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MCL coexpression mm9:407: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0009569!3.50e-10!66;UBERON:0005177!2.18e-09!79;UBERON:0000468!1.16e-08!333;UBERON:0002100!2.13e-08!90;UBERON:0000922!3.48e-08!320;UBERON:0000464!4.22e-08!57;UBERON:0001008!1.99e-07!19;UBERON:0006554!2.29e-07!18;UBERON:0000489!2.83e-07!21;UBERON:0005156!3.28e-07!26;UBERON:0000990!3.28e-07!26;UBERON:0005178!4.14e-07!17;UBERON:0005181!4.14e-07!17;UBERON:0002224!4.14e-07!17;UBERON:0000915!4.14e-07!17;UBERON:0008947!4.14e-07!17;UBERON:0003258!4.14e-07!17;UBERON:0002113!7.79e-07!14;UBERON:0003918!7.79e-07!14;UBERON:0011143!7.79e-07!14;UBERON:0005095!7.79e-07!14;UBERON:0007687!7.79e-07!14
|ontology_enrichment_uberon=UBERON:0009569!3.50e-10!66;UBERON:0005177!2.18e-09!79;UBERON:0000468!1.16e-08!333;UBERON:0002100!2.13e-08!90;UBERON:0000922!3.48e-08!320;UBERON:0000464!4.22e-08!57;UBERON:0001008!1.99e-07!19;UBERON:0006554!2.29e-07!18;UBERON:0000489!2.83e-07!21;UBERON:0005156!3.28e-07!26;UBERON:0000990!3.28e-07!26;UBERON:0005178!4.14e-07!17;UBERON:0005181!4.14e-07!17;UBERON:0002224!4.14e-07!17;UBERON:0000915!4.14e-07!17;UBERON:0008947!4.14e-07!17;UBERON:0003258!4.14e-07!17;UBERON:0002113!7.79e-07!14;UBERON:0003918!7.79e-07!14;UBERON:0011143!7.79e-07!14;UBERON:0005095!7.79e-07!14;UBERON:0007687!7.79e-07!14
|tfbs_overrepresentation_for_novel_motifs=0.149902,0.327473,0.133309,0.178048,0.0709145,1.05122,0.708527,1.28332,0.035291,5.24829,1.18299,0.24561,0.30879,0.73029,0.271754,0,0.42315,0.511529,0.514215,0.951721,0.111207,0.153134,1.34044,0.246461,0.138033,0.285776,0.106674,0.202945,0.0941661,0.0685294,0.192916,0.512187,0.868591,0.0199181,0.0793793,10.5145,1.76234,0.680922,0.052341,3.68633,0.243076,0.196576,0.0569041,0.0801495,0.115796,0.508392,0.355451,1.15441,0.0966826,0.095769,0.408111,0.307229,0.063174,0.641205,0.657376,0.269785,0.330626,0.23598,0.0226113,0.739389,0.494318,1.52699,0.0394494,0.398468,0.762935,0.433342,0.785371,1.12243,0.490165,3.68026,0.386078,0.58423,6.97413,0.6886,0.0208952,4.51296,0.0199002,0.346003,0.479091,2.39503,5.49015,0.438213,0.31368,0.861077,0.582029,6.62901,1.82764,10.7523,1.68475,1.2816,0.851763,0.586575,0.523661,0.256716,0.189143,0.0436985,2.2116,0.526183,0.936209,0.0106182,0.222463,3.24532,0.625103,0.408622,1.85099,3.19998,0.459578,1.14305,0.749789,0.112248,0.145352,0.626748,0.739879,0.640523,0.858505,0.068143,2.04632,1.02142,0.424276,0.0601654,0.693645,0.380657,0.287218,0.345253,0.910454,2.10244,0.722986,4.41637,0.783932,0.0752496,0.609469,0.173056,0.75595,0.280468,0.879201,1.24458,0.15539,1.08889,0.832159,1.64606,1.25025,0.789841,0.296788,0.521565,0.402166,0.572489,0.358053,1.60668,0.156941,2.48518,1.25243,7.0291,0.642658,0.0459937,0.27974,0.718834,0.30804,0.085296,0.14831,0.155206,0.841238,0.581248,0.482758,0.869484,1.03222,1.37878,0.220881,0.244407,4.66833
