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MCL coexpression mm9:2596: Difference between revisions

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{{MCL_coexpression_mm9
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vesicle membrane;0.0360765078419499;27204!GO:0051649;establishment of cellular localization;0.0360765078419499;27204,16564!GO:0051641;cellular localization;0.0360765078419499;27204,16564!GO:0005871;kinesin complex;0.0360765078419499;16564!GO:0005524;ATP binding;0.0360765078419499;27204,16564!GO:0032559;adenyl ribonucleotide binding;0.0360765078419499;27204,16564!GO:0030554;adenyl nucleotide binding;0.0360765078419499;27204,16564!GO:0044433;cytoplasmic vesicle part;0.0360765078419499;27204!GO:0007269;neurotransmitter secretion;0.0360765078419499;27204!GO:0008021;synaptic vesicle;0.0360765078419499;27204!GO:0012506;vesicle membrane;0.0360765078419499;27204!GO:0045055;regulated secretory pathway;0.0360765078419499;27204!GO:0003777;microtubule motor activity;0.0360765078419499;16564!GO:0032553;ribonucleotide binding;0.0360765078419499;27204,16564!GO:0032555;purine ribonucleotide binding;0.0360765078419499;27204,16564!GO:0017076;purine nucleotide binding;0.0360765078419499;27204,16564!GO:0030136;clathrin-coated vesicle;0.0360765078419499;27204!GO:0007018;microtubule-based movement;0.0360765078419499;16564!GO:0003001;generation of a signal involved in cell-cell signaling;0.0360765078419499;27204!GO:0030135;coated vesicle;0.0360765078419499;27204!GO:0001505;regulation of neurotransmitter levels;0.0360765078419499;27204!GO:0000166;nucleotide binding;0.0360765078419499;27204,16564!GO:0030705;cytoskeleton-dependent intracellular transport;0.0366866860417446;16564!GO:0005875;microtubule associated complex;0.0366866860417446;16564!GO:0006810;transport;0.0439919398657478;27204,16564!GO:0044446;intracellular organelle part;0.0439919398657478;27204,16564!GO:0044422;organelle part;0.0439919398657478;27204,16564!GO:0016043;cellular component organization and biogenesis;0.0439919398657478;27204,16564!GO:0051234;establishment of localization;0.0439919398657478;27204,16564!GO:0045045;secretory 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|gostat_on_MCL_coexpression=GO:0030672;synaptic vesicle membrane;0.0360765078419499;27204!GO:0051649;establishment of cellular localization;0.0360765078419499;27204,16564!GO:0051641;cellular localization;0.0360765078419499;27204,16564!GO:0005871;kinesin complex;0.0360765078419499;16564!GO:0005524;ATP binding;0.0360765078419499;27204,16564!GO:0032559;adenyl ribonucleotide binding;0.0360765078419499;27204,16564!GO:0030554;adenyl nucleotide binding;0.0360765078419499;27204,16564!GO:0044433;cytoplasmic vesicle part;0.0360765078419499;27204!GO:0007269;neurotransmitter secretion;0.0360765078419499;27204!GO:0008021;synaptic vesicle;0.0360765078419499;27204!GO:0012506;vesicle membrane;0.0360765078419499;27204!GO:0045055;regulated secretory pathway;0.0360765078419499;27204!GO:0003777;microtubule motor