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MCL coexpression mm9:925: Difference between revisions

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{{MCL_coexpression_mm9
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89226087,0.0422673559395464,0.0648563765085929,-0.0186923385802032|gostat_on_MCL_coexpression=GO:0003708;retinoic acid receptor activity;0.0390406349406792;19401!GO:0016564;transcription repressor activity;0.0390406349406792;11569,19401!GO:0055012;ventricular cardiac muscle cell differentiation;0.0390406349406792;19401!GO:0006355;regulation of transcription, DNA-dependent;0.0390406349406792;228790,11569,19401,71458!GO:0006351;transcription, DNA-dependent;0.0390406349406792;228790,11569,19401,71458!GO:0032774;RNA biosynthetic process;0.0390406349406792;228790,11569,19401,71458!GO:0045449;regulation of transcription;0.0390406349406792;228790,11569,19401,71458!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0390406349406792;228790,11569,19401,71458!GO:0006350;transcription;0.0390406349406792;228790,11569,19401,71458!GO:0055007;cardiac muscle cell differentiation;0.0390406349406792;19401!GO:0010468;regulation of gene expression;0.0390406349406792;228790,11569,19401,71458!GO:0031323;regulation of cellular metabolic process;0.0415385883410495;228790,11569,19401,71458!GO:0019222;regulation of metabolic process;0.042853123543253;228790,11569,19401,71458!GO:0016070;RNA metabolic process;0.042853123543253;228790,11569,19401,71458!GO:0035051;cardiac cell 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|gostat_on_MCL_coexpression=GO:0003708;retinoic acid receptor activity;0.0390406349406792;19401!GO:0016564;transcription repressor activity;0.0390406349406792;11569,19401!GO:0055012;ventricular cardiac muscle cell differentiation;0.0390406349406792;19401!GO:0006355;regulation of transcription, DNA-dependent;0.0390406349406792;228790,11569,19401,71458!GO:0006351;transcription, DNA-dependent;0.0390406349406792;228790,11569,19401,71458!GO:0032774;RNA biosynthetic process;0.0390406349406792;228790,11569,19401,71458!GO:0045449;regulation of transcription;0.0390406349406792;228790,11569,19401,71458!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0390406349406792;228790,11569,19401,71458!GO:0006350;transcription;0.0390406349406792;228790,11569,19401,71458!GO:0055007;cardiac muscle cell differentiation;0.0390406349406792;19401!GO:0010468;regulation of gene expression;0.0390406349406792;228790,11569,19401,71458!GO:0031323;regulation of cellular metabolic process;0.0415385883410495;228790,11569,19401,71458!GO:0019222;regulation of metabolic process;0.042853123543253;228790,11569,19401,71458!GO:0016070;RNA metabolic process;0.042853123543253;228790,11569,19401,71458!GO:0035051;cardiac cell differentiation;0.042853123543253;19401!GO:0005634;nucleus;0.0459484764591356;108911,228790,11569,19401,71458!
|ontology_enrichment_celltype=CL:0000791!2.67e-07!9;CL:0000789!2.67e-07!9;CL:0002420!2.67e-07!9;CL:0002419!2.67e-07!9;CL:0000790!2.67e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002370!1.68e-07!23;UBERON:0000974!1.68e-07!23;UBERON:0004807!1.68e-07!23;UBERON:0005058!1.68e-07!23;UBERON:0003351!1.68e-07!23;UBERON:0009113!1.68e-07!23;UBERON:0003295!1.68e-07!23;UBERON:0009722!1.68e-07!23;UBERON:0005562!1.68e-07!23;UBERON:0007690!1.68e-07!23;UBERON:0006562!2.25e-07!24;UBERON:0001557!2.25e-07!24;UBERON:0001042!2.25e-07!24;UBERON:0008814!2.25e-07!24;UBERON:0009145!2.25e-07!24;UBERON:0003408!7.20e-07!24
}}

Latest revision as of 16:06, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:98798983..98799049,+p1@Rara
Mm9::chr13:3610263..3610280,-p3@BC016423
Mm9::chr14:75347602..75347611,-p3@Lrch1
Mm9::chr2:153171907..153171931,+p4@Asxl1
Mm9::chr4:140258131..140258153,+p@chr4:140258131..140258153
+
Mm9::chr5:32439348..32439350,+p@chr5:32439348..32439350
+
Mm9::chr6:140572167..140572236,+p2@Aebp2
Mm9::chrX:11657701..11657708,-p7@Bcor


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:0003708retinoic acid receptor activity0.0390406349406792
GO:0016564transcription repressor activity0.0390406349406792
GO:0055012ventricular cardiac muscle cell differentiation0.0390406349406792
GO:0006355regulation of transcription, DNA-dependent0.0390406349406792
GO:0006351transcription, DNA-dependent0.0390406349406792
GO:0032774RNA biosynthetic process0.0390406349406792
GO:0045449regulation of transcription0.0390406349406792
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0390406349406792
GO:0006350transcription0.0390406349406792
GO:0055007cardiac muscle cell differentiation0.0390406349406792
GO:0010468regulation of gene expression0.0390406349406792
GO:0031323regulation of cellular metabolic process0.0415385883410495
GO:0019222regulation of metabolic process0.042853123543253
GO:0016070RNA metabolic process0.042853123543253
GO:0035051cardiac cell differentiation0.042853123543253
GO:0005634nucleus0.0459484764591356



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
mature alpha-beta T cell2.67e-079
alpha-beta T cell2.67e-079
immature T cell2.67e-079
mature T cell2.67e-079
immature alpha-beta T cell2.67e-079

Uber Anatomy
Ontology termp-valuen
thymus1.68e-0723
neck1.68e-0723
respiratory system epithelium1.68e-0723
hemolymphoid system gland1.68e-0723
pharyngeal epithelium1.68e-0723
thymic region1.68e-0723
pharyngeal gland1.68e-0723
entire pharyngeal arch endoderm1.68e-0723
thymus primordium1.68e-0723
early pharyngeal endoderm1.68e-0723
pharynx2.25e-0724
upper respiratory tract2.25e-0724
chordate pharynx2.25e-0724
pharyngeal arch system2.25e-0724
pharyngeal region of foregut2.25e-0724
gland of gut7.20e-0724


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)
MA0003.13.57432
MA0004.10.434673
MA0006.12.10678
MA0007.11.07722
MA0009.10.870101
MA0014.12.94923
MA0017.10.804572
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.12.2709
MA0050.12.07056
MA0051.11.43259
MA0052.10.890676
MA0055.13.83726
MA0056.10
MA0057.12.16719
MA0058.10.341628
MA0059.10.931383
MA0060.10.574356
MA0061.11.19505
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.0965831
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.15.21207
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.853781
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.950493
MA0103.10.307078
MA0105.13.33376
MA0106.10.626997
MA0107.10.301222
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.633896
MA0115.10.969632
MA0116.10.27152
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
MA0139.10.977634
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.246409
MA0146.10.385068
MA0147.11.24068
MA0148.10.450593
MA0149.10.962263
MA0062.20.426733
MA0035.20.524137
MA0039.21.07211
MA0138.20.675599
MA0002.20.172399
MA0137.20.32312
MA0104.22.33347
MA0047.20.576767
MA0112.20.527225
MA0065.20.247168
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.330759
MA0155.10.0804339
MA0156.10.843735
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.16.08859
MA0163.11.36861
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.212.7454
MA0102.21.59466
MA0258.10.210437
MA0259.11.87317
MA0442.10
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