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MCL coexpression mm9:734: Difference between revisions

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{{MCL_coexpression_mm9
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transporter activity;0.000749205781920186;170762,234865!GO:0051028;mRNA transport;0.00407034741706452;170762,234865!GO:0050658;RNA transport;0.00407034741706452;170762,234865!GO:0051236;establishment of RNA localization;0.00407034741706452;170762,234865!GO:0050657;nucleic acid transport;0.00407034741706452;170762,234865!GO:0006403;RNA localization;0.00407034741706452;170762,234865!GO:0005643;nuclear pore;0.00407034741706452;170762,234865!GO:0065002;intracellular protein transport across a membrane;0.00407034741706452;170762,234865!GO:0015931;nucleobase, nucleoside, nucleotide and nucleic acid transport;0.00407034741706452;170762,234865!GO:0046930;pore complex;0.00407034741706452;170762,234865!GO:0044453;nuclear membrane part;0.00429391984070031;170762,234865!GO:0031965;nuclear membrane;0.00429391984070031;170762,234865!GO:0044428;nuclear part;0.00746703842105303;70052,170762,234865,101943!GO:0006913;nucleocytoplasmic transport;0.00746703842105303;170762,234865!GO:0051169;nuclear transport;0.00746703842105303;170762,234865!GO:0017056;structural constituent of nuclear pore;0.00764090439970906;170762!GO:0005635;nuclear envelope;0.00886461988172955;170762,234865!GO:0005681;spliceosome;0.0143799144534344;70052,101943!GO:0046540;U4/U6 x U5 tri-snRNP complex;0.0160755416039761;70052!GO:0008380;RNA splicing;0.0197360766737931;70052,101943!GO:0051649;establishment of cellular localization;0.0243803738730018;170762,234865,109658!GO:0051641;cellular localization;0.0244002357987189;170762,234865,109658!GO:0004526;ribonuclease P activity;0.0248546207161951;67724!GO:0006397;mRNA processing;0.0248546207161951;70052,101943!GO:0006406;mRNA export from nucleus;0.0248546207161951;234865!GO:0030532;small nuclear ribonucleoprotein complex;0.0248546207161951;70052!GO:0043123;positive regulation of I-kappaB kinase/NF-kappaB cascade;0.0248546207161951;18572!GO:0004549;tRNA-specific ribonuclease activity;0.0261400419890448;67724!GO:0016071;mRNA metabolic process;0.027836696568666;70052,101943!GO:0043122;regulation of I-kappaB kinase/NF-kappaB cascade;0.0284511320653779;18572!GO:0006405;RNA export from nucleus;0.0294935597533027;234865!GO:0012505;endomembrane system;0.0328158581290779;170762,234865!GO:0016891;endoribonuclease activity, producing 5'-phosphomonoesters;0.0369009904895174;67724!GO:0032991;macromolecular complex;0.0382548377726184;70052,170762,234865,101943!GO:0016893;endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters;0.0382548377726184;67724!GO:0051168;nuclear export;0.0388742433313261;234865!GO:0006396;RNA processing;0.0398025270092647;70052,101943!GO:0031975;envelope;0.0437951567695661;170762,234865!GO:0031967;organelle envelope;0.0437951567695661;170762,234865!GO:0006886;intracellular protein transport;0.0448957993436601;170762,234865!GO:0016070;RNA metabolic 