activity;0.0360765078419499;16564!GO:0032553;ribonucleotide binding;0.0360765078419499;27204,16564!GO:0032555;purine ribonucleotide binding;0.0360765078419499;27204,16564!GO:0017076;purine nucleotide binding;0.0360765078419499;27204,16564!GO:0030136;clathrin-coated vesicle;0.0360765078419499;27204!GO:0007018;microtubule-based movement;0.0360765078419499;16564!GO:0003001;generation of a signal involved in cell-cell signaling;0.0360765078419499;27204!GO:0030135;coated vesicle;0.0360765078419499;27204!GO:0001505;regulation of neurotransmitter levels;0.0360765078419499;27204!GO:0000166;nucleotide binding;0.0360765078419499;27204,16564!GO:0030705;cytoskeleton-dependent intracellular transport;0.0366866860417446;16564!GO:0005875;microtubule associated complex;0.0366866860417446;16564!GO:0006810;transport;0.0439919398657478;27204,16564!GO:0044446;intracellular organelle part;0.0439919398657478;27204,16564!GO:0044422;organelle part;0.0439919398657478;27204,16564!GO:0016043;cellular component organization and biogenesis;0.0439919398657478;27204,16564!GO:0051234;establishment of localization;0.0439919398657478;27204,16564!GO:0045045;secretory pathway;0.0464001961037806;27204!GO:0007017;microtubule-based process;0.0464001961037806;16564!GO:0016023;cytoplasmic membrane-bound vesicle;0.0464001961037806;27204!GO:0051179;localization;0.0464001961037806;27204,16564!GO:0007268;synaptic transmission;0.0464001961037806;27204!GO:0005874;microtubule;0.0464001961037806;16564!GO:0031988;membrane-bound vesicle;0.0464001961037806;27204!GO:0032940;secretion by cell;0.0479228385937083;27204!
|ontology_enrichment_celltype=CL:0000540!4.91e-17!33;CL:0000047!4.91e-17!33;CL:0000031!4.91e-17!33;CL:0000404!4.91e-17!33;CL:0000393!1.57e-11!39;CL:0000211!1.57e-11!39;CL:0000117!3.60e-11!23;CL:0000337!3.60e-11!23;CL:0000221!4.64e-09!44;CL:0000133!4.64e-09!44;CL:0002319!1.00e-08!43
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!1.32e-24!73;UBERON:0004121!1.31e-23!95;UBERON:0000924!1.31e-23!95;UBERON:0006601!1.31e-23!95;UBERON:0001016!2.46e-23!75;UBERON:0002346!6.44e-22!64;UBERON:0003075!6.44e-22!64;UBERON:0007284!6.44e-22!64;UBERON:0010371!5.83e-21!73;UBERON:0000073!5.01e-19!54;UBERON:0001049!8.12e-18!52;UBERON:0005068!8.12e-18!52;UBERON:0006241!8.12e-18!52;UBERON:0007135!8.12e-18!52;UBERON:0003056!2.78e-16!49;UBERON:0000955!2.59e-15!47;UBERON:0006238!2.59e-15!47;UBERON:0002616!9.33e-15!46;UBERON:0003080!2.98e-14!40;UBERON:0002020!8.87e-14!34;UBERON:0002780!1.37e-13!39;UBERON:0001890!1.37e-13!39;UBERON:0006240!1.37e-13!39;UBERON:0003528!1.65e-11!29;UBERON:0002791!1.65e-11!29;UBERON:0001893!1.65e-11!29;UBERON:0010314!4.38e-11!92;UBERON:0000956!9.23e-08!21;UBERON:0001869!9.23e-08!21;UBERON:0000203!9.23e-08!21;UBERON:0000489!4.53e-07!21;UBERON:0002021!5.36e-07!10;UBERON:0000411!5.36e-07!10;UBERON:0001950!5.36e-07!10
