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MCL coexpression mm9:2728: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0003989;acetyl-CoA carboxylase activity;0.00284884676491536;107476!GO:0004075;biotin carboxylase activity;0.00284884676491536;107476!GO:0009374;biotin binding;0.00284884676491536;107476!GO:0016421;CoA carboxylase activity;0.00299128910316113;107476!GO:0016885;ligase activity, forming carbon-carbon bonds;0.00299128910316113;107476!GO:0006633;fatty acid biosynthetic process;0.0194967950473895;107476!GO:0046394;carboxylic acid biosynthetic process;0.0194967950473895;107476!GO:0016053;organic acid biosynthetic process;0.0194967950473895;107476!GO:0019842;vitamin binding;0.0249274091930094;107476!GO:0030145;manganese ion binding;0.0275625924505561;107476!GO:0016879;ligase activity, forming carbon-nitrogen bonds;0.0284884676491536;107476!GO:0006631;fatty acid metabolic process;0.0284884676491536;107476!GO:0032787;monocarboxylic acid metabolic process;0.035007943899633;107476!GO:0008610;lipid biosynthetic process;0.0360175626707156;107476!GO:0016874;ligase activity;0.046008875253383;107476!
}}

Latest revision as of 18:59, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:83993113..83993159,+p2@Acaca
p2@LOC100503180
p2@LOC100503206
Mm9::chr3:96531454..96531495,+p3@Rnf115
Mm9::chrX:153930212..153930272,-p4@Gm14680
p4@Sms


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:0003989acetyl-CoA carboxylase activity0.00284884676491536
GO:0004075biotin carboxylase activity0.00284884676491536
GO:0009374biotin binding0.00284884676491536
GO:0016421CoA carboxylase activity0.00299128910316113
GO:0016885ligase activity, forming carbon-carbon bonds0.00299128910316113
GO:0006633fatty acid biosynthetic process0.0194967950473895
GO:0046394carboxylic acid biosynthetic process0.0194967950473895
GO:0016053organic acid biosynthetic process0.0194967950473895
GO:0019842vitamin binding0.0249274091930094
GO:0030145manganese ion binding0.0275625924505561
GO:0016879ligase activity, forming carbon-nitrogen bonds0.0284884676491536
GO:0006631fatty acid metabolic process0.0284884676491536
GO:0032787monocarboxylic acid metabolic process0.035007943899633
GO:0008610lipid biosynthetic process0.0360175626707156
GO:0016874ligase activity0.046008875253383



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)1.39e-1223
neuroblast (sensu Vertebrata)1.39e-1223
neuron4.15e-0733
neuronal stem cell4.15e-0733
neuroblast4.15e-0733
electrically signaling cell4.15e-0733

Uber Anatomy
Ontology termp-valuen
ecto-epithelium2.00e-1573
neurectoderm5.24e-1564
neural plate5.24e-1564
presumptive neural plate5.24e-1564
regional part of nervous system1.20e-1454
gray matter2.67e-1434
neural tube7.21e-1452
neural rod7.21e-1452
future spinal cord7.21e-1452
neural keel7.21e-1452
pre-chordal neural plate1.37e-1349
ectoderm-derived structure7.60e-1295
ectoderm7.60e-1295
presumptive ectoderm7.60e-1295
anterior neural tube1.89e-1140
brain grey matter2.03e-1129
regional part of telencephalon2.03e-1129
telencephalon2.03e-1129
brain2.38e-1147
future brain2.38e-1147
regional part of forebrain5.56e-1139
forebrain5.56e-1139
future forebrain5.56e-1139
regional part of brain6.33e-1146
central nervous system1.02e-1073
nervous system4.06e-1075
cerebral cortex1.36e-0821
cerebral hemisphere1.36e-0821
pallium1.36e-0821
anterior region of body2.08e-0743
structure with developmental contribution from neural crest3.26e-0792


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)
MA0003.11.87396
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.11.33691
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
MA0048.10.353763
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.190475
MA0056.10
MA0057.10.337566
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
MA0073.10.0430758
MA0074.10.911576
MA0076.11.58243
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
MA0105.11.84392
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.10.537669
MA0115.11.38041
MA0116.11.46662
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
MA0139.10.462282
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.10.292366
MA0146.10.46063
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.21.06145
MA0035.20.903829
MA0039.20.40695
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.21.21648
MA0047.20.962424
MA0112.20.794478
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.11.52001
MA0156.11.58027
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.10.499274
MA0163.10.157796
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.20.166764
MA0102.22.01714
MA0258.10.520639
MA0259.11.34197
MA0442.10
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