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MCL coexpression mm9:544: Difference between revisions

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{{MCL_coexpression_mm9
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5,0.0845301845292944,0,0,0|gostat_on_MCL_coexpression=GO:0016080;synaptic vesicle targeting;0.017307005837869;192167!GO:0006903;vesicle targeting;0.017307005837869;192167!GO:0042043;neurexin binding;0.017307005837869;192167!GO:0016079;synaptic vesicle exocytosis;0.017307005837869;192167!GO:0051650;establishment of vesicle localization;0.017307005837869;192167!GO:0051648;vesicle localization;0.017307005837869;192167!GO:0007416;synaptogenesis;0.0212316856430153;192167!GO:0051656;establishment of organelle localization;0.0212316856430153;192167!GO:0048489;synaptic vesicle transport;0.0212316856430153;192167!GO:0051640;organelle localization;0.0212316856430153;192167!GO:0045664;regulation of neuron differentiation;0.0212316856430153;192167!GO:0050808;synapse organization and biogenesis;0.0317016877136253;192167!GO:0007269;neurotransmitter secretion;0.0339120770595599;192167!GO:0045055;regulated secretory pathway;0.0395025018332462;192167!GO:0006887;exocytosis;0.044701314499151;192167!GO:0003001;generation of a signal involved in cell-cell signaling;0.044701314499151;192167!GO:0001505;regulation of neurotransmitter levels;0.044701314499151;192167!GO:0043062;extracellular structure organization and biogenesis;0.0474808004265753;192167!GO:0045211;postsynaptic 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|gostat_on_MCL_coexpression=GO:0016080;synaptic vesicle targeting;0.017307005837869;192167!GO:0006903;vesicle targeting;0.017307005837869;192167!GO:0042043;neurexin binding;0.017307005837869;192167!GO:0016079;synaptic vesicle exocytosis;0.017307005837869;192167!GO:0051650;establishment of vesicle localization;0.017307005837869;192167!GO:0051648;vesicle localization;0.017307005837869;192167!GO:0007416;synaptogenesis;0.0212316856430153;192167!GO:0051656;establishment of organelle localization;0.0212316856430153;192167!GO:0048489;synaptic vesicle transport;0.0212316856430153;192167!GO:0051640;organelle localization;0.0212316856430153;192167!GO:0045664;regulation of neuron differentiation;0.0212316856430153;192167!GO:0050808;synapse organization and biogenesis;0.0317016877136253;192167!GO:0007269;neurotransmitter secretion;0.0339120770595599;192167!GO:0045055;regulated secretory pathway;0.0395025018332462;192167!GO:0006887;exocytosis;0.044701314499151;192167!GO:0003001;generation of a signal involved in cell-cell signaling;0.044701314499151;192167!GO:0001505;regulation of neurotransmitter levels;0.044701314499151;192167!GO:0043062;extracellular structure organization and biogenesis;0.0474808004265753;192167!GO:0045211;postsynaptic membrane;0.0495118245516327;192167!
|ontology_enrichment_celltype=CL:0000117!1.73e-07!23;CL:0000337!1.73e-07!23
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002346!1.92e-26!64;UBERON:0003075!1.92e-26!64;UBERON:0007284!1.92e-26!64;UBERON:0003056!4.17e-23!49;UBERON:0010371!4.26e-21!73;UBERON:0000073!2.60e-20!54;UBERON:0001049!3.07e-20!52;UBERON:0005068!3.07e-20!52;UBERON:0006241!3.07e-20!52;UBERON:0007135!3.07e-20!52;UBERON:0004121!4.27e-18!95;UBERON:0000924!4.27e-18!95;UBERON:0006601!4.27e-18!95;UBERON:0000955!7.65e-18!47;UBERON:0006238!7.65e-18!47;UBERON:0002616!6.22e-17!46;UBERON:0002020!1.18e-16!34;UBERON:0001017!1.89e-16!73;UBERON:0001016!1.28e-