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.564138,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.66329,0.870507,0.906098,1.18012,0.933025,0.608226,0,1.14208,0.578045,1.138,0.876292,0.679146,0.756749,0.932027,0.585919,0.731217,0.963352,1.1146,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,0.411696,0.608816,0.872889,0.563758,2.08624,1.32715,0.50014,0.582863,0.831295,0.724277,0.610669,0.922882,0.788421,1.05665,0.859154,0.663409,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,1.23806,1.11142,2.19064,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.777706,1.44925,1.882,2.7424,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,0.535545,0.195254,0.99201,1.06194,2.07346,1.62608,1.33496,1.26245,1.4508,2.26459,0.509215,1.17262,1.26539,1.05692,2.50519,1.38502,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,2.53104,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,1.862,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.999018,2.0485,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,1.75703,1.11251,0.94678,0.562367,0.904334,0.833542
|tfbs_overrepresentation_jaspar=MA0003.1;0.245953,MA0004.1;0.801718,MA0006.1;0.60285,MA0007.1;0.784593,MA0009.1;1.27673,MA0014.1;0.825079,MA0017.1;0.635031,MA0019.1;1.08369,MA0024.1;1.23079,MA0025.1;1.51835,MA0027.1;2.9431,MA0028.1;0.61552,MA0029.1;1.20789,MA0030.1;1.21482,MA0031.1;1.17722,MA0038.1;0.963265,MA0040.1;1.28983,MA0041.1;0.714279,MA0042.1;0.69885,MA0043.1;1.3775,MA0046.1;1.31428,MA0048.1;0.353763,MA0050.1;0.845669,MA0051.1;0.973068,MA0052.1;1.29825,MA0055.1;0.190475,MA0056.1;0,MA0057.1;0.896032,MA0058.1;0.690848,MA0059.1;0.705317,MA0060.1;2.1699,MA0061.1;0.5406,MA0063.1;0,MA0066.1;0.951196,MA0067.1;1.63197,MA0068.1;0.343188,MA0069.1;1.29861,MA0070.1;1.28847,MA0071.1;0.844726,MA0072.1;1.2796,MA0073.1;0.439282,MA0074.1;0.911576,MA0076.1;0.657929,MA0077.1;1.2569,MA0078.1;1.0091,MA0081.1;0.732313,MA0083.1;1.37668,MA0084.1;1.96428,MA0087.1;1.33189,MA0088.1;0.27999,MA0089.1;0,MA0090.1;0.762482,MA0091.1;0.816659,MA0092.1;0.762845,MA0093.1;0.62555,MA0095.1;0,MA0098.1;0,MA0100.1;0.89873,MA0101.1;0.71579,MA0103.1;0.647985,MA0105.1;0.405648,MA0106.1;1.01755,MA0107.1;0.640607,MA0108.2;1.10817,MA0109.1;0,MA0111.1;0.778753,MA0113.1;0.986839,MA0114.1;1.3296,MA0115.1;1.38041,MA0116.1;0.602598,MA0117.1;1.34691,MA0119.1;0.716476,MA0122.1;1.36752,MA0124.1;1.57762,MA0125.1;1.5017,MA0130.1;0,MA0131.1;1.07881,MA0132.1;0,MA0133.1;0,MA0135.1;1.4152,MA0136.1;0.933582,MA0139.1;1.16863,MA0140.1;0.898603,MA0141.1;0.671467,MA0142.1;1.16183,MA0143.1;1.00467,MA0144.1;0.541532,MA0145.1;0.292366,MA0146.1;0.151124,MA0147.1;0.556853,MA0148.1;0.820161,MA0149.1;0.722227,MA0062.2;0.412742,MA0035.2;0.903829,MA0039.2;1.10518,MA0138.2;1.07027,MA0002.2;0.466067,MA0137.2;0.668025,MA0104.2;0.48458,MA0047.2;0.962424,MA0112.2;0.29236,MA0065.2;1.44804,MA0150.1;0.784464,MA0151.1;0,MA0152.1;0.962542,MA0153.1;1.43238,MA0154.1;1.65374,MA0155.1;0.840842,MA0156.1;0.656895,MA0157.1;1.12772,MA0158.1;0,MA0159.1;0.569393,MA0160.1;0.823568,MA0161.1;0,MA0162.1;1.53682,MA0163.1;2.12767,MA0164.1;2.15144,MA0080.2;0.64167,MA0018.2;0.944669,MA0099.2;1.06348,MA0079.2;1.4764,MA0102.2;2.01714,MA0258.1;0.520639,MA0259.1;0.543506,MA0442.1;0
}}

