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MCL coexpression mm9:845: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0003682;chromatin binding;0.0100113843144172;13390,13392!GO:0048306;calcium-dependent protein binding;0.0377534594233227;54524!GO:0005667;transcription factor complex;0.0377534594233227;13390,13392!GO:0043565;sequence-specific DNA binding;0.0377534594233227;13390,13392!GO:0007340;acrosome reaction;0.0377534594233227;54524!GO:0003727;single-stranded RNA binding;0.0377534594233227;13392!GO:0044451;nucleoplasm part;0.0377534594233227;13390,13392!GO:0005654;nucleoplasm;0.0377534594233227;13390,13392!GO:0017156;calcium ion-dependent exocytosis;0.039472660718551;54524!GO:0031981;nuclear lumen;0.039472660718551;13390,13392!GO:0043524;negative regulation of neuron apoptosis;0.039472660718551;13390!GO:0031974;membrane-enclosed lumen;0.041487927027033;13390,13392!GO:0043233;organelle lumen;0.041487927027033;13390,13392!GO:0043523;regulation of neuron apoptosis;0.0432655166342465;13390!GO:0003700;transcription factor activity;0.0432655166342465;13390,13392!GO:0051402;neuron apoptosis;0.0447989412981176;13390!GO:0007338;single fertilization;0.0454849411957286;54524!GO:0009566;fertilization;0.0497183098655478;54524!GO:0044428;nuclear part;0.0497183098655478;13390,13392!GO:0008021;synaptic vesicle;0.0499450898651755;54524!}}
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binding;0.0100113843144172;13390,13392!GO:0048306;calcium-dependent protein binding;0.0377534594233227;54524!GO:0005667;transcription factor complex;0.0377534594233227;13390,13392!GO:0043565;sequence-specific DNA binding;0.0377534594233227;13390,13392!GO:0007340;acrosome reaction;0.0377534594233227;54524!GO:0003727;single-stranded RNA binding;0.0377534594233227;13392!GO:0044451;nucleoplasm part;0.0377534594233227;13390,13392!GO:0005654;nucleoplasm;0.0377534594233227;13390,13392!GO:0017156;calcium ion-dependent exocytosis;0.039472660718551;54524!GO:0031981;nuclear lumen;0.039472660718551;13390,13392!GO:0043524;negative regulation of neuron apoptosis;0.039472660718551;13390!GO:0031974;membrane-enclosed lumen;0.041487927027033;13390,13392!GO:0043233;organelle lumen;0.041487927027033;13390,13392!GO:0043523;regulation of neuron apoptosis;0.0432655166342465;13390!GO:0003700;transcription factor activity;0.0432655166342465;13390,13392!GO:0051402;neuron apoptosis;0.0447989412981176;13390!GO:0007338;single fertilization;0.0454849411957286;54524!GO:0009566;fertilization;0.0497183098655478;54524!GO:0044428;nuclear part;0.0497183098655478;13390,13392!GO:0008021;synaptic vesicle;0.0499450898651755;54524!