15!75;UBERON:0003080!3.73e-15!40;UBERON:0010314!8.57e-15!92;UBERON:0003528!2.59e-14!29;UBERON:0002791!2.59e-14!29;UBERON:0001893!2.59e-14!29;UBERON:0002780!2.62e-14!39;UBERON:0001890!2.62e-14!39;UBERON:0006240!2.62e-14!39;UBERON:0002021!1.04e-11!10;UBERON:0000411!1.04e-11!10;UBERON:0001950!1.04e-11!10;UBERON:0000956!3.27e-10!21;UBERON:0001869!3.27e-10!21;UBERON:0000203!3.27e-10!21;UBERON:0000970!1.09e-09!9;UBERON:0000019!1.09e-09!9;UBERON:0000047!1.09e-09!9;UBERON:0010312!1.09e-09!9;UBERON:0004088!1.09e-09!9;UBERON:0002104!1.09e-09!9;UBERON:0001456!1.09e-09!9;UBERON:0003072!1.09e-09!9;UBERON:0004128!1.09e-09!9;UBERON:0003071!1.09e-09!9;UBERON:0002619!2.15e-09!17;UBERON:0001444!2.04e-07!11
|tfbs_overrepresentation_for_novel_motifs=0.224466,0.153651,0.204219,0.25808,0.123731,0.743234,0.346405,0.0669598,0.251553,0.0394224,0.308886,0.336042,0.237599,0.357027,0.830717,0,0.530547,0.377686,0.470307,0.24668,0.176628,0.165365,0.356242,0.388504,0.603782,0.381085,0.448115,0.287195,0.469653,0.145734,0.275529,0.624931,0.117091,0.176308,0.135203,0.850523,0.358314,0.332941,0.322338,0.0808072,0.384293,0.279796,0.0536251,0.136236,0.0379861,0.24907,0.457618,0.300372,0.237017,0.474834,0.514446,0.404841,0.321327,0.759566,0.776306,0.363247,0.163199,0.325117,0.0511827,0.36147,0.606104,0.413233,0.569343,0.504093,0.372973,1.33757,0.908031,1.25063,0.60172,1.10561,0.189925,0.526777,0.351968,0.808562,0.407198,0.37844,0.0464428,0.447339,0.590017,0.531085,0.530081,0.546623,1.05972,0.227715,0.69807,0.132803,4.99085,0.0368325,0.462057,1.41118,0.975915,0.702809,0.636995,0.401201,0.651159,1.01076,0.233568,0.639644,0.457849,0.0288834,0.725622,1.51291,0.742871,0.514993,0.514023,0.279432,0.569344,0.296997,0.183341,0.177945,0.218949,0.744577,0.180573,0.313258,0.982794,0.381263,0.189757,0.26114,0.53175,0.108794,0.813766,0.484912,0.995764,0.446521,1.03573,0.593478,0.353461,0.630607,0.906557,0.406303,0.726634,0.252176,0.877862,0.979261,1.0039,0.012643,0.231086,0.280962,0.955897,1.77738,1.3796,0.91261,0.393303,0.634793,0.508066,0.280171,0.460443,1.73788,0.232952,0.124893,0.0377782,0.0106906,0.761071,0.0882878,0.374365,0.839715,0.405736,0.440483,0.633366,0.230865,0.96517,0.697256,0.593895,0.21719,0.50503,0.367885,0.110426,0.33468,0.0649099
|tfbs_overrepresentation_jaspar=MA0003.1;0.00296851,MA0004.1;0.258473,MA0006.1;0.1319,MA0007.1;0.246385,MA0009.1;0.649874,MA0014.1;0.00638392,MA0017.1;0.895796,MA0019.1;0.480432,MA0024.1;0.608636,MA0025.1;0.873493,MA0027.1;2.275,MA0028.1;0.138956,MA0029.1;2.44985,MA0030.1;0.594419,MA0031.1;0.561217,MA0038.1;0.992094,MA0040.1;0.661716,MA0041.1;0.577334,MA0042.1;0.553522,MA0043.1;0.74191,MA0046.1;0.683926,MA0048.1;0.121113,MA0050.1;0.290354,MA0051.1;0.388883,MA0052.1;0.669354,MA0055.1;0.14835,MA0056.1;0,MA0057.1;0.261486,MA0058.1;0.183941,MA0059.1;0.19314,MA0060.1;0.586951,MA0061.1;0.0995825,MA0063.1;0,MA0066.1;0.371389,MA0067.1;0.981551,MA0068.1;0.0266408,MA0069.1;0.669676,MA0070.1;0.660488,MA0071.1;1.43623,MA0072.1;1.57103,MA0073.1;1.06747,MA0074.1;1.61724,MA0076.1;0.163664,MA0077.1;0.632005,MA0078.1;0.418168,MA0081.1;0.210747,MA0083.1;1.7553,MA0084.1;1.30392,MA0087.1;0.699999,MA0088.1;0.0649199,MA0089.1;0,MA0090.1;0.653402,MA0091.1;1.36127,MA0092.1;0.231323,MA0093.1;0.144649,MA0095.1;0,MA0098.1;0,MA0100.1;0.330364,MA0101.1;0.199903,MA0103.1;0.157724,MA0105.1;0.0444807,MA0106.1;0.425111,MA0107.1;0.153373,MA0108.2;0.50131,MA0109.1;0,MA0111.1;0.242308,MA0113.1;0.400008,MA0114.1;0.323836,MA0115.1;0.744589,MA0116.1;0.131762