|tfbs_overrepresentation_for_novel_motifs=0.149902,0.327473,0.133309,0.178048,0.0709145,1.05122,0.708527,1.28332,0.035291,5.24829,1.18299,0.24561,0.30879,0.73029,0.271754,0,0.42315,0.511529,0.514215,0.951721,0.111207,0.153134,1.34044,0.246461,0.138033,0.285776,0.106674,0.202945,0.0941661,0.0685294,0.192916,0.512187,0.868591,0.0199181,0.0793793,10.5145,1.76234,0.680922,0.052341,3.68633,0.243076,0.196576,0.0569041,0.0801495,0.115796,0.508392,0.355451,1.15441,0.0966826,0.095769,0.408111,0.307229,0.063174,0.641205,0.657376,0.269785,0.330626,0.23598,0.0226113,0.739389,0.494318,1.52699,0.0394494,0.398468,0.762935,0.433342,0.785371,1.12243,0.490165,3.68026,0.386078,0.58423,6.97413,0.6886,0.0208952,4.51296,0.0199002,0.346003,0.479091,2.39503,5.49015,0.438213,0.31368,0.861077,0.582029,6.62901,1.82764,10.7523,1.68475,1.2816,0.851763,0.586575,0.523661,0.256716,0.189143,0.0436985,2.2116,0.526183,0.936209,0.0106182,0.222463,3.24532,0.625103,0.408622,1.85099,3.19998,0.459578,1.14305,0.749789,0.112248,0.145352,0.626748,0.739879,0.640523,0.858505,0.068143,2.04632,1.02142,0.424276,0.0601654,0.693645,0.380657,0.287218,0.345253,0.910454,2.10244,0.722986,4.41637,0.783932,0.0752496,0.609469,0.173056,0.75595,0.280468,0.879201,1.24458,0.15539,1.08889,0.832159,1.64606,1.25025,0.789841,0.296788,0.521565,0.402166,0.572489,0.358053,1.60668,0.156941,2.48518,1.25243,7.0291,0.642658,0.0459937,0.27974,0.718834,0.30804,0.085296,0.14831,0.155206,0.841238,0.581248,0.482758,0.869484,1.03222,1.37878,0.220881,0.244407,4.66833
|tfbs_overrepresentation_jaspar=MA0003.1;0.487861,MA0004.1;0.178381,MA0006.1;3.22261,MA0007.1;0.168178,MA0009.1;0.535932,MA0014.1;0.0736541,MA0017.1;3.46285,MA0019.1;0.376509,MA0024.1;0.496718,MA0025.1;0.751694,MA0027.1;2.14278,MA0028.1;0.0821841,MA0029.1;0.477444,MA0030.1;0.483253,MA0031.1;0.451927,MA0038.1;0.285714,MA0040.1;0.547233,MA0041.1;0.404719,MA0042.1;0.121046,MA0043.1;0.624178,MA0046.1;0.568473,MA0048.1;0.145518,MA0050.1;1.12066,MA0051.1;0.2928,MA0052.1;1.36531,MA0055.1;9.35232,MA0056.1;0,MA0057.1;0.700684,MA0058.1;0.117003,MA0059.1;0.124358,MA0060.1;1.02438,MA0061.1;0.198315,MA0063.1;0,MA0066.1;0.277072,MA0067.1;0.857286,MA0068.1;0.0481248,MA0069.1;0.554839,MA0070.1;1.34738,MA0071.1;0.20507,MA0072.1;0.538403,MA0073.1;5.63812e-07,MA0074.1;0.249359,MA0076.1;0.101055,MA0077.1;0.518913,MA0078.1;0.319336,MA0081.1;0.138626,MA0083.1;12.3246,MA0084.1;1.1752,MA0087.1;0.583879,MA0088.1;0.476626,MA0089.1;0,MA0090.1;0.917865,MA0091.1;0.187483,MA0092.1;0.471747,MA0093.1;0.0864726,MA0095.1;0,MA0098.1;0,MA0100.1;0.675637,MA0101.1;0.12981,MA0103.1;0.0964586,MA0105.1;0.0188009,MA0106.1;0.325663,MA0107.1;0.093115,MA0108.2;0.395878,MA0109.1;0,MA0111.1;0.164756,MA0113.1;0.302851,MA0114.1;1.62985,MA0115.1;0.626759,MA0116.1;0.076822,MA0117.1;0.597086,MA0119.1;0.130171,MA0122.1;0.615314,MA0124.1;0.80652,MA0125.1;0.736412