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MCL coexpression mm9:2546: Difference between revisions

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{{MCL_coexpression_mm9
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618674833,0.141183443972418,0.212664309528237,0.29061047861444,0.170575732287876,0.189702357405233,0.14986111676545,0.180876014666395,0.0693613744957475,0.275859125630462,0.092873634605593,0.213651700149258,0.194418948264644,0.245683575073352,0.135404897539632,0.18359421108913,0.260732069112669,0.134770128022935,0.174783231261599,0.0855960041584459,0,0.15077492661627,0.141704700595215,0.439123241623968,0.108013232228701,0.157391406252458,0.140689222355642,0,0.0318917604078142|gostat_on_MCL_coexpression=GO:0045179;apical cortex;0.00942285039103686;18762!GO:0004700;atypical protein kinase C activity;0.00942285039103686;18762!GO:0004674;protein serine/threonine kinase activity;0.0145566028350312;18762!GO:0004672;protein kinase activity;0.0145566028350312;18762!GO:0006468;protein amino acid phosphorylation;0.0145566028350312;18762!GO:0016773;phosphotransferase activity, alcohol group as acceptor;0.0145566028350312;18762!GO:0016310;phosphorylation;0.0145566028350312;18762!GO:0004697;protein kinase C activity;0.0145566028350312;18762!GO:0006793;phosphorus metabolic process;0.0145566028350312;18762!GO:0006796;phosphate metabolic process;0.0145566028350312;18762!GO:0001565;phorbol ester receptor activity;0.0145566028350312;18762!GO:0016301;kinase activity;0.0153779896151013;18762!GO:0016772;transferase activity, transferring phosphorus-containing groups;0.0185871248635674;18762!GO:0044448;cell cortex part;0.0188322775505494;18762!GO:0005524;ATP binding;0.0221164002125192;18762!GO:0043687;post-translational protein modification;0.0221164002125192;18762!GO:0032559;adenyl ribonucleotide binding;0.0221164002125192;18762!GO:0019992;diacylglycerol binding;0.0221164002125192;18762!GO:0030554;adenyl nucleotide binding;0.0221164002125192;18762!GO:0005938;cell cortex;0.0221164002125192;18762!GO:0006464;protein modification process;0.0249193206754661;18762!GO:0043412;biopolymer modification;0.0249193206754661;18762!GO:0000226;microtubule cytoskeleton organization and biogenesis;0.0249193206754661;18762!GO:0032553;ribonucleotide binding;0.0249193206754661;18762!GO:0032555;purine ribonucleotide binding;0.0249193206754661;18762!GO:0005923;tight junction;0.0249519135053777;18762!GO:0017076;purine nucleotide binding;0.0249519135053777;18762!GO:0045177;apical part of cell;0.0258595973926225;18762!GO:0016740;transferase activity;0.0264410244880735;18762!GO:0043296;apical junction complex;0.0270002977994341;18762!GO:0016327;apicolateral plasma membrane;0.0270002977994341;18762!GO:0000166;nucleotide binding;0.0270002977994341;18762!GO:0005911;intercellular junction;0.0426574809500271;18762!GO:0005768;endosome;0.0455243430674482;18762!GO:0007017;microtubule-based process;0.0471576119431688;18762!GO:0044267;cellular protein metabolic process;0.0486033701908296;18762!GO:0044260;cellular macromolecule metabolic 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|gostat_on_MCL_coexpression=GO:0045179;apical cortex;0.00942285039103686;18762!GO:0004700;atypical protein kinase C activity;0.00942285039103686;18762!GO:0004674;protein serine/threonine kinase activity;0.0145566028350312;18762!GO:0004672;protein kinase activity;0.0145566028350312;18762!GO:0006468;protein amino