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MCL coexpression mm9:991: Difference between revisions

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{{MCL_coexpression_mm9
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619,0.0914477891695676,0.0972522732513006,0.0729583017401753,0.101427320830301,0.0798283833100081,0,0.112346887556877,0.126009132120275,0,0.117229416500102,0.170004882748698,0.0484220980280083,0.091291089277545,0.119893946266008,0.221874956202416,0.0793595409278515,0.128013386275029|gostat_on_MCL_coexpression=GO:0007389;pattern specification process;0.00833645111298099;15438,15434!GO:0005667;transcription factor complex;0.00833645111298099;15438,15434!GO:0043565;sequence-specific DNA binding;0.00833645111298099;15438,15434!GO:0009887;organ morphogenesis;0.00833645111298099;15438,15434!GO:0044451;nucleoplasm part;0.00833645111298099;15438,15434!GO:0005654;nucleoplasm;0.00833645111298099;15438,15434!GO:0030878;thyroid gland development;0.00876352118929734;15434!GO:0031981;nuclear lumen;0.00883635242581507;15438,15434!GO:0031974;membrane-enclosed lumen;0.00899439116634181;15438,15434!GO:0043233;organelle lumen;0.00899439116634181;15438,15434!GO:0003700;transcription factor activity;0.00986557089874141;15438,15434!GO:0044428;nuclear part;0.0132477209712142;15438,15434!GO:0009653;anatomical structure morphogenesis;0.0158880744910698;15438,15434!GO:0048513;organ development;0.0196098476524455;15438,15434!GO:0035270;endocrine system development;0.0196098476524455;15434!GO:0043234;protein complex;0.0239772212963834;15438,15434!GO:0048731;system development;0.0239772212963834;15438,15434!GO:0048732;gland development;0.0239772212963834;15434!GO:0006355;regulation of transcription, DNA-dependent;0.0239772212963834;15438,15434!GO:0006351;transcription, DNA-dependent;0.0239772212963834;15438,15434!GO:0032774;RNA biosynthetic process;0.0239772212963834;15438,15434!GO:0003677;DNA binding;0.0239772212963834;15438,15434!GO:0045449;regulation of transcription;0.0239772212963834;15438,15434!GO:0048856;anatomical structure development;0.0239772212963834;15438,15434!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0239772212963834;15438,15434!GO:0006350;transcription;0.0239772212963834;15438,15434!GO:0032991;macromolecular complex;0.0239772212963834;15438,15434!GO:0010468;regulation of gene expression;0.0240249430055953;15438,15434!GO:0031323;regulation of cellular metabolic process;0.0251371079575476;15438,15434!GO:0007275;multicellular organismal development;0.0252864587535295;15438,15434!GO:0019222;regulation of metabolic process;0.0252864587535295;15438,15434!GO:0016070;RNA metabolic process;0.0258064807770019;15438,15434!GO:0044446;intracellular organelle part;0.0260279821068564;15438,15434!GO:0044422;organelle part;0.0260279821068564;15438,15434!GO:0016563;transcription activator activity;0.0310545188630561;15438!GO:0010467;gene expression;0.032851226006689;15438,15434!GO:0003676;nucleic acid binding;0.0335243983959264;15438,15434!GO:0032502;developmental process;0.0347664881354756;15438,15434!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0369379254886281;15438,15434!GO:0050794;regulation of cellular 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|gostat_on_MCL_coexpression=GO:0007389;pattern specification process;0.00833645111298099;15438,15434!GO:0005667;transcription factor complex;0.00833645111298099;15438,15434!GO:0043565;sequence-specific DNA binding;0.00833645111298099;15438,15434!GO:0009887;organ morphogenesis;0.00833645111298099;15438,15434!GO:0044451;nucleoplasm part;0.00833645111298099;15438,15434!GO:0005654;nucleoplasm;0.00833645111298099;15438,15434!GO:0030878;thyroid gland development;0.00876352118929734;15434!GO:0031981;nuclear lumen;0.00883635242581507;15438,15434!GO:0031974;membrane-enclosed lumen;0.00899439116634181;15438,15434!GO:0043233;organelle lumen;0.00899439116634181;15438,15434!GO:0003700;transcription factor activity;0.00986557089874141;15438,15434!GO:0044428;nuclear part;0.0132477209712142;15438,15434!GO:0009653;anatomical structure morphogenesis;0.0158880744910698;15438,15434!GO:0048513;organ development;0.0196098476524455;15438,15434!GO:0035270;endocrine system development;0.0196098476524455;15434!GO:0043234;protein complex;0.0239772212963834;15438,15434!GO:0048731;system development;0.0239772212963834;15438,15434!GO:0048732;gland development;0.0239772212963834;15434!GO:0006355;regulation of transcription, DNA-dependent;0.0239772212963834;15438,15434!GO:0006351;transcription, DNA-dependent;0.0239772212963834;15438,15434!GO:0032774;RNA biosynthetic process;0.0239772212963834;15438,15434!GO:0003677;DNA binding;0.0239772212963834;15438,15434!GO:0045449;regulation of transcription;0.0239772212963834;15438,15434!GO:0048856;anatomical structure development;0.0239772212963834;15438,15434!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0239772212963834;15438,15434!GO:0006350;transcription;0.0239772212963834;15438,15434!GO:0032991;macromolecular complex;0.0239772212963834;15438,15434!GO:0010468;regulation of gene expression;0.0240249430055953;15438,15434!GO:0031323;regulation of cellular metabolic process;0.0251371079575476;15438,15434!GO:0007275;multicellular organismal development;0.0252864587535295;15438,15434!GO:0019222;regulation of metabolic process;0.0252864587535295;15438,15434!GO:0016070;RNA metabolic process;0.0258064807770019;15438,15434!GO:0044446;intracellular organelle part;0.0260279821068564;15438,15434!GO:0044422;organelle part;0.0260279821068564;15438,15434!GO:0016563;transcription activator activity;0.0310545188630561;15438!GO:0010467;gene expression;0.032851226006689;15438,15434!GO:0003676;nucleic acid binding;0.0335243983959264;15438,15434!GO:0032502;developmental process;0.0347664881354756;15438,15434!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0369379254886281;15438,15434!GO:0050794;regulation of cellular process;0.0414194459809722;15438,15434!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005156!8.52e-20!26;UBERON:0000990!8.52e-20!26;UBERON:0003133!6.10e-19!24;UBERON:0000489!1.59e-18!21;UBERON:0000991!3.38e-15!18;UBERON:0005564!3.38e-15!18;UBERON:0001008!3.95e-15!19;UBERON:0006554!3.97e-15!18;UBERON:0004176!2.32e-14!17;UBERON:0009196!2.32e-14!17;UBERON:0009117!2.32e-14!17;UBERON:0002113!3.09e-13!14;UBERON:0003918!3.09e-13!14;UBERON:0011143!3.09e-13!14;UBERON:0005095!3.09e-13!14;UBERON:0007687!3.09e-13!14;UBERON:0003101!9.76e-13!16;UBERON:0000079!9.76e-13!16;UBERON:0003135!1.02e-12!15;UBERON:0000473!7.23e-12!14;UBERON:0003100!9.28e-09!11;UBERON:0003064!4.67e-08!14;UBERON:0000474!1.94e-07!9;UBERON:0004175!2.52e-07!9;UBERON:0003886!5.80e-07!38
}}

