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MCL coexpression mm9:398: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0009235;cobalamin metabolic process;0.0363227962526708;77697!GO:0008817;cob(I)yrinic acid a,c-diamide adenosyltransferase activity;0.0363227962526708;77697!GO:0016572;histone phosphorylation;0.0363227962526708;26404!GO:0009236;cobalamin biosynthetic process;0.0363227962526708;77697!}}
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metabolic process;0.0363227962526708;77697!GO:0008817;cob(I)yrinic acid a,c-diamide adenosyltransferase activity;0.0363227962526708;77697!GO:0016572;histone phosphorylation;0.0363227962526708;26404!GO:0009236;cobalamin biosynthetic process;0.0363227962526708;77697!|ontology_enrichment_celltype=CL:0000221!1.43e-16!44;CL:0000133!1.43e-16!44;CL:0002319!2.24e-16!43;CL:0000540!2.79e-15!33;CL:0000047!2.79e-15!33;CL:0000031!2.79e-15!33;CL:0000404!2.79e-15!33;CL:0000055!1.88e-14!49;CL:0000393!5.09e-13!39;CL:0000211!5.09e-13!39;CL:0000117!1.72e-12!23;CL:0000337!1.72e-12!23|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0001017!1.90e-31!73;UBERON:0001016!1.87e-30!75;UBERON:0004121!7.48e-28!95;UBERON:0000924!7.48e-28!95;UBERON:0006601!7.48e-28!95;UBERON:0002346!2.65e-26!64;UBERON:0003075!2.65e-26!64;UBERON:0007284!2.65e-26!64;UBERON:0010371!1.20e-23!73;UBERON:0000073!4.38e-23!54;UBERON:0001049!7.13e-23!52;UBERON:0005068!7.13e-23!52;UBERON:0006241!7.13e-23!52;UBERON:0007135!7.13e-23!52;UBERON:0010314!1.30e-20!92;UBERON:0003056!4.00e-20!49;UBERON:0000955!9.99e-20!47;UBERON:0006238!9.99e-20!47;UBERON:0002616!3.66e-19!46;UBERON:0003080!6.18e-18!40;UBERON:0002780!9.70e-18!39;UBERON:0001890!9.70e-18!39;UBERON:0006240!9.70e-18!39;UBERON:0002020!3.28e-17!34;UBERON:0003528!7.83e-14!29;UBERON:0002791!7.83e-14!29;UBERON:0001893!7.83e-14!29;UBERON:0000956!1.56e-10!21;UBERON:0001869!1.56e-10!21;UBERON:0000203!1.56e-10!21;UBERON:0002619!2.46e-08!17;UBERON:0000468!3.20e-07!333|tfbs_overrepresentation_for_novel_motifs=0.457576,1.18192,0.823928,0.178048,0.24857,0.188081,1.30793,0.308279,0.32877,0.0966197,0.631542,0.24561,0.30879,0.264234,0.572973,0,1.08407,0.0671461,0.514215,0.245228,0.358501,0.685027,2.06478,0.070175,0.427698,0.285776,1.14076,0.586946,0.646362,0.884629,1.07045,0.512187,0.868591,0.221918,0.970517,0.0928537,0.483264,1.26328,0.194199,0.159278,0.243076,1.08493,0.131909,0.0801495,0.199883,0.508392,0.355451,1.15441,0.0115058,0.317394,0.408111,0.828085,0.167462,0.641205,0.657376,0.743028,0.100694,0.664869,0.0979835,0.739389,0.494318,0.314847,0.637374,1.03032,0.278491,1.93806,0.785371,1.12243,0.490165,0.979213,0.386078,0.919753,1.69069,1.64631,0.229359,0.660397,0.088252,0.346003,0.479091,0.113666,0.138314,1.11671,0.31368,0.123739,0.582029,2.35273,0.114191,0.35371,0.359539,1.2816,0.851763,0.586575,0.523661,0.0737837,1.59853,0.167694,0.127918,0.526183,0.355664,0.0526066,0.483457,0.511936,0.625103,0.408622,0.407717,0.570967,0.459578,0.211422,0.372426,0.730452,0.44617,0.626748,0.114328,0.640523,0.858505,0.240644,0.402332,0.533284,1.08652,0.474273,0.693645,0.380657,0.287218,0.345253,0.910454,0.482363,0.722986,0.517583,1.84366,0.0752496,0.609469,0.173056,0.75595,0.280468,0.879201,0.0658603,0.15539,0.197578,0.832159,1.64606,1.25025,0.789841,0.296788,0.521565,0.402166,0.196898,0.358053,1.60668,1.47