acid phosphorylation;0.0145566028350312;18762!GO:0016773;phosphotransferase activity, alcohol group as acceptor;0.0145566028350312;18762!GO:0016310;phosphorylation;0.0145566028350312;18762!GO:0004697;protein kinase C activity;0.0145566028350312;18762!GO:0006793;phosphorus metabolic process;0.0145566028350312;18762!GO:0006796;phosphate metabolic process;0.0145566028350312;18762!GO:0001565;phorbol ester receptor activity;0.0145566028350312;18762!GO:0016301;kinase activity;0.0153779896151013;18762!GO:0016772;transferase activity, transferring phosphorus-containing groups;0.0185871248635674;18762!GO:0044448;cell cortex part;0.0188322775505494;18762!GO:0005524;ATP binding;0.0221164002125192;18762!GO:0043687;post-translational protein modification;0.0221164002125192;18762!GO:0032559;adenyl ribonucleotide binding;0.0221164002125192;18762!GO:0019992;diacylglycerol binding;0.0221164002125192;18762!GO:0030554;adenyl nucleotide binding;0.0221164002125192;18762!GO:0005938;cell cortex;0.0221164002125192;18762!GO:0006464;protein modification process;0.0249193206754661;18762!GO:0043412;biopolymer modification;0.0249193206754661;18762!GO:0000226;microtubule cytoskeleton organization and biogenesis;0.0249193206754661;18762!GO:0032553;ribonucleotide binding;0.0249193206754661;18762!GO:0032555;purine ribonucleotide binding;0.0249193206754661;18762!GO:0005923;tight junction;0.0249519135053777;18762!GO:0017076;purine nucleotide binding;0.0249519135053777;18762!GO:0045177;apical part of cell;0.0258595973926225;18762!GO:0016740;transferase activity;0.0264410244880735;18762!GO:0043296;apical junction complex;0.0270002977994341;18762!GO:0016327;apicolateral plasma membrane;0.0270002977994341;18762!GO:0000166;nucleotide binding;0.0270002977994341;18762!GO:0005911;intercellular junction;0.0426574809500271;18762!GO:0005768;endosome;0.0455243430674482;18762!GO:0007017;microtubule-based process;0.0471576119431688;18762!GO:0044267;cellular protein metabolic process;0.0486033701908296;18762!GO:0044260;cellular macromolecule metabolic process;0.0487909349677067;18762!
|ontology_enrichment_celltype=CL:0000117!5.48e-16!23;CL:0000337!5.48e-16!23;CL:0000540!6.44e-10!33;CL:0000047!6.44e-10!33;CL:0000031!6.44e-10!33;CL:0000404!6.44e-10!33;CL:0000393!4.45e-07!39;CL:0000211!4.45e-07!39
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002346!2.14e-29!64;UBERON:0003075!2.14e-29!64;UBERON:0007284!2.14e-29!64;UBERON:0000073!1.50e-28!54;UBERON:0001049!4.41e-27!52;UBERON:0005068!4.41e-27!52;UBERON:0006241!4.41e-27!52;UBERON:0007135!4.41e-27!52;UBERON:0010371!9.86e-26!73;UBERON:0001017!2.87e-24!73;UBERON:0004121!4.47e-24!95;UBERON:0000924!4.47e-24!95;UBERON:0006601!4.47e-24!95;UBERON:0001016!9.12e-24!75;UBERON:0003056!1.26e-23!49;UBERON:0000955!1.84e-22!47;UBERON:0006238!1.84e-22!47;UBERON:0002616!9.83e-22!46;UBERON:0002020!1.18e-20!34;UBERON:0003080!4.09e-20!40;UBERON:0002780!3.58e-19!39;UBERON:0001890!3.58e-19!39;UBERON:0006240!3.58e-19!39;UBERON:0010314!3.03e-18!92;UBERON:0003528!2.64e-16!29;UBERON:0002791!2.64e-16!29;UBERON:0001893!2.64e-16!29;UBERON:0000956!1.21e-10!21;UBERON:0001869!1.21e-10!21;UBERON:0000203!1.21e-10!21;UBERON:0002619!2.12e-09!17;UBERON:0002021!4.44e-09!10;UBERON:0000411!4.44e-09!10;UBERON:0001950!4.44e-09!10;UBERON:0003076!1.89e-07!12;UBERON:0003057!1.89e-07!12;UBERON:0002420!4.40e-07!8;UBERON:0007245!4.40e-07!8;UBERON:0010009!4.40e-07!8;UBERON:0010011!4.40e-07!8;UBERON:0000454!4.40e-07!8
}}