|ontology_enrichment_celltype=CL:0000221!6.32e-12!44;CL:0000133!6.32e-12!44;CL:0002319!2.99e-11!43;CL:0000055!3.53e-11!49;CL:0000540!3.96e-11!33;CL:0000047!3.96e-11!33;CL:0000031!3.96e-11!33;CL:0000404!3.96e-11!33;CL:0000393!7.66e-11!39;CL:0000211!7.66e-11!39;CL:0000107!3.24e-10!9;CL:0002609!2.99e-07!6|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0004121!6.70e-16!95;UBERON:0000924!6.70e-16!95;UBERON:0006601!6.70e-16!95;UBERON:0001016!7.94e-14!75;UBERON:0001017!6.47e-13!73;UBERON:0003056!1.00e-12!49;UBERON:0010371!5.07e-12!73;UBERON:0003528!2.13e-11!29;UBERON:0002791!2.13e-11!29;UBERON:0001893!2.13e-11!29;UBERON:0000010!5.44e-11!11;UBERON:0002346!6.93e-11!64;UBERON:0003075!6.93e-11!64;UBERON:0007284!6.93e-11!64;UBERON:0003080!1.38e-10!40;UBERON:0002780!2.58e-10!39;UBERON:0001890!2.58e-10!39;UBERON:0006240!2.58e-10!39;UBERON:0002410!3.24e-10!9;UBERON:0000955!8.22e-10!47;UBERON:0006238!8.22e-10!47;UBERON:0002616!4.23e-09!46;UBERON:0002020!1.25e-08!34;UBERON:0001049!4.61e-07!52;UBERON:0005068!4.61e-07!52;UBERON:0006241!4.61e-07!52;UBERON:0007135!4.61e-07!52;UBERON:0000073!5.07e-07!54;UBERON:0000956!7.49e-07!21;UBERON:0001869!7.49e-07!21;UBERON:0000203!7.49e-07!21|tfbs_overrepresentation_for_novel_motifs=0.354643,2.88442,0.330161,1.02163,0.227651,0.40827,1.24018,0.146465,0.154135,1.29998,0.453212,0.484001,4.30989,0.507558,0.24249,0,0.696644,0.22065,1.94334,0.247067,0.296085,0.403891,0.50668,0.226287,0.337218,0.534339,0.402559,0.428336,3.80935,0.656973,0.414842,0.796599,0.624261,0.113369,1.95748,0.482999,0.210533,0.480503,0.191662,0.967553,0.224094,0.419787,0.371854,0.244285,0.536558,0.383899,0.618203,0.443479,0.904531,1.36808,0.679429,0.560572,0.30602,0.937018,0.954342,0.514504,0.279148,0.471658,0.770972,0.512521,0.776777,0.569793,0.492158,0.668331,0.525334,1.68713,1.08987,1.43807,0.772155,1.29123,0.840217,0.460931,1.14319,0.987652,3.87232,1.71614,0.113315,0.607043,0.759798,0.299972,0.152219,0.713779,0.568383,1.38499,0.873141,0.967095,0.439624,0.0965007,0.623015,1.60001,1.15927,0.878077,0.809272,0.232894,0.551605,0.17334,0.14449,0.812053,0.618454,4.02533,1.13987,0.796322,0.919715,0.680015,0.678976,0.419366,0.737915,0.439611,0.30446,0.297733,0.348012,0.921485,0.301014,0.458194,1.16629,0.222515,0.265919,0.398075,0.697928,0.207304,0.993019,1.56109,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.663857,0.90286,0.387557,1.05894,0.527782,1.18781,0.0467191,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,1.89109,0.672593,0.420221,0.621266,1.92834,0.364791,0.229209,2.22198,0.041769,0.938577,0.527659,0.526881,1.01974,1.38016,0.253271,0.928824,0.950885,1.1483,0.872292,0.763895,1.63697,0.669337,0.519673,0.209556,0.482466,5.37833|tfbs_overrepresentation_jaspar=MA0003.1;0.0854318,MA0004.1;0.394951,MA0006.1;0.238555,MA0007.1;0.38073,MA0009.1;0.82278,MA0014.1;0.67203,MA0017.1;0.26239,MA0019.1;0.642876,MA0024.1;0.779446,MA0025.1;1.05446,MA0027.1;2.46647,MA0028.1;0.24786,MA0029.1;0.757957,MA0030.1;0.764448,MA0031.1;0.729293,MA0038.1;1.32237,MA0040.1;0.835181,MA0041.1;0.323687,MA0042.1;0.311486,MA0043.1;0.918718,MA0046.1;0.858391,MA0048.1;0.993388,MA0050.1;1.93344,MA0051.1;1.34084,MA0052.1;0.84317,MA0055.1;6.70696,MA0056.1;0,MA0057.1;1.39929,MA0058.1;0.305206,MA0059.1;0.316585,MA0060.1;2.95149,MA0061.1;0.194456,MA0063.1;0,MA0066.1;0.523573,MA0067.1;1.16502,MA0068.1;0.266547,MA0069.1;0.843506