921,0.0717633,1.25243,3.60579,0.642658,0.174823,0.27974,0.718834,0.30804,0.085296,0.14831,0.917139,0.841238,0.581248,0.482758,0.869484,0.39934,0.273933,0.220881,0.244407,5.136|tfbs_overrepresentation_jaspar=MA0003.1;1.4082,MA0004.1;0.527785,MA0006.1;1.42327,MA0007.1;0.502851,MA0009.1;0.535932,MA0014.1;1.06573,MA0017.1;0.0906268,MA0019.1;0.376509,MA0024.1;0.496718,MA0025.1;0.751694,MA0027.1;2.14278,MA0028.1;2.03047,MA0029.1;0.477444,MA0030.1;0.483253,MA0031.1;0.451927,MA0038.1;0.779388,MA0040.1;0.547233,MA0041.1;1.30829,MA0042.1;0.770017,MA0043.1;0.624178,MA0046.1;0.568473,MA0048.1;1.0852,MA0050.1;0.205672,MA0051.1;0.2928,MA0052.1;0.554531,MA0055.1;0.666797,MA0056.1;0,MA0057.1;0.998407,MA0058.1;0.751937,MA0059.1;0.392739,MA0060.1;3.0778,MA0061.1;0.438647,MA0063.1;0,MA0066.1;0.277072,MA0067.1;0.857286,MA0068.1;0.0481248,MA0069.1;0.554839,MA0070.1;0.54606,MA0071.1;0.20507,MA0072.1;0.538403,MA0073.1;0.0405835,MA0074.1;0.249359,MA0076.1;3.63477,MA0077.1;0.518913,MA0078.1;0.319336,MA0081.1;0.8469,MA0083.1;0.623446,MA0084.1;1.1752,MA0087.1;0.583879,MA0088.1;1.29308,MA0089.1;0,MA0090.1;0.471234,MA0091.1;0.187483,MA0092.1;0.471747,MA0093.1;1.02245,MA0095.1;0,MA0098.1;0,MA0100.1;0.2406,MA0101.1;0.40675,MA0103.1;0.0964586,MA0105.1;0.410191,MA0106.1;5.30356,MA0107.1;0.310214,MA0108.2;0.395878,MA0109.1;0,MA0111.1;0.494436,MA0113.1;0.302851,MA0114.1;0.195359,MA0115.1;0.626759,MA0116.1;0.561344,MA0117.1;0.597086,MA0119.1;2.5698,MA0122.1;0.615314,MA0124.1;0.80652,MA0125.1;0.736412,MA0130.1;0,MA0131.1;1.73046,MA0132.1;0,MA0133.1;0,MA0135.1;0.657882,MA0136.1;0.264624,MA0139.1;0.299978,MA0140.1;0.240513,MA0141.1;0.10748,MA0142.1;0.439269,MA0143.1;0.31603,MA0144.1;1.17542,MA0145.1;1.38577,MA0146.1;2.20416,MA0147.1;0.813958,MA0148.1;0.189643,MA0149.1;0.133214,MA0062.2;4.02084,MA0035.2;0.244063,MA0039.2;2.19819,MA0138.2;0.366012,MA0002.2;0.0318175,MA0137.2;0.105829,MA0104.2;0.955719,MA0047.2;0.285109,MA0112.2;1.05475,MA0065.2;0.0821754,MA0150.1;0.168102,MA0151.1;0,MA0152.1;0.285194,MA0153.1;1.61457,MA0154.1;0.0518625,MA0155.1;1.54192,MA0156.1;1.12151,MA0157.1;0.411541,MA0158.1;0,MA0159.1;0.228388,MA0160.1;0.191754,MA0161.1;0,MA0162.1;1.18735,MA0163.1;4.39034,MA0164.1;0.264905,MA0080.2;0.0935932,MA0018.2;0.272436,MA0099.2;0.360735,MA0079.2;2.79991,MA0102.2;1.22663,MA0258.1;0.178572,MA0259.1;0.444163,MA0442.1;0}}

Latest revision as of 15:14, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:120328644..120328685,-p2@Arl16
Mm9::chr15:102341112..102341136,-p5@Map3k12
Mm9::chr15:99288189..99288208,-p2@Nckap5l
Mm9::chr17:36116182..36116253,-p1@Prr3
Mm9::chr4:117556033..117556112,-p1@B4galt2
Mm9::chr5:114893964..114893987,-p3@Mmab
Mm9::chr7:134592623..134592680,-p1@Zfp689
Mm9::chr7:150239284..150239364,-p1@ENSMUST00000133630
Mm9::chr7:19661591..19661622,+p2@Dmwd
Mm9::chr7:25372631..25372684,-p1@Zfp575
Mm9::chr7:28043859..28043878,+p2@Numbl
Mm9::chr7:5003102..5003113,+p4@Zfp580
Mm9::chr7:5003117..5003159,+p1@Zfp580
Mm9::chr7:5003165..5003203,+p2@Zfp580
Mm9::chr7:5003205..5003234,+p3@Zfp580
Mm9::chr7:69565028..69565043,-p1@Mkrn3
Mm9::chr8:13869673..13869740,+p1@Zfp828
Mm9::chr8:81923412..81923431,-p2@Smad1
Mm9::chrX:148803223..148803283,-p1@Gpr173


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:0009235cobalamin metabolic process0.0363227962526708