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|gostat_on_MCL_coexpression=GO:0005487;nucleocytoplasmic transporter activity;0.000749205781920186;170762,234865!GO:0051028;mRNA transport;0.00407034741706452;170762,234865!GO:0050658;RNA transport;0.00407034741706452;170762,234865!GO:0051236;establishment of RNA localization;0.00407034741706452;170762,234865!GO:0050657;nucleic acid transport;0.00407034741706452;170762,234865!GO:0006403;RNA localization;0.00407034741706452;170762,234865!GO:0005643;nuclear pore;0.00407034741706452;170762,234865!GO:0065002;intracellular protein transport across a membrane;0.00407034741706452;170762,234865!GO:0015931;nucleobase, nucleoside, nucleotide and nucleic acid transport;0.00407034741706452;170762,234865!GO:0046930;pore complex;0.00407034741706452;170762,234865!GO:0044453;nuclear membrane part;0.00429391984070031;170762,234865!GO:0031965;nuclear membrane;0.00429391984070031;170762,234865!GO:0044428;nuclear part;0.00746703842105303;70052,170762,234865,101943!GO:0006913;nucleocytoplasmic transport;0.00746703842105303;170762,234865!GO:0051169;nuclear transport;0.00746703842105303;170762,234865!GO:0017056;structural constituent of nuclear pore;0.00764090439970906;170762!GO:0005635;nuclear envelope;0.00886461988172955;170762,234865!GO:0005681;spliceosome;0.0143799144534344;70052,101943!GO:0046540;U4/U6 x U5 tri-snRNP complex;0.0160755416039761;70052!GO:0008380;RNA splicing;0.0197360766737931;70052,101943!GO:0051649;establishment of cellular localization;0.0243803738730018;170762,234865,109658!GO:0051641;cellular localization;0.0244002357987189;170762,234865,109658!GO:0004526;ribonuclease P activity;0.0248546207161951;67724!GO:0006397;mRNA processing;0.0248546207161951;70052,101943!GO:0006406;mRNA export from nucleus;0.0248546207161951;234865!GO:0030532;small nuclear ribonucleoprotein complex;0.0248546207161951;70052!GO:0043123;positive regulation of I-kappaB kinase/NF-kappaB cascade;0.0248546207161951;18572!GO:0004549;tRNA-specific ribonuclease activity;0.0261400419890448;67724!GO:0016071;mRNA metabolic process;0.027836696568666;70052,101943!GO:0043122;regulation of I-kappaB kinase/NF-kappaB cascade;0.0284511320653779;18572!GO:0006405;RNA export from nucleus;0.0294935597533027;234865!GO:0012505;endomembrane system;0.0328158581290779;170762,234865!GO:0016891;endoribonuclease activity, producing 5'-phosphomonoesters;0.0369009904895174;67724!GO:0032991;macromolecular complex;0.0382548377726184;70052,170762,234865,101943!GO:0016893;endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters;0.0382548377726184;67724!GO:0051168;nuclear export;0.0388742433313261;234865!GO:0006396;RNA processing;0.0398025270092647;70052,101943!GO:0031975;envelope;0.0437951567695661;170762,234865!GO:0031967;organelle envelope;0.0437951567695661;170762,234865!GO:0006886;intracellular protein transport;0.0448957993436601;170762,234865!GO:0016070;RNA metabolic process;0.0499137677017831;70052,230908,18572,101943!
|ontology_enrichment_celltype=CL:0002242!1.39e-07!16