,MA0070.1;0.833895,MA0071.1;0.431174,MA0072.1;0.825495,MA0073.1;0.126434,MA0074.1;0.488775,MA0076.1;0.279739,MA0077.1;1.88507,MA0078.1;2.40745,MA0081.1;0.897217,MA0083.1;0.917931,MA0084.1;1.49188,MA0087.1;0.87515,MA0088.1;0.728131,MA0089.1;0,MA0090.1;0.362551,MA0091.1;0.407455,MA0092.1;0.362847,MA0093.1;0.709711,MA0095.1;0,MA0098.1;0,MA0100.1;0.477594,MA0101.1;0.324888,MA0103.1;0.272167,MA0105.1;0.109964,MA0106.1;0.582805,MA0107.1;0.266586,MA0108.2;0.665343,MA0109.1;0,MA0111.1;0.375908,MA0113.1;0.555251,MA0114.1;0.19245,MA0115.1;0.921497,MA0116.1;0.670446,MA0117.1;0.88947,MA0119.1;0.325434,MA0122.1;0.909168,MA0124.1;1.11203,MA0125.1;1.03833,MA0130.1;0,MA0131.1;0.638414,MA0132.1;0,MA0133.1;0,MA0135.1;0.954884,MA0136.1;0.508047,MA0139.1;0.143341,MA0140.1;0.477483,MA0141.1;2.20026,MA0142.1;0.714976,MA0143.1;0.571221,MA0144.1;0.195095,MA0145.1;0.77191,MA0146.1;2.33537,MA0147.1;0.205697,MA0148.1;0.410398,MA0149.1;0.330018,MA0062.2;0.113962,MA0035.2;0.482026,MA0039.2;0.288731,MA0138.2;0.630612,MA0002.2;0.145685,MA0137.2;0.287486,MA0104.2;0.157347,MA0047.2;0.533516,MA0112.2;2.77674,MA0065.2;0.44341,MA0150.1;0.380623,MA0151.1;0,MA0152.1;0.53362,MA0153.1;0.971406,MA0154.1;1.46345,MA0155.1;0.490492,MA0156.1;0.278949,MA0157.1;0.683365,MA0158.1;0,MA0159.1;0.614411,MA0160.1;0.413266,MA0161.1;0,MA0162.1;0.0672805,MA0163.1;1.53225,MA0164.1;0.508398,MA0080.2;0.267388,MA0018.2;0.51781,MA0099.2;1.51239,MA0079.2;2.46822,MA0102.2;1.5442,MA0258.1;0.180934,MA0259.1;1.08444,MA0442.1;0}}

Latest revision as of 15:59, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr2:71367605..71367621,+p9@Dlx1
Mm9::chr2:71367646..71367658,+p11@Dlx1
Mm9::chr2:71367712..71367725,-p@chr2:71367712..71367725
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Mm9::chr2:71367855..71367864,+p6@Dlx1
Mm9::chr2:71367871..71367898,+p1@Dlx1
Mm9::chr2:71384401..71384424,-p3@Dlx2
Mm9::chr2:71384425..71384456,-p4@Dlx2
Mm9::chr2:71384458..71384526,-p2@Dlx2
Mm9::chr3:103379198..103379209,+p2@Syt6


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:0003682chromatin binding0.0100113843144172
GO:0048306calcium-dependent protein binding0.0377534594233227
GO:0005667transcription factor complex0.0377534594233227
GO:0043565sequence-specific DNA binding0.0377534594233227
GO:0007340acrosome reaction0.0377534594233227
GO:0003727single-stranded RNA binding0.0377534594233227
GO:0044451nucleoplasm part0.0377534594233227
GO:0005654nucleoplasm0.0377534594233227
GO:0017156calcium ion-dependent exocytosis0.039472660718551
GO:0031981nuclear lumen0.039472660718551
GO:0043524negative regulation of neuron apoptosis0.039472660718551
GO:0031974membrane-enclosed lumen0.041487927027033
GO:0043233organelle lumen0.041487927027033
GO:0043523regulation of neuron apoptosis0.0432655166342465
GO:0003700transcription factor activity0.0432655166342465
GO:0051402neuron apoptosis0.0447989412981176
GO:0007338single fertilization0.0454849411957286
GO:0009566fertilization0.0497183098655478
GO:0044428nuclear part0.0497183098655478
