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MCL coexpression mm9:605: Difference between revisions

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{{MCL_coexpression_mm9
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ion binding;0.0101926500573792;22758,94093,22757,244219,22646,22697!GO:0005643;nuclear pore;0.0101926500573792;16211,19069!GO:0046930;pore complex;0.0101926500573792;16211,19069!GO:0044453;nuclear membrane part;0.0101926500573792;16211,19069!GO:0046914;transition metal ion binding;0.0101926500573792;22758,94093,22757,244219,22646,22697!GO:0031965;nuclear membrane;0.0101926500573792;16211,19069!GO:0003676;nucleic acid binding;0.0154739663567033;22758,94093,22757,244219,22646,22697!GO:0005634;nucleus;0.0154739663567033;22758,16211,94093,19069,22757,244219,22697!GO:0005635;nuclear envelope;0.0154739663567033;16211,19069!GO:0006355;regulation of transcription, DNA-dependent;0.0154739663567033;22758,94093,22757,244219,22697!GO:0006351;transcription, DNA-dependent;0.0154739663567033;22758,94093,22757,244219,22697!GO:0032774;RNA biosynthetic process;0.0154739663567033;22758,94093,22757,244219,22697!GO:0003677;DNA binding;0.0154739663567033;22758,94093,22757,244219,22697!GO:0045449;regulation of transcription;0.0154739663567033;22758,94093,22757,244219,22697!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0156932195626997;22758,94093,22757,244219,22697!GO:0006350;transcription;0.0156932195626997;22758,94093,22757,244219,22697!GO:0010468;regulation of gene expression;0.0171464204925708;22758,94093,22757,244219,22697!GO:0006610;ribosomal protein import into nucleus;0.0174735340687904;16211!GO:0031323;regulation of cellular metabolic process;0.0174735340687904;22758,94093,22757,244219,22697!GO:0043169;cation binding;0.0174735340687904;22758,94093,22757,244219,22646,22697!GO:0019222;regulation of metabolic process;0.0195620152981443;22758,94093,22757,244219,22697!GO:0016070;RNA metabolic process;0.0209717005586246;22758,94093,22757,244219,22697!GO:0046872;metal ion binding;0.0234416485775474;22758,94093,22757,244219,22646,22697!GO:0043167;ion binding;0.0250128630190543;22758,94093,22757,244219,22646,22697!GO:0003700;transcription 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|gostat_on_MCL_coexpression=GO:0008270;zinc ion binding;0.0101926500573792;22758,94093,22757,244219,22646,22697!GO:0005643;nuclear pore;0.0101926500573792;16211,19069!GO:0046930;pore complex;0.0101926500573792;16211,19069!GO:0044453;nuclear membrane part;0.0101926500573792;16211,19069!GO:0046914;transition metal ion binding;0.0101926500573792;22758,94093,22757,244219,22646,22697!GO:0031965;nuclear membrane;0.0101926500573792;16211,19069!GO:0003676;nucleic acid binding;0.0154739663567033;22758,94093,22757,244219,22646,22697!GO:0005634;nucleus;0.0154739663567033;22758,16211,94093,19069,22757,244219,22697!GO:0005635;nuclear envelope;0.0154739663567033;16211,19069!GO:0006355;regulation of transcription, DNA-dependent;0.0154739663567033;22758,94093,22757,244219,22697!GO:0006351;transcription, DNA-dependent;0.0154739663567033;22758,94093,22757,244219,22697!GO:0032774;RNA biosynthetic process;0.0154739663567033;22758,94093,22757,244219,22697!GO:0003677;DNA binding;0.0154739663567033;22758,94093,22757,244219,22697!GO:0045449;regulation of transcription;0.0154739663567033;22758,94093,22757,244219,22697!