,MA0130.1;0,MA0131.1;2.60364,MA0132.1;0,MA0133.1;0,MA0135.1;0.657882,MA0136.1;0.264624,MA0139.1;0.872959,MA0140.1;1.25438,MA0141.1;0.10748,MA0142.1;0.439269,MA0143.1;0.31603,MA0144.1;0.19926,MA0145.1;0.0269479,MA0146.1;0.00163181,MA0147.1;1.23635,MA0148.1;0.555053,MA0149.1;0.133214,MA0062.2;0.0201154,MA0035.2;0.244063,MA0039.2;0.00524431,MA0138.2;0.366012,MA0002.2;0.886864,MA0137.2;0.3443,MA0104.2;1.83601,MA0047.2;0.285109,MA0112.2;2.16314,MA0065.2;0.524507,MA0150.1;0.168102,MA0151.1;0,MA0152.1;0.778204,MA0153.1;0.67335,MA0154.1;0.0104371,MA0155.1;0.034627,MA0156.1;0.100572,MA0157.1;0.411541,MA0158.1;0,MA0159.1;0.0638985,MA0160.1;0.191754,MA0161.1;0,MA0162.1;0.710666,MA0163.1;1.09217,MA0164.1;0.264905,MA0080.2;0.0935932,MA0018.2;0.272436,MA0099.2;0.360735,MA0079.2;2.60165,MA0102.2;1.22663,MA0258.1;2.05467,MA0259.1;1.65933,MA0442.1;0
}}
}}

Revision as of 11:42, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr7:77497803..77497808,-p@chr7:77497803..77497808
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Mm9::chr7:77498870..77498885,-p@chr7:77498870..77498885
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Mm9::chr7:77499419..77499424,-p@chr7:77499419..77499424
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Mm9::chr7:77499564..77499602,-p@chr7:77499564..77499602
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Mm9::chr7:77505617..77505632,-p1@Nr2f2
Mm9::chr7:77506311..77506323,-p@chr7:77506311..77506323
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Mm9::chr7:77506341..77506350,-p@chr7:77506341..77506350
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Mm9::chr7:77506414..77506435,-p@chr7:77506414..77506435
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Mm9::chr7:77506457..77506462,-p@chr7:77506457..77506462
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Mm9::chr7:77506483..77506497,-p@chr7:77506483..77506497
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Mm9::chr7:77506520..77506570,-p@chr7:77506520..77506570
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Mm9::chr7:77506586..77506593,-p@chr7:77506586..77506593
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Mm9::chr7:77506609..77506634,-p@chr7:77506609..77506634
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Mm9::chr7:77506636..77506663,-p@chr7:77506636..77506663
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Mm9::chr7:77506683..77506696,-p@chr7:77506683..77506696
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Mm9::chr7:77511234..77511302,-p2@Nr2f2
Mm9::chr7:77511311..77511352,-p4@Nr2f2
Mm9::chr7:77511403..77511450,-p3@Nr2f2
Mm9::chr7:77511622..77511657,-p5@Nr2f2


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

no results for this coexpression

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
non-terminally differentiated cell6.16e-0749
ectodermal cell7.16e-0744
