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MCL coexpression mm9:2774: Difference between revisions

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{{MCL_coexpression_mm9
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of histone H3-K4 methylation;0.00602640661809018;214162!GO:0051568;histone H3-K4 methylation;0.00602640661809018;214162!GO:0031060;regulation of histone methylation;0.00803498870553531;214162!GO:0031056;regulation of histone modification;0.0120518227025482;214162!GO:0035162;embryonic hemopoiesis;0.0144613948161521;214162!GO:0006306;DNA methylation;0.0225903576485567;214162!GO:0006305;DNA alkylation;0.0225903576485567;214162!GO:0016571;histone methylation;0.0225903576485567;214162!GO:0006304;DNA modification;0.0240944004245295;214162!GO:0051052;regulation of DNA metabolic process;0.0246237656104948;214162!GO:0044428;nuclear part;0.0246237656104948;214162,20688!GO:0008213;protein amino acid alkylation;0.0246237656104948;214162!GO:0006479;protein amino acid methylation;0.0246237656104948;214162!GO:0016570;histone modification;0.0246237656104948;214162!GO:0008016;regulation of heart contraction;0.0246237656104948;20688!GO:0048568;embryonic organ development;0.0246237656104948;214162!GO:0016569;covalent chromatin modification;0.0246237656104948;214162!GO:0043414;biopolymer methylation;0.0246237656104948;214162!GO:0040029;regulation of gene expression, epigenetic;0.0246237656104948;214162!GO:0060047;heart contraction;0.0246237656104948;20688!GO:0003015;heart process;0.0246237656104948;20688!GO:0032259;methylation;0.0246237656104948;214162!GO:0051128;regulation of cellular component organization and biogenesis;0.0282568237247241;214162!GO:0003713;transcription coactivator activity;0.033112143142528;20688!GO:0003702;RNA polymerase II transcription factor activity;0.033112143142528;20688!GO:0006730;one-carbon compound metabolic process;0.033112143142528;214162!GO:0006355;regulation of transcription, DNA-dependent;0.033112143142528;214162,20688!GO:0006351;transcription, DNA-dependent;0.033112143142528;214162,20688!GO:0032774;RNA biosynthetic process;0.033112143142528;214162,20688!GO:0008270;zinc ion binding;0.033112143142528;214162,20688!GO:0003677;DNA binding;0.033112143142528;214162,20688!GO:0009952;anterior/posterior pattern formation;0.033112143142528;214162!GO:0008015;blood circulation;0.033112143142528;20688!GO:0003013;circulatory system process;0.033112143142528;20688!GO:0045449;regulation of transcription;0.033112143142528;214162,20688!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.033429706950182;214162,20688!GO:0006350;transcription;0.033429706950182;214162,20688!GO:0010468;regulation of gene expression;0.0347729438238879;214162,20688!GO:0031323;regulation of cellular metabolic process;0.0367158307621688;214162,20688!GO:0019222;regulation of metabolic process;0.0383625493068262;214162,20688!GO:0016070;RNA metabolic process;0.0383625493068262;214162,20688!GO:0003712;transcription cofactor activity;0.0383625493068262;20688!GO:0046914;transition metal ion binding;0.0383625493068262;214162,20688!GO:0044446;intracellular organelle part;0.0383625493068262;214162,20688!GO:0044422;organelle part;0.0383625493068262;214162,20688!GO:0003002;regionalization;0.0383625493068262;214162!GO:0016568;chromatin modification;0.0421229695873964;214162!GO:0016563;transcription activator activity;0.044479128579898;20688!GO:0008134;transcription factor binding;0.045763098535396;20688!GO:0010467;gene expression;0.0464610196380316;214162,20688!GO:0003676;nucleic