Latest revision as of 18:47, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:85961581..85961603,-p2@Syn3
Mm9::chr10:85961617..85961654,-p1@Syn3
Mm9::chr15:90880254..90880298,-p1@Kif21a


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:0030672synaptic vesicle membrane0.0360765078419499
GO:0051649establishment of cellular localization0.0360765078419499
GO:0051641cellular localization0.0360765078419499
GO:0005871kinesin complex0.0360765078419499
GO:0005524ATP binding0.0360765078419499
GO:0032559adenyl ribonucleotide binding0.0360765078419499
GO:0030554adenyl nucleotide binding0.0360765078419499
GO:0044433cytoplasmic vesicle part0.0360765078419499
GO:0007269neurotransmitter secretion0.0360765078419499
GO:0008021synaptic vesicle0.0360765078419499
GO:0012506vesicle membrane0.0360765078419499
GO:0045055regulated secretory pathway0.0360765078419499
GO:0003777microtubule motor activity0.0360765078419499
GO:0032553ribonucleotide binding0.0360765078419499
GO:0032555purine ribonucleotide binding0.0360765078419499
GO:0017076purine nucleotide binding0.0360765078419499
GO:0030136clathrin-coated vesicle0.0360765078419499
GO:0007018microtubule-based movement0.0360765078419499
GO:0003001generation of a signal involved in cell-cell signaling0.0360765078419499
GO:0030135coated vesicle0.0360765078419499
GO:0001505regulation of neurotransmitter levels0.0360765078419499
GO:0000166nucleotide binding0.0360765078419499
GO:0030705cytoskeleton-dependent intracellular transport0.0366866860417446
GO:0005875microtubule associated complex0.0366866860417446
GO:0006810transport0.0439919398657478
GO:0044446intracellular organelle part0.0439919398657478
GO:0044422organelle part0.0439919398657478
GO:0016043cellular component organization and biogenesis0.0439919398657478
GO:0051234establishment of localization0.0439919398657478
GO:0045045secretory pathway0.0464001961037806
GO:0007017microtubule-based process0.0464001961037806
GO:0016023cytoplasmic membrane-bound vesicle0.0464001961037806
GO:0051179localization0.0464001961037806
GO:0007268synaptic transmission0.0464001961037806
GO:0005874microtubule0.0464001961037806
GO:0031988membrane-bound vesicle0.0464001961037806
GO:0032940secretion by cell0.0479228385937083



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>

Cell Type
Ontology termp-valuen
neuron4.91e-1733
neuronal stem cell4.91e-1733
neuroblast4.91e-1733
electrically signaling cell4.91e-1733
electrically responsive cell1.57e-1139
electrically active cell1.57e-1139
CNS neuron (sensu Vertebrata)3.60e-1123
neuroblast (sensu Vertebrata)3.60e-1123
ectodermal cell4.64e-0944
neurectodermal cell4.64e-0944
neural cell1.00e-0843

Uber Anatomy
Ontology termp-valuen
central nervous system1.32e-2473
ectoderm-derived structure1.31e-2395
ectoderm1.31e-2395
presumptive ectoderm1.31e-2395
nervous system2.46e-2375
neurectoderm6.44e-2264
neural plate6.44e-2264
presumptive neural plate6.44e-2264
ecto-epithelium5.83e-2173
regional part of nervous system5.01e-1954
neural tube8.12e-1852
neural rod8.12e-1852
future spinal cord8.12e-1852
neural keel8.12e-1852
pre-chordal neural plate2.78e-1649
brain2.59e-1547
future brain2.59e-1547
regional part of brain9.33e-1546
anterior neural tube2.98e-1440
gray matter8.87e-1434
regional part of forebrain1.37e-1339
forebrain1.37e-1339
future forebrain1.37e-1339
brain grey matter1.65e-1129
regional part of telencephalon1.65e-1129
telencephalon1.65e-1129
structure with developmental contribution from neural crest4.38e-1192
cerebral cortex9.23e-0821
cerebral hemisphere9.23e-0821
pallium9.23e-0821
cavitated compound organ4.53e-0721
occipital lobe5.36e-0710
visual cortex5.36e-0710
neocortex5.36e-0710


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)
MA0003.10.245953
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.10.825079
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.10.61552
MA0029.11.20789
MA0030.11.21482
MA0031.11.17722
MA0038.10.963265
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.10.353763
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.190475
MA0056.10
MA0057.10.896032
MA0058.10.690848
MA0059.10.705317
MA0060.12.1699
MA0061.10.5406
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.343188
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.439282
MA0074.10.911576
MA0076.10.657929
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.27999
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.10.62555
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.10.71579
MA0103.10.647985
MA0105.10.405648
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.11.3296
MA0115.11.38041
MA0116.10.602598
MA0117.11.34691
MA0119.10.716476
MA0122.11.36752
MA0124.11.57762
MA0125.11.5017
MA0130.10
MA0131.11.07881
MA0132.10
MA0133.10
MA0135.11.4152
MA0136.10.933582
MA0139.11.16863
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.10.292366
MA0146.10.151124
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.21.10518
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.20.48458
MA0047.20.962424
MA0112.20.29236
MA0065.21.44804
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.11.65374
MA0155.10.840842
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.11.53682
MA0163.12.12767
MA0164.12.15144
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.21.4764
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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