neurectodermal cell7.16e-0744
neural cell9.48e-0743

Uber Anatomy
Ontology termp-valuen
subdivision of trunk3.50e-1066
trunk region element2.18e-0979
multi-cellular organism1.16e-08333
trunk2.13e-0890
embryo3.48e-08320
anatomical space4.22e-0857
renal system1.99e-0719
urinary system structure2.29e-0718
cavitated compound organ2.83e-0721
reproductive structure3.28e-0726
reproductive system3.28e-0726
thoracic cavity element4.14e-0717
thoracic segment organ4.14e-0717
thoracic cavity4.14e-0717
thoracic segment of trunk4.14e-0717
respiratory primordium4.14e-0717
endoderm of foregut4.14e-0717
kidney7.79e-0714
kidney mesenchyme7.79e-0714
upper urinary tract7.79e-0714
kidney rudiment7.79e-0714
kidney field7.79e-0714


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)
MA0003.10.487861
MA0004.10.178381
MA0006.13.22261
MA0007.10.168178
MA0009.10.535932
MA0014.10.0736541
MA0017.13.46285
MA0019.10.376509
MA0024.10.496718
MA0025.10.751694
MA0027.12.14278
MA0028.10.0821841
MA0029.10.477444
MA0030.10.483253
MA0031.10.451927
MA0038.10.285714
MA0040.10.547233
MA0041.10.404719
MA0042.10.121046
MA0043.10.624178
MA0046.10.568473
MA0048.10.145518
MA0050.11.12066
MA0051.10.2928
MA0052.11.36531
MA0055.19.35232
MA0056.10
MA0057.10.700684
MA0058.10.117003
MA0059.10.124358
MA0060.11.02438
MA0061.10.198315
MA0063.10
MA0066.10.277072
MA0067.10.857286
MA0068.10.0481248
MA0069.10.554839
MA0070.11.34738
MA0071.10.20507
MA0072.10.538403
MA0073.15.63812e-07
MA0074.10.249359
MA0076.10.101055
MA0077.10.518913
MA0078.10.319336
MA0081.10.138626
MA0083.112.3246
MA0084.11.1752
MA0087.10.583879
MA0088.10.476626
MA0089.10
MA0090.10.917865
MA0091.10.187483
MA0092.10.471747
MA0093.10.0864726
MA0095.10
MA0098.10
MA0100.10.675637
MA0101.10.12981
MA0103.10.0964586
MA0105.10.0188009
MA0106.10.325663
MA0107.10.093115
MA0108.20.395878
MA0109.10
MA0111.10.164756
MA0113.10.302851
MA0114.11.62985
MA0115.10.626759
MA0116.10.076822
MA0117.10.597086
MA0119.10.130171
MA0122.10.615314
MA0124.10.80652
MA0125.10.736412
MA0130.10
MA0131.12.60364
MA0132.10
MA0133.10
MA0135.10.657882
MA0136.10.264624
MA0139.10.872959
MA0140.11.25438
MA0141.10.10748
MA0142.10.439269
MA0143.10.31603
MA0144.10.19926
MA0145.10.0269479
MA0146.10.00163181
MA0147.11.23635
MA0148.10.555053
MA0149.10.133214
MA0062.20.0201154
MA0035.20.244063
MA0039.20.00524431
MA0138.20.366012
MA0002.20.886864
MA0137.20.3443
MA0104.21.83601
MA0047.20.285109
MA0112.22.16314
MA0065.20.524507
MA0150.10.168102
MA0151.10
MA0152.10.778204
MA0153.10.67335
MA0154.10.0104371
MA0155.10.034627
MA0156.10.100572
MA0157.10.411541
MA0158.10
MA0159.10.0638985
MA0160.10.191754
MA0161.10
MA0162.10.710666
MA0163.11.09217
MA0164.10.264905
MA0080.20.0935932
MA0018.20.272436
MA0099.20.360735
MA0079.22.60165
MA0102.21.22663
MA0258.12.05467
MA0259.11.65933
MA0442.10
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