acid 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|gostat_on_MCL_coexpression=GO:0051569;regulation of histone H3-K4 methylation;0.00602640661809018;214162!GO:0051568;histone H3-K4 methylation;0.00602640661809018;214162!GO:0031060;regulation of histone methylation;0.00803498870553531;214162!GO:0031056;regulation of histone modification;0.0120518227025482;214162!GO:0035162;embryonic hemopoiesis;0.0144613948161521;214162!GO:0006306;DNA methylation;0.0225903576485567;214162!GO:0006305;DNA alkylation;0.0225903576485567;214162!GO:0016571;histone methylation;0.0225903576485567;214162!GO:0006304;DNA modification;0.0240944004245295;214162!GO:0051052;regulation of DNA metabolic process;0.0246237656104948;214162!GO:0044428;nuclear part;0.0246237656104948;214162,20688!GO:0008213;protein amino acid alkylation;0.0246237656104948;214162!GO:0006479;protein amino acid methylation;0.0246237656104948;214162!GO:0016570;histone modification;0.0246237656104948;214162!GO:0008016;regulation of heart contraction;0.0246237656104948;20688!GO:0048568;embryonic organ development;0.0246237656104948;214162!GO:0016569;covalent chromatin modification;0.0246237656104948;214162!GO:0043414;biopolymer methylation;0.0246237656104948;214162!GO:0040029;regulation of gene expression, epigenetic;0.0246237656104948;214162!GO:0060047;heart contraction;0.0246237656104948;20688!GO:0003015;heart process;0.0246237656104948;20688!GO:0032259;methylation;0.0246237656104948;214162!GO:0051128;regulation of cellular component organization and biogenesis;0.0282568237247241;214162!GO:0003713;transcription coactivator activity;0.033112143142528;20688!GO:0003702;RNA polymerase II transcription factor activity;0.033112143142528;20688!GO:0006730;one-carbon compound metabolic process;0.033112143142528;214162!GO:0006355;regulation of transcription, DNA-dependent;0.033112143142528;214162,20688!GO:0006351;transcription, DNA-dependent;0.033112143142528;214162,20688!GO:0032774;RNA biosynthetic process;0.033112143142528;214162,20688!GO:0008270;zinc ion binding;0.033112143142528;214162,20688!GO:0003677;DNA binding;0.033112143142528;214162,20688!GO:0009952;anterior/posterior pattern formation;0.033112143142528;214162!GO:0008015;blood circulation;0.033112143142528;20688!GO:0003013;circulatory system process;0.033112143142528;20688!GO:0045449;regulation of transcription;0.033112143142528;214162,20688!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.033429706950182;214162,20688!GO:0006350;transcription;0.033429706950182;214162,20688!GO:0010468;regulation of gene expression;0.0347729438238879;214162,20688!GO:0031323;regulation of cellular metabolic process;0.0367158307621688;214162,20688!GO:0019222;regulation of metabolic process;0.0383625493068262;214162,20688!GO:0016070;RNA metabolic process;0.0383625493068262;214162,20688!GO:0003712;transcription cofactor activity;0.0383625493068262;20688!GO:0046914;transition metal ion binding;0.0383625493068262;214162,20688!GO:0044446;intracellular organelle part;0.0383625493068262;214162,20688!GO:0044422;organelle part;0.0383625493068262;214162,20688!GO:0003002;regionalization;0.0383625493068262;214162!GO:0016568;chromatin modification;0.0421229695873964;214162!GO:0016563;transcription activator activity;0.044479128579898;20688!GO:0008134;transcription factor binding;0.045763098535396;20688!GO:0010467;gene expression;0.0464610196380316;214162,20688!GO:0003676;nucleic acid binding;0.0477746153611416;214162,20688!GO:0030097;hemopoiesis;0.0479378656622439;214162!
}}