,MA0117.1;0.713754,MA0119.1;0.200349,MA0122.1;0.732707,MA0124.1;0.929684,MA0125.1;0.857794,MA0130.1;0,MA0131.1;0.476296,MA0132.1;0,MA0133.1;0,MA0135.1;0.77683,MA0136.1;0.357464,MA0139.1;0.231431,MA0140.1;0.330266,MA0141.1;0.511953,MA0142.1;0.547747,MA0143.1;0.414534,MA0144.1;0.328866,MA0145.1;0.0731548,MA0146.1;0.00143436,MA0147.1;0.107632,MA0148.1;0.271704,MA0149.1;0.204102,MA0062.2;0.046824,MA0035.2;1.5961,MA0039.2;0.00913764,MA0138.2;0.469076,MA0002.2;0.235791,MA0137.2;0.169785,MA0104.2;0.0740839,MA0047.2;0.380343,MA0112.2;0.0731504,MA0065.2;0.0735294,MA0150.1;0.246295,MA0151.1;0,MA0152.1;0.380437,MA0153.1;0.792819,MA0154.1;0.118426,MA0155.1;0.0879017,MA0156.1;0.490212,MA0157.1;0.518122,MA0158.1;0,MA0159.1;0.114033,MA0160.1;0.274172,MA0161.1;0,MA0162.1;0.0134677,MA0163.1;0.0388292,MA0164.1;0.357779,MA0080.2;0.153997,MA0018.2;0.366212,MA0099.2;0.463355,MA0079.2;0.000476405,MA0102.2;1.35579,MA0258.1;0.0900907,MA0259.1;0.101001,MA0442.1;0
}}

Latest revision as of 15:29, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr16:75092953..75092979,-p@chr16:75092953..75092979
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Mm9::chr18:23200112..23200123,-p4@Nol4
Mm9::chr18:77800445..77800450,-p@chr18:77800445..77800450
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Mm9::chr1:106677500..106677503,+p@chr1:106677500..106677503
+
Mm9::chr3:25330641..25330645,-p@chr3:25330641..25330645
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Mm9::chr3:25497991..25497995,-p@chr3:25497991..25497995
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Mm9::chr3:25746206..25746219,-p@chr3:25746206..25746219
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Mm9::chr3:25835662..25835666,-p@chr3:25835662..25835666
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Mm9::chr3:26001283..26001284,-p@chr3:26001283..26001284
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Mm9::chr3:26015244..26015245,-p@chr3:26015244..26015245
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Mm9::chr3:26230752..26230771,-p7@Nlgn1
Mm9::chr5:99792484..99792489,-p@chr5:99792484..99792489
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Mm9::chr7:129814314..129814341,+p@chr7:129814314..129814341
+
Mm9::chr7:71650246..71650250,+p@chr7:71650246..71650250
+


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:0016080synaptic vesicle targeting0.017307005837869
GO:0006903vesicle targeting0.017307005837869
GO:0042043neurexin binding0.017307005837869
GO:0016079synaptic vesicle exocytosis0.017307005837869
GO:0051650establishment of vesicle localization0.017307005837869
GO:0051648vesicle localization0.017307005837869
GO:0007416synaptogenesis0.0212316856430153
GO:0051656establishment of organelle localization0.0212316856430153
GO:0048489synaptic vesicle transport0.0212316856430153
GO:0051640organelle localization0.0212316856430153
GO:0045664regulation of neuron differentiation0.0212316856430153
GO:0050808synapse organization and biogenesis0.0317016877136253
GO:0007269neurotransmitter secretion0.0339120770595599
GO:0045055regulated secretory pathway0.0395025018332462
GO:0006887exocytosis0.044701314499151
GO:0003001generation of a signal involved in cell-cell signaling0.044701314499151
GO:0001505regulation of neurotransmitter levels0.044701314499151
GO:0043062extracellular structure organization and biogenesis0.0474808004265753
GO:0045211postsynaptic membrane0.0495118245516327



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
