09!52;UBERON:0005068!5.03e-09!52;UBERON:0006241!5.03e-09!52;UBERON:0007135!5.03e-09!52;UBERON:0010371!5.37e-09!73;UBERON:0004121!1.21e-08!95;UBERON:0000924!1.21e-08!95;UBERON:0006601!1.21e-08!95;UBERON:0000955!2.69e-08!47;UBERON:0006238!2.69e-08!47;UBERON:0001017!6.90e-08!73;UBERON:0002616!8.23e-08!46;UBERON:0001016!8.56e-08!75;UBERON:0000479!2.31e-07!349;UBERON:0003056!4.17e-07!49;UBERON:0002048!6.52e-07!14;UBERON:0000117!6.52e-07!14;UBERON:0000171!6.52e-07!14;UBERON:0000170!6.52e-07!14;UBERON:0005597!6.52e-07!14;UBERON:0000118!6.52e-07!14
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.612204,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.310789,0.370407,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.283802,0.185796,1.22707,0.145201,0.727684,0.404661,1.32977,0.757752,0.274609,0.641282,1.15581,0.227599,0.626183,1.03545,0.395107,0.704734,0.425309,0.454919,1.00043,0.699032,0.360612,0.876199,0.401916,0.631725,0.134724,0.426986,0.227872,0.591277,0.847828,0.658142,0.115788,0.459555,0.912738,0.786094,0.220111,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.827208,1.45025,1.23259,0.714607,0.245132,0.70455,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.293164,1.1148,1.44773,0.0882907,0.227755,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,2.43005,0.297538,1.05152,0.848095,0.20438,0.384901,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,1.23125,0.550229,1.16464,0.495367,0.674448,1.41481,1.03353,1.11665,0.607321,0.932233,0.380707,1.23809,0.879184,1.7936,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,1.21592,3.34092,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.745913
}}

Latest revision as of 17:26, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr1:181890115..181890211,+p1@Cdc42bpa
Mm9::chr5:8567093..8567110,+p@chr5:8567093..8567110
+
Mm9::chr5:8567113..8567123,+p@chr5:8567113..8567123
+
Mm9::chr5:8606564..8606568,+p@chr5:8606564..8606568
+
Mm9::chr9:42914037..42914109,-p1@Arhgef12


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:0005083small GTPase regulator activity0.00509899699284794
GO:0030695GTPase regulator activity0.00821737696392652
GO:0007097nuclear migration0.00821737696392652
GO:0040023establishment of nucleus localization0.00986004192010371
GO:0051647nucleus localization0.00986004192010371
GO:0051656establishment of organelle localization0.027715412429569
GO:0007242intracellular signaling cascade0.027715412429569
GO:0051640organelle localization0.027715412429569
GO:0019992diacylglycerol binding0.0403401200135352
GO:0005089Rho guanyl-nucleotide exchange factor activity0.0403401200135352
GO:0035023regulation of Rho protein signal transduction0.0403401200135352
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0403401200135352
GO:0000226microtubule cytoskeleton organization and biogenesis0.0403871732472332
GO:0007266Rho protein signal transduction0.0468573864306494



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>

Uber Anatomy
Ontology termp-valuen
anatomical conduit1.60e-16122
tube1.73e-15114
structure with developmental contribution from neural crest1.86e-1192
multi-cellular organism2.27e-10333
regional part of nervous system5.30e-1054
neurectoderm4.27e-0964
neural plate4.27e-0964
presumptive neural plate4.27e-0964
neural tube5.03e-0952
neural rod5.03e-0952
future spinal cord5.03e-0952
neural keel5.03e-0952
ecto-epithelium5.37e-0973
ectoderm-derived structure1.21e-0895
ectoderm1.21e-0895
presumptive ectoderm1.21e-0895
brain2.69e-0847
future brain2.69e-0847
central nervous system6.90e-0873
regional part of brain8.23e-0846
nervous system8.56e-0875
tissue2.31e-07349
pre-chordal neural plate4.17e-0749
lung6.52e-0714
respiratory tube6.52e-0714
respiration organ6.52e-0714
pair of lungs6.52e-0714
lung primordium6.52e-0714
lung bud6.52e-0714


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)
MA0003.11.36559
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
MA0031.12.2151
MA0038.10.757669
MA0040.11.07552
MA0041.10.522007
MA0042.10.507715
MA0043.11.1618
MA0046.11.09955
MA0048.10.593503
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.0851423
MA0056.10
MA0057.10.562607
MA0058.10.50032
MA0059.10.513699
MA0060.10.330907
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
MA0073.10.0481612
MA0074.10.708108
MA0076.11.1853
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
MA0105.11.28296
MA0106.10.809991
MA0107.10.454197
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.10.780358
MA0114.10.361633
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
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.956957
MA0145.10.157686
MA0146.10.21827
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.20.706751
MA0035.20.700704
MA0039.20.489701
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.20.315156
MA0047.20.75686
MA0112.20.157681
MA0065.20.158101
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.11.11105
MA0155.10.173445
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.11.87338
MA0163.10.497328
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.22.32359
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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