Latest revision as of 19:03, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:119539843..119539899,-p1@Sp4
Mm9::chr12:119539902..119539931,-p2@Sp4
Mm9::chr9:44689360..44689406,-p1@Mll1


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:0051569regulation of histone H3-K4 methylation0.00602640661809018
GO:0051568histone H3-K4 methylation0.00602640661809018
GO:0031060regulation of histone methylation0.00803498870553531
GO:0031056regulation of histone modification0.0120518227025482
GO:0035162embryonic hemopoiesis0.0144613948161521
GO:0006306DNA methylation0.0225903576485567
GO:0006305DNA alkylation0.0225903576485567
GO:0016571histone methylation0.0225903576485567
GO:0006304DNA modification0.0240944004245295
GO:0051052regulation of DNA metabolic process0.0246237656104948
GO:0044428nuclear part0.0246237656104948
GO:0008213protein amino acid alkylation0.0246237656104948
GO:0006479protein amino acid methylation0.0246237656104948
GO:0016570histone modification0.0246237656104948
GO:0008016regulation of heart contraction0.0246237656104948
GO:0048568embryonic organ development0.0246237656104948
GO:0016569covalent chromatin modification0.0246237656104948
GO:0043414biopolymer methylation0.0246237656104948
GO:0040029regulation of gene expression, epigenetic0.0246237656104948
GO:0060047heart contraction0.0246237656104948
GO:0003015heart process0.0246237656104948
GO:0032259methylation0.0246237656104948
GO:0051128regulation of cellular component organization and biogenesis0.0282568237247241
GO:0003713transcription coactivator activity0.033112143142528
GO:0003702RNA polymerase II transcription factor activity0.033112143142528
GO:0006730one-carbon compound metabolic process0.033112143142528
GO:0006355regulation of transcription, DNA-dependent0.033112143142528
GO:0006351transcription, DNA-dependent0.033112143142528
GO:0032774RNA biosynthetic process0.033112143142528
GO:0008270zinc ion binding0.033112143142528
GO:0003677DNA binding0.033112143142528
GO:0009952anterior/posterior pattern formation0.033112143142528
GO:0008015blood circulation0.033112143142528
GO:0003013circulatory system process0.033112143142528
GO:0045449regulation of transcription0.033112143142528
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.033429706950182
GO:0006350transcription0.033429706950182
GO:0010468regulation of gene expression0.0347729438238879
GO:0031323regulation of cellular metabolic process0.0367158307621688
GO:0019222regulation of metabolic process0.0383625493068262
GO:0016070RNA metabolic process0.0383625493068262
GO:0003712transcription cofactor activity0.0383625493068262
GO:0046914transition metal ion binding0.0383625493068262
GO:0044446intracellular organelle part0.0383625493068262
GO:0044422organelle part0.0383625493068262
GO:0003002regionalization0.0383625493068262
GO:0016568chromatin modification0.0421229695873964
GO:0016563transcription activator activity0.044479128579898
GO:0008134transcription factor binding0.045763098535396
GO:0010467gene expression0.0464610196380316
GO:0003676nucleic acid binding0.0477746153611416
GO:0030097hemopoiesis0.0479378656622439



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
CNS neuron (sensu Vertebrata)4.36e-0923
neuroblast (sensu Vertebrata)4.36e-0923
neuron2.08e-0733
neuronal stem cell2.08e-0733
neuroblast2.08e-0733
electrically signaling cell2.08e-0733

Uber Anatomy
Ontology termp-valuen
neurectoderm5.30e-1464
neural plate5.30e-1464
presumptive neural plate5.30e-1464
regional part of nervous system7.86e-1354
pre-chordal neural plate3.08e-1249
neural tube6.54e-1252
neural rod6.54e-1252
future spinal cord6.54e-1252
neural keel6.54e-1252
central nervous system2.87e-1173
brain6.80e-1147
future brain6.80e-1147
ecto-epithelium8.50e-1173
gray matter2.25e-1034
regional part of brain2.57e-1046
nervous system3.65e-1075
anterior neural tube5.32e-1040
regional part of forebrain1.40e-0939
forebrain1.40e-0939
future forebrain1.40e-0939
ectoderm-derived structure3.08e-0995
ectoderm3.08e-0995
presumptive ectoderm3.08e-0995
brain grey matter3.21e-0929
regional part of telencephalon3.21e-0929
telencephalon3.21e-0929
structure with developmental contribution from neural crest6.77e-0892


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)
MA0003.13.77865
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.14.96439
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.10.61552
MA0029.11.20789
MA0030.11.21482
MA0031.11.17722
MA0038.10.963265
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.10.932001
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.190475
MA0056.10
MA0057.11.60767
MA0058.10.690848
MA0059.10.705317
MA0060.11.25521
MA0061.10.5406
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.343188
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.14.16062
MA0074.10.911576
MA0076.10.657929
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.27999
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.10.62555
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.10.71579
MA0103.10.647985
MA0105.12.75918
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.11.3296
MA0115.11.38041
MA0116.10.602598
MA0117.11.34691
MA0119.10.716476
MA0122.11.36752
MA0124.11.57762
MA0125.11.5017
MA0130.10
MA0131.11.07881
MA0132.10
MA0133.10
MA0135.11.4152
MA0136.10.933582
MA0139.12.03543
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.13.06815
MA0146.12.07553
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.23.25387
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.20.48458
MA0047.20.962424
MA0112.20.29236
MA0065.23.07166
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.11.52001
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.11.53682
MA0163.14.46088
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.211.3089
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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