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MCL coexpression mm9:1677: Difference between revisions

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{{MCL_coexpression_mm9
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9254686258,0,0.0476191773904887,0.0766073954291401,0.14986111676545,0.112067779638927,0,0.155803124474447,0,0.110822898586572,0.0615880961136666,0.0678996586311492,0,0,0.104353329269123,0.116274076590891,0.0486884105045233,0.0408018333703219,0,0.0625582350728301,0,0.0196757891998992,0,0.0845301845292944,0.33197968197362,0.0865703124974023,0.01339570897577|gostat_on_MCL_coexpression=GO:0008253;5'-nucleotidase activity;0.0242162498772717;230718!GO:0005452;inorganic anion exchanger activity;0.0242162498772717;20536!GO:0008252;nucleotidase activity;0.0242162498772717;230718!GO:0015380;anion exchanger activity;0.0242162498772717;20536!GO:0015106;bicarbonate transmembrane transporter activity;0.0242162498772717;20536!GO:0015301;anion:anion antiporter activity;0.0242162498772717;20536!GO:0015108;chloride transmembrane transporter activity;0.0242162498772717;20536!GO:0017137;Rab GTPase binding;0.0313776749010759;116838!GO:0017156;calcium ion-dependent exocytosis;0.0313776749010759;116838!GO:0030073;insulin secretion;0.0314828234138316;116838!GO:0030072;peptide hormone secretion;0.0314828234138316;116838!GO:0015103;inorganic anion transmembrane transporter activity;0.0314828234138316;20536!GO:0002790;peptide secretion;0.0314828234138316;116838!GO:0015297;antiporter activity;0.035735271435484;20536!GO:0015833;peptide transport;0.035735271435484;116838!GO:0046879;hormone secretion;0.0361407521892148;116838!GO:0006836;neurotransmitter transport;0.0378365687345399;116838!GO:0017016;Ras GTPase binding;0.0378365687345399;116838!GO:0031267;small GTPase binding;0.0378365687345399;116838!GO:0051020;GTPase binding;0.038755433051013;116838!GO:0019933;cAMP-mediated signaling;0.0402543445152911;116838!GO:0019935;cyclic-nucleotide-mediated 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|gostat_on_MCL_coexpression=GO:0008253;5'-nucleotidase activity;0.0242162498772717;230718!GO:0005452;inorganic anion exchanger activity;0.0242162498772717;20536!GO:0008252;nucleotidase activity;0.0242162498772717;230718!GO:0015380;anion exchanger activity;0.0242162498772717;20536!GO:0015106;bicarbonate transmembrane transporter activity;0.0242162498772717;20536!GO:0015301;anion:anion antiporter activity;0.0242162498772717;20536!GO:0015108;chloride transmembrane transporter activity;0.0242162498772717;20536!GO:0017137;Rab GTPase binding;0.0313776749010759;116838!GO:0017156;calcium ion-dependent exocytosis;0.0313776749010759;116838!GO:0030073;insulin secretion;0.0314828234138316;116838!GO:0030072;peptide hormone secretion;0.0314828234138316;116838!GO:0015103;inorganic anion transmembrane transporter activity;0.0314828234138316;20536!GO:0002790;peptide secretion;0.0314828234138316;116838!GO:0015297;antiporter activity;0.035735271435484;20536!GO:0015833;peptide transport;0.035735271435484;116838!GO:0046879;hormone secretion;0.0361407521892148;116838!GO:0006836;neurotransmitter transport;0.0378365687345399;116838!GO:0017016;Ras GTPase binding;0.0378365687345399;116838!GO:0031267;small GTPase binding;0.0378365687345399;116838!GO:0051020;GTPase binding;0.038755433051013;116838!GO:0019933;cAMP-mediated signaling;0.0402543445152911;116838!GO:0019935;cyclic-nucleotide-mediated signaling;0.040339193295129;116838!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0010314!3.71e-23!92;UBERON:0001017!6.97e-19!73;UBERON:0001016!1.48e-18!75;UBERON:0000073!3.51e-18!54;UBERON:0002346!1.35e-16!64;UBERON:0003075!1.35e-16!64;UBERON:0007284!1.35e-16!64;UBERON:0001049!1.83e-16!52;UBERON:0005068!1.83e-16!52;UBERON:0006241!1.83e-16!52;UBERON:0007135!1.83e-16!52;UBERON:0004121!5.68e-15!95;UBERON:0000924!5.68e-15!95;UBERON:0006601!5.68e-15!95;UBERON:0000955!6.05e-15!47;UBERON:0006238!6.05e-15!47;UBERON:0002616!4.13e-14!46;UBERON:0010371!1.60e-12!73;UBERON:0003080!3.19e-12!40;UBERON:0003056!5.25e-12!49;UBERON:0002780!1.60e-11!39;UBERON:0001890!1.60e-11!39;UBERON:0006240!1.60e-11!39;UBERON:0002020!7.75e-10!34;UBERON:0002021!8.24e-10!10;UBERON:0000411!8.24e-10!10;UBERON:0001950!8.24e-10!10;UBERON:0003528!2.19e-08!29;UBERON:0002791!2.19e-08!29;UBERON:0001893!2.19e-08!29;UBERON:0002619!1.97e-07!17
|tfbs_overrepresentation_for_novel_motifs=0.557864,1.52338,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.310789,0.370407,0.668936,0.702872,1.47559,0.728641,0.424775,0,0.930881,0.397593,0.283802,1.0421,0.489529,0.44579,0.727684,0.404661,0.537749,1.78963,0.754069,0.641282,0.456327,0.645258,0.626183,1.03545,0.395107,0.704734,0.425309,0.20704,0.384813,0.699032,0.360612,0.328675,0.401916,0.631725,0.134724,0.426986,1.78875,0.591277,1.97509,0.658142,0.115788,0.459555,0.912738,0.786094,0.627649,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,0.46305,1.23259,1.31774,0.245132,0.70455,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.293164,1.1148,0.574099,0.297068,1.20595,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.3366,0.806207,1.05152,0.848095,1.11561,0.384901,1.03517,1.16282,0.913356,0.91226,1.52669,0.97421,0.653843,0.499439,0.491483,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,0.328405,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.44142,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.230371,0.826123,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,2.71086
}}