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004177!1.06e-09!29;UBERON:0005057!1.06e-09!29;UBERON:0000153!2.15e-09!43;UBERON:0001048!2.09e-08!134;UBERON:0002370!1.70e-07!23;UBERON:0000974!1.70e-07!23;UBERON:0004807!1.70e-07!23;UBERON:0005058!1.70e-07!23;UBERON:0003351!1.70e-07!23;UBERON:0009113!1.70e-07!23;UBERON:0003295!1.70e-07!23;UBERON:0009722!1.70e-07!23;UBERON:0005562!1.70e-07!23;UBERON:0007690!1.70e-07!23;UBERON:0000065!5.02e-07!41;UBERON:0000077!6.08e-07!35;UBERON:0006562!6.25e-07!24;UBERON:0001557!6.25e-07!24;UBERON:0001042!6.25e-07!24;UBERON:0008814!6.25e-07!24;UBERON:0009145!6.25e-07!24;UBERON:0007811!7.77e-07!36;UBERON:0000072!8.81e-07!27
|tfbs_overrepresentation_for_novel_motifs=0.860199,0.352573,0.807108,0.360062,0.200163,0.373426,0.458558,0.392928,0.411053,0.771958,1.071,0.447169,0.124608,2.06188,0.214197,0,1.57859,0.19356,0.113609,0.205418,0.26524,0.145076,2.05901,0.198877,0.304728,0.496413,0.107695,0.392919,0.67135,0.572447,0.989437,0.754912,0.191698,0.646834,1.1554,0.6066,0.541514,1.12869,0.166348,0.143746,0.196807,0.38461,0.307718,0.617704,0.249283,0.349801,1.41649,0.407653,0.104497,0.677281,0.639101,0.522137,0.0747297,0.894161,0.911367,1.20022,0.249055,0.435119,0.101408,0.47505,1.74318,0.531188,0.140453,0.628155,0.487593,0.667546,1.04613,1.3932,0.730718,1.24673,0.281085,0.404236,0.996746,0.944464,1.09617,0.623453,0.0942164,0.567793,0.718494,0.268962,0.129727,0.673009,0.529804,0.119727,0.830765,0.318393,0.0149522,0.271714,1.42647,1.55487,1.11522,0.835661,0.767462,0.205117,0.490417,0.149272,0.777003,0.770215,0.57902,1.30903,0.184103,0.754637,0.87698,0.639679,0.638654,0.3842,0.696857,0.403887,0.273261,0.266818,0.315128,0.878738,0.26996,1.08155,1.12221,0.5687,0.212667,0.953611,0.657356,0.181004,0.949798,0.607824,0.498153,0.566919,1.17594,0.722111,0.466292,0.760818,1.04463,0.59809,0.86025,0.353344,1.01535,0.48999,1.14365,0.0358067,0.329172,0.385921,2.47881,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,0.385031,0.581788,1.88287,0.331322,1.73501,0.580497,1.72175,0.895708,0.153911,0.489108,0.976367,2.23719,0.637798,0.319291,1.57707,1.1043,0.829923,0.722546,0.313083,0.629147,0.482049,0.18312,0.445669,0.350088
|tfbs_overrepresentation_jaspar=MA0003.1;1.23085,MA0004.1;0.360508,MA0006.1;1.13936,MA0007.1;0.346734,MA0009.1;0.780842,MA0014.1;0.544988,MA0017.1;0.658116,MA0019.1;0.603066,MA0024.1;0.737933,MA0025.1;1.01089,MA0027.1;2.42079,MA0028.1;2.57895,MA0029.1;0.716673,MA0030.1;0.723093,MA0031.1;0.688336,MA0038.1;0.496338,MA0040.1;0.79313,MA0041.1;0.291712,MA0042.1;0.279998,MA0043.1;0.875991,MA0046.1;0.816137,MA0048.1;0.236433,MA0050.1;0.396459,MA0051.1;0.504875,MA0052.1;0.801048,MA0055.1;0.0660514,MA0056.1;0,MA0057.1;0.471918,MA0058.1;0.752621,MA0059.1;0.28489,MA0060.1;0.8754,MA0061.1;0.504772,MA0063.1;0,MA0066.1;0.485868,MA0067.1;1.12095,MA0068.1;0.22316,MA0069.1;0.801381,MA0070.1;0.791856,MA0071.1;0.395679,MA0072.1;0.783532,MA0073.1;0.0215953,MA0074.1;0.451832,MA0076.1;3.65654,MA0077.1;0.762273,MA0078.1;0.536502,MA0081.1;0.305576,MA0083.1;0.875209,MA0084.1;1.44691,MA0087.1;0.832758,MA0088.1;1.86507,MA0089.1;0,MA0090.1;0.329158,MA0091.1;0.372635,MA0092.1;0.329444,MA0093.1;0.642324,MA0095.1;0