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MCL coexpression mm9:949: Difference between revisions

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{{MCL_coexpression_mm9
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of transcription, DNA-dependent;0.000846250591911452;17135,67150,23849,16478!GO:0006351;transcription, DNA-dependent;0.000846250591911452;17135,67150,23849,16478!GO:0032774;RNA biosynthetic process;0.000846250591911452;17135,67150,23849,16478!GO:0003677;DNA binding;0.000846250591911452;17135,67150,23849,16478!GO:0045449;regulation of transcription;0.000846250591911452;17135,67150,23849,16478!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.000846250591911452;17135,67150,23849,16478!GO:0006350;transcription;0.000846250591911452;17135,67150,23849,16478!GO:0010468;regulation of gene expression;0.000846250591911452;17135,67150,23849,16478!GO:0031323;regulation of cellular metabolic process;0.000883418543246339;17135,67150,23849,16478!GO:0019222;regulation of metabolic process;0.000919415008920835;17135,67150,23849,16478!GO:0016070;RNA metabolic process;0.000927678990891804;17135,67150,23849,16478!GO:0010467;gene expression;0.00174457134770867;17135,67150,23849,16478!GO:0003676;nucleic acid binding;0.00177157416827755;17135,67150,23849,16478!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0021697329344756;17135,67150,23849,16478!GO:0046983;protein dimerization activity;0.0021697329344756;17135,16478!GO:0050794;regulation of cellular process;0.00256845552065455;17135,67150,23849,16478!GO:0050789;regulation of biological process;0.0037195622018551;17135,67150,23849,16478!GO:0065007;biological regulation;0.00517786401692624;17135,67150,23849,16478!GO:0051726;regulation of cell cycle;0.0053044587446759;17135,16478!GO:0043283;biopolymer metabolic process;0.00571734313471222;17135,67150,23849,16478!GO:0043565;sequence-specific DNA binding;0.00713917179461032;17135,16478!GO:0022402;cell cycle process;0.0112374307265607;17135,16478!GO:0043170;macromolecule metabolic process;0.0148121223912388;17135,67150,23849,16478!GO:0007049;cell cycle;0.0162530989024509;17135,16478!GO:0019221;cytokine and chemokine mediated signaling pathway;0.0184724840990229;23849!GO:0003700;transcription factor activity;0.0198073286152921;17135,16478!GO:0044238;primary metabolic process;0.021900994017295;17135,67150,23849,16478!GO:0044237;cellular metabolic 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|gostat_on_MCL_coexpression=GO:0006355;regulation of transcription, DNA-dependent;0.000846250591911452;17135,67150,23849,16478!GO:0006351;transcription, DNA-dependent;0.000846250591911452;17135,67150,23849,16478!GO:0032774;RNA biosynthetic process;0.000846250591911452;17135,67150,23849,16478!GO:0003677;DNA binding;0.000846250591911452;17135,67150,23849,16478!GO:0045449;regulation of transcription;0.000846250591911452;17135,67150,23849,16478!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.000846250591911452;17135,67150,23849,16478!GO:0006350;transcription;0.000846250591911452;17135,67150,23849,16478!GO:0010468;regulation of gene expression;0.000846250591911452;17135,67150,23849,16478!GO:0031323;regulation of cellular metabolic process;0.000883418543246339;17135,67150,23849,16478!GO:0019222;regulation of metabolic process;0.000919415008920835;17135,67150,23849,16478!GO:0016070;RNA metabolic process;0.000927678990891804;17135,67150,23849,16478!GO:0010467;gene expression;0.00174457134770867;17135,67150,23849,16478!GO:0003676;nucleic acid binding;0.00177157416827755;17135,67150,23849,16478!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0021697329344756;17135,67150,23849,16478!GO:0046983;protein dimerization activity;0.0021697329344756;17135,16478!GO:0050794;regulation of cellular process;0.00256845552065455;17135,67150,23849,16478!GO:0050789;regulation of biological process;0.0037195622018551;17135,67150,23849,16478!GO:0065007;biological regulation;0.00517786401692624;17135,67150,23849,16478!GO:0051726;regulation of cell cycle;0.0053044587446759;17135,16478!GO:0043283;biopolymer metabolic process;0.00571734313471222;17135,67150,23849,16478!GO:0043565;sequence-specific DNA binding;0.00713917179461032;17135,16478!GO:0022402;cell cycle process;0.0112374307265607;17135,16478!GO:0043170;macromolecule metabolic process;0.0148121223912388;17135,67150,23849,16478!GO:0007049;cell cycle;0.0162530989024509;17135,16478!GO:0019221;cytokine and chemokine mediated signaling pathway;0.0184724840990229;23849!GO:0003700;transcription factor activity;0.0198073286152921;17135,16478!GO:0044238;primary metabolic process;0.021900994017295;17135,67150,23849,16478!GO:0044237;cellular metabolic process;0.021900994017295;17135,67150,23849,16478!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002204!9.77e-08!32
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.84953,0.367606,0.434198,0.260188,0.448401,0.538088,0.173246,0.535519,0.170907,0.494602,0.526159,0.992329,0.550255,0.275867,0,0.742571,0.252772,0.160384,0.29826,0.332107,1.76861,2.32326,0.258745,0.978733,0.577606,0.466037,0.469052,0.818708,1.23861,0.455168,0.843667,0.250677,0.425071,0.276324,0.60397,1.95279,0.522578,0.221921,0.570041,0.256422,0.460258,1.19668,0.27776,0.0183213,0.423266,0.662995,0.484612,0.386968,0.825035,0.725127,0.604356,0.362495,0.985264,1.00271,0.557354,0.314394,0.513517,0.447041,0.555328,0.823643,1.49002,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.922232,0.527912,0.236196,1.03623,0.433216,0.813951,0.42492,0.651651,0.806481,0.336166,1.01677,0.759925,0.612313,0.167672,0.920903,3.10739,0.123242,0.376919,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.202284,0.510015,0.859272,0.663249,0.332938,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.333829,0.386136,0.96962,0.337254,0.499714,1.21576,0.254749,0.333069,0.437894,1.76093,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,2.6678,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,1.33415,0.766041,0.203102,0.986833,1.76809,0.569994,1.06851,1.47241,0.287226,0.39061,2.73712,1.1977,0.920047,0.810622,0.998505,0.714896,0.562634,0.676555,0.524587,0.558175
}}