Latest revision as of 16:13, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr2:74535720..74535731,+p6@Hoxd9
Mm9::chr2:74535796..74535808,+p3@Hoxd9
Mm9::chr2:74536003..74536008,+p7@Hoxd9
Mm9::chr2:74536026..74536039,+p1@Hoxd9
Mm9::chr2:74536050..74536065,+p2@Hoxd9
Mm9::chr2:74536071..74536083,+p4@Hoxd9
Mm9::chr2:74547770..74547771,+p@chr2:74547770..74547771
+
Mm9::chr2:74549968..74549996,+p1@Hoxd3


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:0007389pattern specification process0.00833645111298099
GO:0005667transcription factor complex0.00833645111298099
GO:0043565sequence-specific DNA binding0.00833645111298099
GO:0009887organ morphogenesis0.00833645111298099
GO:0044451nucleoplasm part0.00833645111298099
GO:0005654nucleoplasm0.00833645111298099
GO:0030878thyroid gland development0.00876352118929734
GO:0031981nuclear lumen0.00883635242581507
GO:0031974membrane-enclosed lumen0.00899439116634181
GO:0043233organelle lumen0.00899439116634181
GO:0003700transcription factor activity0.00986557089874141
GO:0044428nuclear part0.0132477209712142
GO:0009653anatomical structure morphogenesis0.0158880744910698
GO:0048513organ development0.0196098476524455
GO:0035270endocrine system development0.0196098476524455
GO:0043234protein complex0.0239772212963834
GO:0048731system development0.0239772212963834
GO:0048732gland development0.0239772212963834
GO:0006355regulation of transcription, DNA-dependent0.0239772212963834
GO:0006351transcription, DNA-dependent0.0239772212963834
GO:0032774RNA biosynthetic process0.0239772212963834
GO:0003677DNA binding0.0239772212963834
GO:0045449regulation of transcription0.0239772212963834
GO:0048856anatomical structure development0.0239772212963834
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0239772212963834
GO:0006350transcription0.0239772212963834
GO:0032991macromolecular complex0.0239772212963834
GO:0010468regulation of gene expression0.0240249430055953
GO:0031323regulation of cellular metabolic process0.0251371079575476
GO:0007275multicellular organismal development0.0252864587535295
GO:0019222regulation of metabolic process0.0252864587535295
GO:0016070RNA metabolic process0.0258064807770019
GO:0044446intracellular organelle part0.0260279821068564
GO:0044422organelle part0.0260279821068564
GO:0016563transcription activator activity0.0310545188630561
GO:0010467gene expression0.032851226006689
GO:0003676nucleic acid binding0.0335243983959264
GO:0032502developmental process0.0347664881354756
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0369379254886281
GO:0050794regulation of cellular process0.0414194459809722



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>


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)
MA0003.10.400153
MA0004.11.94256
MA0006.10.747445
MA0007.10.419994
MA0009.12.02076
MA0014.10.325341
MA0017.10.296816
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.12.415
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.102483
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.834608
MA0056.10
MA0057.10.0935008
MA0058.14.38029
MA0059.12.51175
MA0060.12.42557
MA0061.10.224905
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.11.09399
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.12.20974
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.064239
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.13.97711
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.10.133231
MA0106.12.57478
MA0107.10.301222
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.12.10578
MA0117.10.937363
MA0119.10.362692
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.169849
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.13.0966
MA0146.13.23209
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.20.137653
MA0035.20.524137
MA0039.20.00752803
MA0138.20.675599
MA0002.20.988033
MA0137.20.32312
MA0104.21.03907
MA0047.20.576767
MA0112.28.6977
MA0065.20.0704227
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.330759
MA0155.10.275377
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.10.230918
MA0163.10.0186439
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.26.8848e-05
MA0102.21.59466
MA0258.13.32479
MA0259.10.227035
MA0442.10
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