,MA0098.1;0,MA0100.1;0.440912,MA0101.1;0.292867,MA0103.1;0.242398,MA0105.1;0.304995,MA0106.1;0.543967,MA0107.1;0.237082,MA0108.2;0.625209,MA0109.1;0,MA0111.1;0.342068,MA0113.1;0.516916,MA0114.1;0.500166,MA0115.1;0.878749,MA0116.1;0.210297,MA0117.1;0.846964,MA0119.1;0.796817,MA0122.1;0.866511,MA0124.1;1.06819,MA0125.1;0.994853,MA0130.1;0,MA0131.1;0.598671,MA0132.1;0,MA0133.1;0,MA0135.1;0.911905,MA0136.1;0.470672,MA0139.1;0.772315,MA0140.1;0.440804,MA0141.1;0.719522,MA0142.1;0.674191,MA0143.1;0.53259,MA0144.1;0.506239,MA0145.1;0.163161,MA0146.1;0.923066,MA0147.1;1.01679,MA0148.1;0.375491,MA0149.1;0.2978,MA0062.2;2.18244,MA0035.2;0.44524,MA0039.2;0.647421,MA0138.2;0.590987,MA0002.2;0.391079,MA0137.2;0.257017,MA0104.2;1.34242,MA0047.2;0.495607,MA0112.2;0.163154,MA0065.2;0.163769,MA0150.1;0.346631,MA0151.1;0,MA0152.1;0.495709,MA0153.1;0.92832,MA0154.1;0.232525,MA0155.1;0.416651,MA0156.1;0.694831,MA0157.1;0.642984,MA0158.1;0,MA0159.1;0.550545,MA0160.1;0.378276,MA0161.1;0,MA0162.1;0.27679,MA0163.1;0.439212,MA0164.1;0.471016,MA0080.2;0.669221,MA0018.2;2.09533,MA0099.2;0.584892,MA0079.2;0.432474,MA0102.2;1.49914,MA0258.1;0.473611,MA0259.1;1.56071,MA0442.1;0
}}

Latest revision as of 15:48, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr15:34425057..34425102,+p1@Pop1
Mm9::chr15:8059322..8059356,+p1@Nup155
Mm9::chr17:35378730..35378782,+p1@Ddx39b
Mm9::chr19:47165238..47165290,+p1@Pdcd11
Mm9::chr4:129318235..129318295,-p1@Txlna
Mm9::chr4:148000865..148000884,-p1@Tardbp
Mm9::chr4:62069804..62069899,+p1@Prpf4
Mm9::chr6:35127610..35127627,+p1@Nup205
Mm9::chr8:113370670..113370698,-p1@Sf3b3
Mm9::chr8:126473101..126473187,-p1@Nup133


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:0005487nucleocytoplasmic transporter activity0.000749205781920186
GO:0051028mRNA transport0.00407034741706452
GO:0050658RNA transport0.00407034741706452
GO:0051236establishment of RNA localization0.00407034741706452
GO:0050657nucleic acid transport0.00407034741706452
GO:0006403RNA localization0.00407034741706452
GO:0005643nuclear pore0.00407034741706452
GO:0065002intracellular protein transport across a membrane0.00407034741706452
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.00407034741706452
GO:0046930pore complex0.00407034741706452
GO:0044453nuclear membrane part0.00429391984070031
GO:0031965nuclear membrane0.00429391984070031
GO:0044428nuclear part0.00746703842105303
GO:0006913nucleocytoplasmic transport0.00746703842105303
GO:0051169nuclear transport0.00746703842105303
GO:0017056structural constituent of nuclear pore0.00764090439970906
GO:0005635nuclear envelope0.00886461988172955
GO:0005681spliceosome0.0143799144534344
GO:0046540U4/U6 x U5 tri-snRNP complex0.0160755416039761
GO:0008380RNA splicing0.0197360766737931
GO:0051649establishment of cellular localization0.0243803738730018
GO:0051641cellular localization0.0244002357987189
GO:0004526ribonuclease P activity0.0248546207161951
GO:0006397mRNA processing0.0248546207161951
GO:0006406mRNA export from nucleus0.0248546207161951
GO:0030532small nuclear ribonucleoprotein complex0.0248546207161951