GO:0008817cob(I)yrinic acid a,c-diamide adenosyltransferase activity0.0363227962526708
GO:0016572histone phosphorylation0.0363227962526708
GO:0009236cobalamin biosynthetic process0.0363227962526708



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
central nervous system1.90e-3173
nervous system1.87e-3075
ectoderm-derived structure7.48e-2895
ectoderm7.48e-2895
presumptive ectoderm7.48e-2895
neurectoderm2.65e-2664
neural plate2.65e-2664
presumptive neural plate2.65e-2664
ecto-epithelium1.20e-2373
regional part of nervous system4.38e-2354
neural tube7.13e-2352
neural rod7.13e-2352
future spinal cord7.13e-2352
neural keel7.13e-2352
structure with developmental contribution from neural crest1.30e-2092
pre-chordal neural plate4.00e-2049
brain9.99e-2047
future brain9.99e-2047
regional part of brain3.66e-1946
anterior neural tube6.18e-1840
regional part of forebrain9.70e-1839
forebrain9.70e-1839
future forebrain9.70e-1839
gray matter3.28e-1734
brain grey matter7.83e-1429
regional part of telencephalon7.83e-1429
telencephalon7.83e-1429
cerebral cortex1.56e-1021
cerebral hemisphere1.56e-1021
pallium1.56e-1021
regional part of cerebral cortex2.46e-0817
multi-cellular organism3.20e-07333


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)
MA0003.11.4082
MA0004.10.527785
MA0006.11.42327
MA0007.10.502851
MA0009.10.535932
MA0014.11.06573
MA0017.10.0906268
MA0019.10.376509
MA0024.10.496718
MA0025.10.751694
MA0027.12.14278
MA0028.12.03047
MA0029.10.477444
MA0030.10.483253
MA0031.10.451927
MA0038.10.779388
MA0040.10.547233
MA0041.11.30829
MA0042.10.770017
MA0043.10.624178
MA0046.10.568473
MA0048.11.0852
MA0050.10.205672
MA0051.10.2928
MA0052.10.554531
MA0055.10.666797
MA0056.10
MA0057.10.998407
MA0058.10.751937
MA0059.10.392739
MA0060.13.0778
MA0061.10.438647
MA0063.10
MA0066.10.277072
MA0067.10.857286
MA0068.10.0481248
MA0069.10.554839
MA0070.10.54606
MA0071.10.20507
MA0072.10.538403
MA0073.10.0405835
MA0074.10.249359
MA0076.13.63477
MA0077.10.518913
MA0078.10.319336
MA0081.10.8469
MA0083.10.623446
MA0084.11.1752
MA0087.10.583879
MA0088.11.29308
MA0089.10
MA0090.10.471234
MA0091.10.187483
MA0092.10.471747
MA0093.11.02245
MA0095.10
MA0098.10
MA0100.10.2406
MA0101.10.40675
MA0103.10.0964586
MA0105.10.410191
MA0106.15.30356
MA0107.10.310214
MA0108.20.395878
MA0109.10
MA0111.10.494436
MA0113.10.302851
MA0114.10.195359
MA0115.10.626759
MA0116.10.561344
MA0117.10.597086
MA0119.12.5698
MA0122.10.615314
MA0124.10.80652
MA0125.10.736412
MA0130.10
MA0131.11.73046
MA0132.10
MA0133.10
MA0135.10.657882
MA0136.10.264624
MA0139.10.299978
MA0140.10.240513
MA0141.10.10748
MA0142.10.439269
MA0143.10.31603
MA0144.11.17542
MA0145.11.38577
MA0146.12.20416
MA0147.10.813958
MA0148.10.189643
MA0149.10.133214
MA0062.24.02084
MA0035.20.244063
MA0039.22.19819
MA0138.20.366012
MA0002.20.0318175
MA0137.20.105829
MA0104.20.955719
MA0047.20.285109
MA0112.21.05475
MA0065.20.0821754
MA0150.10.168102
MA0151.10
MA0152.10.285194
MA0153.11.61457
MA0154.10.0518625
MA0155.11.54192
MA0156.11.12151
MA0157.10.411541
MA0158.10
MA0159.10.228388
MA0160.10.191754
MA0161.10
MA0162.11.18735
MA0163.14.39034
MA0164.10.264905
MA0080.20.0935932
MA0018.20.272436
MA0099.20.360735
MA0079.22.79991
MA0102.21.22663
MA0258.10.178572
MA0259.10.444163
MA0442.10
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