CNS neuron (sensu Vertebrata)1.73e-0723
neuroblast (sensu Vertebrata)1.73e-0723

Uber Anatomy
Ontology termp-valuen
neurectoderm1.92e-2664
neural plate1.92e-2664
presumptive neural plate1.92e-2664
pre-chordal neural plate4.17e-2349
ecto-epithelium4.26e-2173
regional part of nervous system2.60e-2054
neural tube3.07e-2052
neural rod3.07e-2052
future spinal cord3.07e-2052
neural keel3.07e-2052
ectoderm-derived structure4.27e-1895
ectoderm4.27e-1895
presumptive ectoderm4.27e-1895
brain7.65e-1847
future brain7.65e-1847
regional part of brain6.22e-1746
gray matter1.18e-1634
central nervous system1.89e-1673
nervous system1.28e-1575
anterior neural tube3.73e-1540
structure with developmental contribution from neural crest8.57e-1592
brain grey matter2.59e-1429
regional part of telencephalon2.59e-1429
telencephalon2.59e-1429
regional part of forebrain2.62e-1439
forebrain2.62e-1439
future forebrain2.62e-1439
occipital lobe1.04e-1110
visual cortex1.04e-1110
neocortex1.04e-1110
cerebral cortex3.27e-1021
cerebral hemisphere3.27e-1021
pallium3.27e-1021
eye1.09e-099
camera-type eye1.09e-099
simple eye1.09e-099
immature eye1.09e-099
ocular region1.09e-099
visual system1.09e-099
face1.09e-099
optic cup1.09e-099
optic vesicle1.09e-099
eye primordium1.09e-099
regional part of cerebral cortex2.15e-0917
subdivision of head2.04e-0711


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)
MA0003.10.00296851
MA0004.10.258473
MA0006.10.1319
MA0007.10.246385
MA0009.10.649874
MA0014.10.00638392
MA0017.10.895796
MA0019.10.480432
MA0024.10.608636
MA0025.10.873493
MA0027.12.275
MA0028.10.138956
MA0029.12.44985
MA0030.10.594419
MA0031.10.561217
MA0038.10.992094
MA0040.10.661716
MA0041.10.577334
MA0042.10.553522
MA0043.10.74191
MA0046.10.683926
MA0048.10.121113
MA0050.10.290354
MA0051.10.388883
MA0052.10.669354
MA0055.10.14835
MA0056.10
MA0057.10.261486
MA0058.10.183941
MA0059.10.19314
MA0060.10.586951
MA0061.10.0995825
MA0063.10
MA0066.10.371389
MA0067.10.981551
MA0068.10.0266408
MA0069.10.669676
MA0070.10.660488
MA0071.11.43623
MA0072.11.57103
MA0073.11.06747
MA0074.11.61724
MA0076.10.163664
MA0077.10.632005
MA0078.10.418168
MA0081.10.210747
MA0083.11.7553
MA0084.11.30392
MA0087.10.699999
MA0088.10.0649199
MA0089.10
MA0090.10.653402
MA0091.11.36127
MA0092.10.231323
MA0093.10.144649
MA0095.10
MA0098.10
MA0100.10.330364
MA0101.10.199903
MA0103.10.157724
MA0105.10.0444807
MA0106.10.425111
MA0107.10.153373
MA0108.20.50131
MA0109.10
MA0111.10.242308
MA0113.10.400008
MA0114.10.323836
MA0115.10.744589
MA0116.10.131762
MA0117.10.713754
MA0119.10.200349
MA0122.10.732707
MA0124.10.929684
MA0125.10.857794
MA0130.10
MA0131.10.476296
MA0132.10
MA0133.10
MA0135.10.77683
MA0136.10.357464
MA0139.10.231431
MA0140.10.330266
MA0141.10.511953
MA0142.10.547747
MA0143.10.414534
MA0144.10.328866
MA0145.10.0731548
MA0146.10.00143436
MA0147.10.107632
MA0148.10.271704
MA0149.10.204102
MA0062.20.046824
MA0035.21.5961
MA0039.20.00913764
MA0138.20.469076
MA0002.20.235791
MA0137.20.169785
MA0104.20.0740839
MA0047.20.380343
MA0112.20.0731504
MA0065.20.0735294
MA0150.10.246295
MA0151.10
MA0152.10.380437
MA0153.10.792819
MA0154.10.118426
MA0155.10.0879017
MA0156.10.490212
MA0157.10.518122
MA0158.10
MA0159.10.114033
MA0160.10.274172
MA0161.10
MA0162.10.0134677
MA0163.10.0388292
MA0164.10.357779
MA0080.20.153997
MA0018.20.366212
MA0099.20.463355
MA0079.20.000476405
MA0102.21.35579
MA0258.10.0900907
MA0259.10.101001
MA0442.10
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