Latest revision as of 16:09, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:5860749..5860772,+p2@Klf6
Mm9::chr13:5860776..5860796,+p1@Klf6
Mm9::chr13:5860872..5860883,+p3@Klf6
Mm9::chr19:5850004..5850014,-p@chr19:5850004..5850014
-
Mm9::chr5:140267510..140267555,+p2@Mafk
Mm9::chr7:29162636..29162650,-p@chr7:29162636..29162650
-
Mm9::chr7:29164266..29164282,-p1@Zfp36
Mm9::chr8:73222830..73222844,+p1@Jund


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:0006355regulation of transcription, DNA-dependent0.000846250591911452
GO:0006351transcription, DNA-dependent0.000846250591911452
GO:0032774RNA biosynthetic process0.000846250591911452
GO:0003677DNA binding0.000846250591911452
GO:0045449regulation of transcription0.000846250591911452
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.000846250591911452
GO:0006350transcription0.000846250591911452
GO:0010468regulation of gene expression0.000846250591911452
GO:0031323regulation of cellular metabolic process0.000883418543246339
GO:0019222regulation of metabolic process0.000919415008920835
GO:0016070RNA metabolic process0.000927678990891804
GO:0010467gene expression0.00174457134770867
GO:0003676nucleic acid binding0.00177157416827755
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0021697329344756
GO:0046983protein dimerization activity0.0021697329344756
GO:0050794regulation of cellular process0.00256845552065455
GO:0050789regulation of biological process0.0037195622018551
GO:0065007biological regulation0.00517786401692624
GO:0051726regulation of cell cycle0.0053044587446759
GO:0043283biopolymer metabolic process0.00571734313471222
GO:0043565sequence-specific DNA binding0.00713917179461032
GO:0022402cell cycle process0.0112374307265607
GO:0043170macromolecule metabolic process0.0148121223912388
GO:0007049cell cycle0.0162530989024509
GO:0019221cytokine and chemokine mediated signaling pathway0.0184724840990229
GO:0003700transcription factor activity0.0198073286152921
GO:0044238primary metabolic process0.021900994017295
GO:0044237cellular metabolic process0.021900994017295



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
musculoskeletal system9.77e-0832


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)
MA0003.11.81836
MA0004.11.94256
MA0006.10.271714
MA0007.11.89281
MA0009.10.870101
MA0014.13.49148
MA0017.10.804572
MA0019.11.64517
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.769859
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.11.41387
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.335404
MA0050.10.472794
MA0051.10.586414
MA0052.12.06291
MA0055.10.834608
MA0056.10
MA0057.11.58436
MA0058.11.62198
MA0059.10.353484
MA0060.11.08928
MA0061.10.224905
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.0965831
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.0449725
MA0074.10.531046
MA0076.10.845594
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.853781
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.13.04876
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.10.823589
MA0106.10.626997
MA0107.10.301222
MA0108.21.69252
MA0109.10
MA0111.10.415012
MA0113.11.45892
MA0114.10.222763
MA0115.10.969632
MA0116.12.93249
MA0117.10.937363
MA0119.10.951747
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.977634
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.527241
MA0146.10.0771944
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.20.84271
MA0035.20.524137
MA0039.22.04793
MA0138.20.675599
MA0002.20.172399
MA0137.20.32312
MA0104.21.03907
MA0047.20.576767
MA0112.20.90045
MA0065.20.902537
MA0150.11.07698
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.11.65123
MA0155.11.45843
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.13.47629
MA0163.111.3413
MA0164.10.551114
MA0080.20.302064
MA0018.21.37842
MA0099.20.669311
MA0079.22.91632
MA0102.21.59466
MA0258.10.60477
MA0259.10.643936
MA0442.10
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