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MCL coexpression mm9:760: Difference between revisions

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{{MCL_coexpression_mm9
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exchange factor activity;0.0242392330827444;102075,110596!GO:0048666;neuron development;0.0242392330827444;110596,18742!GO:0007417;central nervous system development;0.0242392330827444;110596,18742!GO:0030182;neuron differentiation;0.0242392330827444;110596,18742!GO:0030695;GTPase regulator activity;0.0242392330827444;102075,110596!GO:0048699;generation of neurons;0.0242392330827444;110596,18742!GO:0060052;neurofilament cytoskeleton organization and biogenesis;0.0242392330827444;110596!GO:0021955;central nervous system neuron axonogenesis;0.0242392330827444;110596!GO:0022008;neurogenesis;0.0242392330827444;110596,18742!GO:0030901;midbrain development;0.0262535463198016;18742!GO:0045104;intermediate filament cytoskeleton organization and biogenesis;0.0368669614433751;110596!GO:0045103;intermediate filament-based process;0.038522481583093;110596!GO:0021954;central nervous system neuron development;0.038522481583093;110596!GO:0021953;central nervous system neuron 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|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002102!4.58e-09!7;UBERON:0004710!4.58e-09!7;UBERON:0005419!4.58e-09!7;UBERON:0005417!4.58e-09!7;UBERON:0005729!4.58e-09!7;UBERON:0000026!8.74e-09!12;UBERON:0004708!8.74e-09!12;UBERON:0002101!8.74e-09!12;UBERON:0004357!8.74e-09!12;UBERON:0004347!8.74e-09!12;UBERON:0005732!8.74e-09!12;UBERON:0005733!8.74e-09!12;UBERON:0010707!5.49e-08!13;UBERON:0010708!8.02e-08!8
|tfbs_overrepresentation_for_novel_motifs=0.93395,0.227469,0.330161,1.02163,1.20555,1.05171,0.495658,0.146465,0.468136,0.133458,0.453212,0.484001,0.449446,0.507558,0.680035,0,0.696644,0.22065,0.419123,0.528436,0.296085,0.713323,0.50668,0.226287,0.337218,0.534339,0.801525,0.428336,0.268347,0.656973,0.414842,0.796599,1.17111,0.113369,0.242923,0.482999,0.210533,0.480503,0.559915,0.500908,0.224094,0.419787,0.163087,0.244285,0.536558,0.383899,0.618203,0.443479,0.573356,0.745859,0.679429,0.560572,0.30602,0.937018,0.954342,0.514504,0.764433,1.18878,0.384731,0.512521,0.776777,0.569793,0.952934,0.668331,0.525334,0.708248,1.08987,1.43807,0.772155,1.29123,0.31262,0.900535,0.424998,0.987652,0.116281,0.107966,1.20707,0.607043,0.759798,0.299972,0.463363,0.713779,0.568383,0.14134,0.873141,0.0800961,0.0211263,1.09342,0.623015,1.60001,1.15927,0.878077,0.809272,0.232894,0.188213,0.991864,0.871972,0.812053,0.618454,0.278788,0.210602,0.796322,0.919715,0.680015,0.678976,0.419366,0.737915,0.439611,0.821842,0.297733,0.348012,0.921485,0.301014,1.15983,1.16629,0.222515,0.0259088,1.02946,0.697928,0.207304,0.993019,0.647706,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.235546,0.90286,0.387557,1.05894,0.527782,1.18781,0.398576,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,0.621266,1.92834,0.956381,0.229209,0.32395,0.369078,0.938577,1.01208,0.526881,1.01974,0.561556,0.253271,0.352329,0.950885,1.1483,0.872292,0.763895,0.914544,0.669337,0.519673,1.77857,0.482466,0.442118
|tfbs_overrepresentation_jaspar=MA0003.1;0.0854318,MA0004.1;0.394951,MA0006.1;0.238555,MA0007.1;0.38073,MA0009.1;0.82278,MA0014.1;0.0421798,MA0017.1;0.26239,MA0019.1;0.642876,MA0024.1;0.779446,MA0025.1;1.05446,MA0027.1;2.46647,MA0028.1;0.24786,MA0029.1;0.757957,MA0030.1;0.764448,MA0031.1;0.729293,MA0038.1;0.534262,MA0040.1;0.835181,MA0041.1;0.323687,MA0042.1;0.837668,MA0043.1;2.12026,MA0046.1;0.858391,MA0048.1;0.281053,MA0050.1;0.431976,MA0051.1;0.542972,MA0052.1;0.84317,MA0055.1;0.0198867,MA0056.1;0,MA0057.1;0.549903,MA0058.1;0.305206,MA0059.1;0.316585,MA0060.1;0.169058,MA0061.1;1.07655,MA0063.1;0,MA0066.1;0.523573,MA0067.1;1.16502,MA0068.1;1.4268,MA0069.1;0.843506,MA0070.1;0.833895,MA0071.1;0.431174,MA0072.1;0.825495,MA0073.1;2.88566,MA0074.1;0.488775,MA0076.1;0.279739,MA0077.1;1.88507,MA0078.1;0.575205,MA0081.1;0.338098,MA0083.1;0.917931,MA0084.1;1.49188,MA0087.1;0.87515,MA0088.1;0.413524,MA0089.1;0,MA0090.1;0.362551,MA0091.1;0.407455,MA0092.1;0.362847,MA0093.1;0.2553,MA0095.1;0,MA0098.1;0,MA0100.1;0.477594,MA0101.1;0.324888,MA0103.1;0.272167,MA0105.1;0.720048,MA0106.1;0.582805,MA0107.1;0.73569,MA0108.2;0.665343,MA0109.1;0,MA0111.1;0.375908,MA0113.1;0.555251,MA0114.1;0.19245,MA0115.1;0.921497,MA0116.1;0.238371,MA0117.1;0.88947,MA0119.1;0.868953,MA0122.1;0.909168,MA0124.1;1.11203,MA0125.1;1.03833,MA0130.1;0,MA0131.1;0.638414,MA0132.1;0,MA0133.1;0,MA0135.1;0.954884,MA0136.1;0.508047,MA0139.1;0.143341,MA0140.1;0.477483,MA0141.1;0.29014,MA0142.1;0.714976,MA0143.1;0.571221,MA0144.1;0.195095,MA0145.1;0.200183,MA0146.1;0.148686,MA0147.1;0.205697,MA0148.1;1.05634,MA0149.1;0.879199,MA0062.2;0.113962,MA0035.2;0.482026,MA0039.2;0.0946163,MA0138.2;0.630612,MA0002.2;0.877049,MA0137.2;0.287486,MA0104.2;0.157347,MA0047.2;0.533516,MA0112.2;0.200175,MA0065.2;0.44341,MA0150.1;0.380623,MA0151.1;0,MA0152.1;0.53362,MA0153.1;0.971406,MA0154.1;0.581988,MA0155.1;0.226288,MA0156.1;0.278949,MA0157.1;0.683365,MA0158.1;0,MA0159.1;0.214506,MA0160.1;0.413266,MA0161.1;0,MA0162.1;0.176565,MA0163.1;0.160428,MA0164.1;0.508398,MA0080.2;0.267388,MA0018.2;0.51781,MA0099.2;0.624421,MA0079.2;1.32649,MA0102.2;1.5442,MA0258.1;0.180934,MA0259.1;0.196451,MA0442.1;0
}}