Latest revision as of 17:19, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr15:39491058..39491131,+p1@Rims2
Mm9::chr15:72378118..72378137,-p@chr15:72378118..72378137
-
Mm9::chr1:75543215..75543229,+p6@Slc4a3
Mm9::chr4:122878468..122878513,+p4@Nt5c1a
Mm9::chr4:122878746..122878772,+p2@Nt5c1a


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:00082535'-nucleotidase activity0.0242162498772717
GO:0005452inorganic anion exchanger activity0.0242162498772717
GO:0008252nucleotidase activity0.0242162498772717
GO:0015380anion exchanger activity0.0242162498772717
GO:0015106bicarbonate transmembrane transporter activity0.0242162498772717
GO:0015301anion:anion antiporter activity0.0242162498772717
GO:0015108chloride transmembrane transporter activity0.0242162498772717
GO:0017137Rab GTPase binding0.0313776749010759
GO:0017156calcium ion-dependent exocytosis0.0313776749010759
GO:0030073insulin secretion0.0314828234138316
GO:0030072peptide hormone secretion0.0314828234138316
GO:0015103inorganic anion transmembrane transporter activity0.0314828234138316
GO:0002790peptide secretion0.0314828234138316
GO:0015297antiporter activity0.035735271435484
GO:0015833peptide transport0.035735271435484
GO:0046879hormone secretion0.0361407521892148
GO:0006836neurotransmitter transport0.0378365687345399
GO:0017016Ras GTPase binding0.0378365687345399
GO:0031267small GTPase binding0.0378365687345399
GO:0051020GTPase binding0.038755433051013
GO:0019933cAMP-mediated signaling0.0402543445152911
GO:0019935cyclic-nucleotide-mediated signaling0.040339193295129



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
structure with developmental contribution from neural crest3.71e-2392
central nervous system6.97e-1973
nervous system1.48e-1875
regional part of nervous system3.51e-1854
neurectoderm1.35e-1664
neural plate1.35e-1664
presumptive neural plate1.35e-1664
neural tube1.83e-1652
neural rod1.83e-1652
future spinal cord1.83e-1652
neural keel1.83e-1652
ectoderm-derived structure5.68e-1595
ectoderm5.68e-1595
presumptive ectoderm5.68e-1595
brain6.05e-1547
future brain6.05e-1547
regional part of brain4.13e-1446
ecto-epithelium1.60e-1273
anterior neural tube3.19e-1240
pre-chordal neural plate5.25e-1249
regional part of forebrain1.60e-1139
forebrain1.60e-1139
future forebrain1.60e-1139
gray matter7.75e-1034
occipital lobe8.24e-1010
visual cortex8.24e-1010
neocortex8.24e-1010
brain grey matter2.19e-0829
regional part of telencephalon2.19e-0829
telencephalon2.19e-0829
regional part of cerebral cortex1.97e-0717


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)
MA0003.10.989123
MA0004.10.603793
MA0006.11.07705
MA0007.10.587678
MA0009.11.06266
MA0014.12.11217
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
MA0055.12.6907
MA0056.10
MA0057.11.68574
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
MA0073.10.310158
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.888325
MA0089.10
MA0090.12.38058
MA0091.11.4987
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
MA0116.10.419688
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
MA0139.10.8026
MA0140.10.695713
MA0141.11.21195
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.10.157686
MA0146.10.822925
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.20.254018
MA0035.20.700704
MA0039.20.489701
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.20.315156
MA0047.20.75686
MA0112.20.927461
MA0065.20.158101
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.203217
MA0155.10.515751
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.10.526186
MA0163.10.855539
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.22.6586
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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