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0156932195626997;22758,94093,22757,244219,22697!GO:0006350;transcription;0.0156932195626997;22758,94093,22757,244219,22697!GO:0010468;regulation of gene expression;0.0171464204925708;22758,94093,22757,244219,22697!GO:0006610;ribosomal protein import into nucleus;0.0174735340687904;16211!GO:0031323;regulation of cellular metabolic process;0.0174735340687904;22758,94093,22757,244219,22697!GO:0043169;cation binding;0.0174735340687904;22758,94093,22757,244219,22646,22697!GO:0019222;regulation of metabolic process;0.0195620152981443;22758,94093,22757,244219,22697!GO:0016070;RNA metabolic process;0.0209717005586246;22758,94093,22757,244219,22697!GO:0046872;metal ion binding;0.0234416485775474;22758,94093,22757,244219,22646,22697!GO:0043167;ion binding;0.0250128630190543;22758,94093,22757,244219,22646,22697!GO:0003700;transcription factor activity;0.0371678022108795;22758,22757,22697!GO:0000059;protein import into nucleus, docking;0.0371678022108795;16211!GO:0010467;gene expression;0.0375873581488371;22758,94093,22757,244219,22697!GO:0012505;endomembrane system;0.0441447714819657;16211,19069!GO:0048477;oogenesis;0.046583082755119;22697!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000468!2.37e-08!333;UBERON:0000991!1.28e-07!18;UBERON:0005564!1.28e-07!18;UBERON:0004176!4.18e-07!17;UBERON:0009196!4.18e-07!17;UBERON:0009117!4.18e-07!17;UBERON:0000922!4.73e-07!320
|tfbs_overrepresentation_for_novel_motifs=1.35389,0.2332,0.686572,0.818969,0.1565,0.315748,1.02601,0.303924,0.658686,0.336879,0.939294,0.385627,1.05446,1.05028,0.169024,0,1.43434,0.150639,0.279039,0.33293,0.215242,0.0948826,1.04849,0.155356,0.701128,0.432737,0.0768517,0.334131,0.558665,0.766158,0.321757,0.683831,0.14899,0.234079,0.169391,0.130126,1.39042,0.995071,0.126724,0.347926,0.153518,0.870859,0.0834993,0.508662,1.99457,0.797213,0.512146,0.919381,0.0642028,0.564214,0.570705,0.457464,0.419161,0.82076,0.837732,1.06445,0.200484,0.977003,0.250759,1.0604,0.664611,1.17701,0.104381,0.560059,0.424276,1.45782,0.970969,1.3158,0.660133,1.17005,0.229771,0.313987,9.42818,0.870406,0.883633,0.835139,0.233965,0.50152,0.648171,0.218647,0.0952669,0.60374,0.464847,0.0868537,0.758319,2.31993,0.0395547,0.43877,1.28512,1.47691,1.03946,0.763136,0.696137,0.16091,5.66615,0.11194,0.299765,0.698838,0.512384,0.0434558,0.862562,0.683562,0.803823,0.571268,0.57027,0.869995,0.627019,0.344504,1.84928,1.16343,0.261228,0.805555,0.219561,0.949483,1.04639,0.463309,0.278854,0.826326,0.58848,0.139554,0.875675,0.540309,0.434408,0.500675,1.09972,0.651709,0.403884,0.689622,0.969481,0.163147,0.787341,0.296885,0.940498,0.426575,1.06766,0.0212043,0.274293,0.327523,1.01927,1.84381,1.44523,0.975592,0.445463,0.693891,1.38563,0.326684,0.515065,1.80426,0.276297,0.477267,1.18603,8.05334,0.822286,0.115938,0.425729,0.901933,0.458393,0.178202,0.265096,2.11874,1.02862,0.757491,0.652135,0.25933,0.561023,0.418964,0.141416,0.384198,0.365903
}}