Latest revision as of 15:50, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:23069666..23069687,-p5@Eya4
Mm9::chr10:37035191..37035196,+p@chr10:37035191..37035196
+
Mm9::chr13:98786130..98786139,-p11@Rgnef
Mm9::chr14:112177430..112177435,-p@chr14:112177430..112177435
-
Mm9::chr3:66023831..66023849,+p2@Ptx3
Mm9::chr3:66023864..66023873,+p3@Ptx3
Mm9::chr3:66029440..66029442,+p@chr3:66029440..66029442
+
Mm9::chr4:140268695..140268697,+p@chr4:140268695..140268697
+
Mm9::chr8:107897165..107897177,+p1@Plekhg4


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:0005085guanyl-nucleotide exchange factor activity0.0242392330827444
GO:0048666neuron development0.0242392330827444
GO:0007417central nervous system development0.0242392330827444
GO:0030182neuron differentiation0.0242392330827444
GO:0030695GTPase regulator activity0.0242392330827444
GO:0048699generation of neurons0.0242392330827444
GO:0060052neurofilament cytoskeleton organization and biogenesis0.0242392330827444
GO:0021955central nervous system neuron axonogenesis0.0242392330827444
GO:0022008neurogenesis0.0242392330827444
GO:0030901midbrain development0.0262535463198016
GO:0045104intermediate filament cytoskeleton organization and biogenesis0.0368669614433751
GO:0045103intermediate filament-based process0.038522481583093
GO:0021954central nervous system neuron development0.038522481583093
GO:0021953central nervous system neuron differentiation0.0408709206211934
GO:0007275multicellular organismal development0.0421558894881009
GO:0007399nervous system development0.0447041300673786



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
forelimb4.58e-097
pectoral appendage4.58e-097
pectoral appendage bud4.58e-097
forelimb bud4.58e-097
forelimb/pectoral fin field4.58e-097
appendage8.74e-0912
paired limb/fin8.74e-0912
limb8.74e-0912
paired limb/fin bud8.74e-0912
limb bud8.74e-0912
limb/fin field8.74e-0912
limb field8.74e-0912
appendage girdle complex5.49e-0813
pectoral complex8.02e-088


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)
MA0003.10.0854318
MA0004.10.394951
MA0006.10.238555
MA0007.10.38073
MA0009.10.82278
MA0014.10.0421798
MA0017.10.26239
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.10.24786
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.10.534262
MA0040.10.835181
MA0041.10.323687
MA0042.10.837668
MA0043.12.12026
MA0046.10.858391
MA0048.10.281053
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.10.0198867
MA0056.10
MA0057.10.549903
MA0058.10.305206
MA0059.10.316585
MA0060.10.169058
MA0061.11.07655
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.11.4268
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.12.88566
MA0074.10.488775
MA0076.10.279739
MA0077.11.88507
MA0078.10.575205
MA0081.10.338098
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.413524
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.362847
MA0093.10.2553
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.324888
MA0103.10.272167
MA0105.10.720048
MA0106.10.582805
MA0107.10.73569
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.10.19245
MA0115.10.921497
MA0116.10.238371
MA0117.10.88947
MA0119.10.868953
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.10.638414
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.143341
MA0140.10.477483
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.10.195095
MA0145.10.200183
MA0146.10.148686
MA0147.10.205697
MA0148.11.05634
MA0149.10.879199
MA0062.20.113962
MA0035.20.482026
MA0039.20.0946163
MA0138.20.630612
MA0002.20.877049
MA0137.20.287486
MA0104.20.157347
MA0047.20.533516
MA0112.20.200175
MA0065.20.44341
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.581988
MA0155.10.226288
MA0156.10.278949
MA0157.10.683365
MA0158.10
MA0159.10.214506
MA0160.10.413266
MA0161.10
MA0162.10.176565
MA0163.10.160428
MA0164.10.508398
MA0080.20.267388
MA0018.20.51781
MA0099.20.624421
MA0079.21.32649
MA0102.21.5442
MA0258.10.180934
MA0259.10.196451
MA0442.10
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