Latest revision as of 18:42, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:21602020..21602045,+p8@Sgk1
Mm9::chr4:154719749..154719758,-p4@Prkcz
Mm9::chr9:81527119..81527171,-p@chr9:81527119..81527171
-


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:0045179apical cortex0.00942285039103686
GO:0004700atypical protein kinase C activity0.00942285039103686
GO:0004674protein serine/threonine kinase activity0.0145566028350312
GO:0004672protein kinase activity0.0145566028350312
GO:0006468protein amino acid phosphorylation0.0145566028350312
GO:0016773phosphotransferase activity, alcohol group as acceptor0.0145566028350312
GO:0016310phosphorylation0.0145566028350312
GO:0004697protein kinase C activity0.0145566028350312
GO:0006793phosphorus metabolic process0.0145566028350312
GO:0006796phosphate metabolic process0.0145566028350312
GO:0001565phorbol ester receptor activity0.0145566028350312
GO:0016301kinase activity0.0153779896151013
GO:0016772transferase activity, transferring phosphorus-containing groups0.0185871248635674
GO:0044448cell cortex part0.0188322775505494
GO:0005524ATP binding0.0221164002125192
GO:0043687post-translational protein modification0.0221164002125192
GO:0032559adenyl ribonucleotide binding0.0221164002125192
GO:0019992diacylglycerol binding0.0221164002125192
GO:0030554adenyl nucleotide binding0.0221164002125192
GO:0005938cell cortex0.0221164002125192
GO:0006464protein modification process0.0249193206754661
GO:0043412biopolymer modification0.0249193206754661
GO:0000226microtubule cytoskeleton organization and biogenesis0.0249193206754661
GO:0032553ribonucleotide binding0.0249193206754661
GO:0032555purine ribonucleotide binding0.0249193206754661
GO:0005923tight junction0.0249519135053777
GO:0017076purine nucleotide binding0.0249519135053777
GO:0045177apical part of cell0.0258595973926225
GO:0016740transferase activity0.0264410244880735
GO:0043296apical junction complex0.0270002977994341
GO:0016327apicolateral plasma membrane0.0270002977994341
GO:0000166nucleotide binding0.0270002977994341
GO:0005911intercellular junction0.0426574809500271
GO:0005768endosome0.0455243430674482
GO:0007017microtubule-based process0.0471576119431688
GO:0044267cellular protein metabolic process0.0486033701908296
GO:0044260cellular macromolecule metabolic process0.0487909349677067



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)5.48e-1623
neuroblast (sensu Vertebrata)5.48e-1623
neuron6.44e-1033
neuronal stem cell6.44e-1033
neuroblast6.44e-1033
electrically signaling cell6.44e-1033
electrically responsive cell4.45e-0739
electrically active cell4.45e-0739

Uber Anatomy
Ontology termp-valuen
neurectoderm2.14e-2964
neural plate2.14e-2964
presumptive neural plate2.14e-2964
regional part of nervous system1.50e-2854
neural tube4.41e-2752
neural rod4.41e-2752
future spinal cord4.41e-2752
neural keel4.41e-2752
ecto-epithelium9.86e-2673
central nervous system2.87e-2473
ectoderm-derived structure4.47e-2495
ectoderm4.47e-2495
presumptive ectoderm4.47e-2495
nervous system9.12e-2475
pre-chordal neural plate1.26e-2349
brain1.84e-2247
future brain1.84e-2247
regional part of brain9.83e-2246
gray matter1.18e-2034
anterior neural tube4.09e-2040
regional part of forebrain3.58e-1939
forebrain3.58e-1939
future forebrain3.58e-1939
structure with developmental contribution from neural crest3.03e-1892
brain grey matter2.64e-1629
regional part of telencephalon2.64e-1629
telencephalon2.64e-1629
cerebral cortex1.21e-1021
cerebral hemisphere1.21e-1021
pallium1.21e-1021
regional part of cerebral cortex2.12e-0917
occipital lobe4.44e-0910
visual cortex4.44e-0910
neocortex4.44e-0910
posterior neural tube1.89e-0712
chordal neural plate1.89e-0712
basal ganglion4.40e-078
nuclear complex of neuraxis4.40e-078
aggregate regional part of brain4.40e-078
collection of basal ganglia4.40e-078
cerebral subcortex4.40e-078


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)
MA0003.10.245953
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.10.133574
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
MA0055.10.557057
MA0056.10
MA0057.10.337566
MA0058.10.690848
MA0059.10.705317
MA0060.10.502699
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
MA0073.10.00834468
MA0074.10.911576
MA0076.10.657929
MA0077.11.2569
MA0078.12.30458
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.766354
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
MA0105.10.405648
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.10.537669
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
MA0139.10.462282
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.11.44606
MA0146.10.46063
MA0147.10.556853
MA0148.10.820161
MA0149.15.54197
MA0062.20.412742
MA0035.20.903829
MA0039.20.181475
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.20.48458
MA0047.20.962424
MA0112.20.29236
MA0065.20.79573
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.925147
MA0155.10.840842
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.10.166722
MA0163.10.157796
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.21.81944
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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