GO:0043123positive regulation of I-kappaB kinase/NF-kappaB cascade0.0248546207161951
GO:0004549tRNA-specific ribonuclease activity0.0261400419890448
GO:0016071mRNA metabolic process0.027836696568666
GO:0043122regulation of I-kappaB kinase/NF-kappaB cascade0.0284511320653779
GO:0006405RNA export from nucleus0.0294935597533027
GO:0012505endomembrane system0.0328158581290779
GO:0016891endoribonuclease activity, producing 5'-phosphomonoesters0.0369009904895174
GO:0032991macromolecular complex0.0382548377726184
GO:0016893endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters0.0382548377726184
GO:0051168nuclear export0.0388742433313261
GO:0006396RNA processing0.0398025270092647
GO:0031975envelope0.0437951567695661
GO:0031967organelle envelope0.0437951567695661
GO:0006886intracellular protein transport0.0448957993436601
GO:0016070RNA metabolic process0.0499137677017831



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
nucleate cell1.39e-0716


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)
MA0003.11.23085
MA0004.10.360508
MA0006.11.13936
MA0007.10.346734
MA0009.10.780842
MA0014.10.544988
MA0017.10.658116
MA0019.10.603066
MA0024.10.737933
MA0025.11.01089
MA0027.12.42079
MA0028.12.57895
MA0029.10.716673
MA0030.10.723093
MA0031.10.688336
MA0038.10.496338
MA0040.10.79313
MA0041.10.291712
MA0042.10.279998
MA0043.10.875991
MA0046.10.816137
MA0048.10.236433
MA0050.10.396459
MA0051.10.504875
MA0052.10.801048
MA0055.10.0660514
MA0056.10
MA0057.10.471918
MA0058.10.752621
MA0059.10.28489
MA0060.10.8754
MA0061.10.504772
MA0063.10
MA0066.10.485868
MA0067.11.12095
MA0068.10.22316
MA0069.10.801381
MA0070.10.791856
MA0071.10.395679
MA0072.10.783532
MA0073.10.0215953
MA0074.10.451832
MA0076.13.65654
MA0077.10.762273
MA0078.10.536502
MA0081.10.305576
MA0083.10.875209
MA0084.11.44691
MA0087.10.832758
MA0088.11.86507
MA0089.10
MA0090.10.329158
MA0091.10.372635
MA0092.10.329444
MA0093.10.642324
MA0095.10
MA0098.10
MA0100.10.440912
MA0101.10.292867
MA0103.10.242398
MA0105.10.304995
MA0106.10.543967
MA0107.10.237082
MA0108.20.625209
MA0109.10
MA0111.10.342068
MA0113.10.516916
MA0114.10.500166
MA0115.10.878749
MA0116.10.210297
MA0117.10.846964
MA0119.10.796817
MA0122.10.866511
MA0124.11.06819
MA0125.10.994853
MA0130.10
MA0131.10.598671
MA0132.10
MA0133.10
MA0135.10.911905
MA0136.10.470672
MA0139.10.772315
MA0140.10.440804
MA0141.10.719522
MA0142.10.674191
MA0143.10.53259
MA0144.10.506239
MA0145.10.163161
MA0146.10.923066
MA0147.11.01679
MA0148.10.375491
MA0149.10.2978
MA0062.22.18244
MA0035.20.44524
MA0039.20.647421
MA0138.20.590987
MA0002.20.391079
MA0137.20.257017
MA0104.21.34242
MA0047.20.495607
MA0112.20.163154
MA0065.20.163769
MA0150.10.346631
MA0151.10
MA0152.10.495709
MA0153.10.92832
MA0154.10.232525
MA0155.10.416651
MA0156.10.694831
MA0157.10.642984
MA0158.10
MA0159.10.550545
MA0160.10.378276
MA0161.10
MA0162.10.27679
MA0163.10.439212
MA0164.10.471016
MA0080.20.669221
MA0018.22.09533
MA0099.20.584892
MA0079.20.432474
MA0102.21.49914
MA0258.10.473611
MA0259.11.56071
MA0442.10
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