GO:0008021synaptic vesicle0.0499450898651755



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 structure6.70e-1695
ectoderm6.70e-1695
presumptive ectoderm6.70e-1695
nervous system7.94e-1475
central nervous system6.47e-1373
pre-chordal neural plate1.00e-1249
ecto-epithelium5.07e-1273
brain grey matter2.13e-1129
regional part of telencephalon2.13e-1129
telencephalon2.13e-1129
peripheral nervous system5.44e-1111
neurectoderm6.93e-1164
neural plate6.93e-1164
presumptive neural plate6.93e-1164
anterior neural tube1.38e-1040
regional part of forebrain2.58e-1039
forebrain2.58e-1039
future forebrain2.58e-1039
autonomic nervous system3.24e-109
brain8.22e-1047
future brain8.22e-1047
regional part of brain4.23e-0946
gray matter1.25e-0834
neural tube4.61e-0752
neural rod4.61e-0752
future spinal cord4.61e-0752
neural keel4.61e-0752
regional part of nervous system5.07e-0754
cerebral cortex7.49e-0721
cerebral hemisphere7.49e-0721
pallium7.49e-0721


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)
MA0003.10.0854318
MA0004.10.394951
MA0006.10.238555
MA0007.10.38073
MA0009.10.82278
MA0014.10.67203
MA0017.10.26239
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.10.24786
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.11.32237
MA0040.10.835181
MA0041.10.323687
MA0042.10.311486
MA0043.10.918718
MA0046.10.858391
MA0048.10.993388
MA0050.11.93344
MA0051.11.34084
MA0052.10.84317
MA0055.16.70696
MA0056.10
MA0057.11.39929
MA0058.10.305206
MA0059.10.316585
MA0060.12.95149
MA0061.10.194456
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.266547
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.10.126434
MA0074.10.488775
MA0076.10.279739
MA0077.11.88507
MA0078.12.40745
MA0081.10.897217
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.728131
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.362847
MA0093.10.709711
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.324888
MA0103.10.272167
MA0105.10.109964
MA0106.10.582805
MA0107.10.266586
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.10.19245
MA0115.10.921497
MA0116.10.670446
MA0117.10.88947
MA0119.10.325434
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.10.638414
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.143341
MA0140.10.477483
MA0141.12.20026
MA0142.10.714976
MA0143.10.571221
MA0144.10.195095
MA0145.10.77191
MA0146.12.33537
MA0147.10.205697
MA0148.10.410398
MA0149.10.330018
MA0062.20.113962
MA0035.20.482026
MA0039.20.288731
MA0138.20.630612
MA0002.20.145685
MA0137.20.287486
MA0104.20.157347
MA0047.20.533516
MA0112.22.77674
MA0065.20.44341
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.11.46345
MA0155.10.490492
MA0156.10.278949
MA0157.10.683365
MA0158.10
MA0159.10.614411
MA0160.10.413266
MA0161.10
MA0162.10.0672805
MA0163.11.53225
MA0164.10.508398
MA0080.20.267388
MA0018.20.51781
MA0099.21.51239
MA0079.22.46822
MA0102.21.5442
MA0258.10.180934
MA0259.11.08444
MA0442.10
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