Latest revision as of 15:35, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:70783455..70783480,-p1@Nup88
Mm9::chr11:93747451..93747468,+p4@Mbtd1
Mm9::chr11:97048962..97048994,-p5@Kpnb1
Mm9::chr13:21454695..21454752,+p1@Zscan12
Mm9::chr15:98957049..98957071,+p4@Spats2
Mm9::chr3:103083772..103083796,+p@chr3:103083772..103083796
+
Mm9::chr5:138558139..138558214,+p1@Zscan21
Mm9::chr5:145965392..145965443,+p1@Zkscan5
Mm9::chr7:135019439..135019462,+p@chr7:135019439..135019462
+
Mm9::chr7:54051401..54051455,-p2@Hps5
Mm9::chr9:122832168..122832210,+p1@Zfp105
Mm9::chrX:109714433..109714444,+p2@Zfp711


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:0008270zinc ion binding0.0101926500573792
GO:0005643nuclear pore0.0101926500573792
GO:0046930pore complex0.0101926500573792
GO:0044453nuclear membrane part0.0101926500573792
GO:0046914transition metal ion binding0.0101926500573792
GO:0031965nuclear membrane0.0101926500573792
GO:0003676nucleic acid binding0.0154739663567033
GO:0005634nucleus0.0154739663567033
GO:0005635nuclear envelope0.0154739663567033
GO:0006355regulation of transcription, DNA-dependent0.0154739663567033
GO:0006351transcription, DNA-dependent0.0154739663567033
GO:0032774RNA biosynthetic process0.0154739663567033
GO:0003677DNA binding0.0154739663567033
GO:0045449regulation of transcription0.0154739663567033
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0156932195626997
GO:0006350transcription0.0156932195626997
GO:0010468regulation of gene expression0.0171464204925708
GO:0006610ribosomal protein import into nucleus0.0174735340687904
GO:0031323regulation of cellular metabolic process0.0174735340687904
GO:0043169cation binding0.0174735340687904
GO:0019222regulation of metabolic process0.0195620152981443
GO:0016070RNA metabolic process0.0209717005586246
GO:0046872metal ion binding0.0234416485775474
GO:0043167ion binding0.0250128630190543
GO:0003700transcription factor activity0.0371678022108795
GO:0000059protein import into nucleus, docking0.0371678022108795
GO:0010467gene expression0.0375873581488371
GO:0012505endomembrane system0.0441447714819657
GO:0048477oogenesis0.046583082755119



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
multi-cellular organism2.37e-08333
gonad1.28e-0718
gonad primordium1.28e-0718
external genitalia4.18e-0717
indifferent external genitalia4.18e-0717
indifferent gonad4.18e-0717
embryo4.73e-07320


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)
MA0003.13.86695
MA0004.10.819913
MA0006.10.496735
MA0007.11.43999
MA0009.10.709264
MA0014.12.06593
MA0017.10.186015
MA0019.10.535691
MA0024.10.667197
MA0025.10.936082
MA0027.12.34178
MA0028.12.24825
MA0029.10.64639
MA0030.10.65267
MA0031.10.618697
MA0038.10.432665
MA0040.10.721328
MA0041.10.673209
MA0042.10.648006
MA0043.10.802848
MA0046.10.743934
MA0048.10.680396
MA0050.10.337476
MA0051.10.440863
MA0052.10.729105
MA0055.10.624457
MA0056.10
MA0057.11.40292
MA0058.11.18867
MA0059.10.658541
MA0060.11.7211
MA0061.10.129002
MA0063.10
MA0066.10.422624
MA0067.11.04514
MA0068.11.00777
MA0069.10.729433
MA0070.10.720077
MA0071.10.336739
MA0072.10.711905
MA0073.12.71868
MA0074.11.01196
MA0076.13.24198
MA0077.10.691048
MA0078.10.471303
MA0081.10.252371
MA0083.10.802078
MA0084.11.3693
MA0087.10.760279
MA0088.10.459114
MA0089.10
MA0090.10.27428
MA0091.10.315003
MA0092.10.274547
MA0093.11.01857
MA0095.10
MA0098.10
MA0100.10.989129
MA0101.10.240622
MA0103.10.19444
MA0105.10.226879
MA0106.10.478503
MA0107.10.555009
MA0108.20.557195
MA0109.10
MA0111.10.78079
MA0113.10.452439
MA0114.10.400482
MA0115.10.805567
MA0116.10.496352
MA0117.10.774259
MA0119.10.241106
MA0122.10.793507
MA0124.10.992825
MA0125.10.920215
MA0130.10
MA0131.10.531427
MA0132.10
MA0133.10
MA0135.10.838263
MA0136.10.408073
MA0139.10.297344
MA0140.10.379562
MA0141.10.210047
MA0142.10.604892
MA0143.10.467531
MA0144.10.129525
MA0145.10.793629
MA0146.10.436286
MA0147.10.845188
MA0148.10.317692
MA0149.11.27195
MA0062.23.02214
MA0035.20.383789
MA0039.20.701947
MA0138.20.523978
MA0002.20.302282
MA0137.20.207733
MA0104.21.63782
MA0047.20.431964
MA0112.20.793603
MA0065.20.265926
MA0150.10.290598
MA0151.10
MA0152.10.432062
MA0153.10.854464
MA0154.10.376318
MA0155.10.30272
MA0156.10.580656
MA0157.10.574484
MA0158.10
MA0159.10.145521
MA0160.10.320315
MA0161.10
MA0162.10.748622
MA0163.10.692813
MA0164.10.408402
MA0080.20.556674
MA0018.20.417217
MA0099.20.518072
MA0079.23.07806
MA0102.21.42135
MA0258.10.376353
MA0259.11.31847
MA0442.10
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