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MCL coexpression mm9:624: Difference between revisions

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{{MCL_coexpression_mm9
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phosphatase type 1 regulator activity;0.0403056258892532;74100!GO:0001784;phosphotyrosine binding;0.0403056258892532;26417!GO:0045309;protein phosphorylated amino acid binding;0.0403056258892532;26417!GO:0043330;response to exogenous dsRNA;0.0403056258892532;26417!GO:0031663;lipopolysaccharide-mediated signaling pathway;0.0403056258892532;26417!GO:0032496;response to lipopolysaccharide;0.0403056258892532;26417!GO:0051219;phosphoprotein binding;0.0403056258892532;26417!GO:0004707;MAP kinase activity;0.0403056258892532;26417!GO:0043331;response to dsRNA;0.0403056258892532;26417!GO:0002237;response to molecule of bacterial 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|gostat_on_MCL_coexpression=GO:0008599;protein phosphatase type 1 regulator activity;0.0403056258892532;74100!GO:0001784;phosphotyrosine binding;0.0403056258892532;26417!GO:0045309;protein phosphorylated amino acid binding;0.0403056258892532;26417!GO:0043330;response to exogenous dsRNA;0.0403056258892532;26417!GO:0031663;lipopolysaccharide-mediated signaling pathway;0.0403056258892532;26417!GO:0032496;response to lipopolysaccharide;0.0403056258892532;26417!GO:0051219;phosphoprotein binding;0.0403056258892532;26417!GO:0004707;MAP kinase activity;0.0403056258892532;26417!GO:0043331;response to dsRNA;0.0403056258892532;26417!GO:0002237;response to molecule of bacterial origin;0.0474158328063201;26417!
|ontology_enrichment_celltype=CL:0000117!1.77e-16!23;CL:0000337!1.77e-16!23;CL:0000540!9.96e-10!33;CL:0000047!9.96e-10!33;CL:0000031!9.96e-10!33;CL:0000404!9.96e-10!33;CL:0000393!4.52e-07!39;CL:0000211!4.52e-07!39
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!1.59e-29!54;UBERON:0001049!2.00e-27!52;UBERON:0005068!2.00e-27!52;UBERON:0006241!2.00e-27!52;UBERON:0007135!2.00e-27!52;UBERON:0002346!1.80e-26!64;UBERON:0003075!1.80e-26!64;UBERON:0007284!1.80e-26!64;UBERON:0002020!1.12e-24!34;UBERON:0010371!2.98e-24!73;UBERON:0000955!4.61e-24!47;UBERON:0006238!4.61e-24!47;UBERON:0001017!5.87e-24!73;UBERON:0001016!1.23e-23!75;UBERON:0003056!2.42e-23!49;UBERON:0002616!5.07e-23!46;UBERON:0004121!2.07e-22!95;UBERON:0000924!2.07e-22!95;UBERON:0006601!2.07e-22!95;UBERON:0003080!2.62e-22!40;UBERON:0002780!2.03e-21!39;UBERON:0001890!2.03e-21!39;UBERON:0006240!2.03e-21!39;UBERON:0003528!6.33e-21!29;UBERON:0002791!6.33e-21!29;UBERON:0001893!6.33e-21!29;UBERON:0010314!5.30e-16!92;UBERON:0000956!9.50e-16!21;UBERON:0001869!9.50e-16!21;UBERON:0000203!9.50e-16!21;UBERON:0002619!5.05e-13!17;UBERON:0002021!3.45e-11!10;UBERON:0000411!3.45e-11!10;UBERON:0001950!3.45e-11!10
|tfbs_overrepresentation_for_novel_motifs=0.267173,0.409645,0.245304,0.303186,0.474017,0.315748,0.396495,0.630239,0.320069,0.336879,0.357058,1.00221,0.304329,0.407615,0.169024,0,0.587245,0.897987,0.0817508,1.35406,0.616152,0.0948826,0.406794,0.155356,0.251585,0.432737,0.0768517,0.334131,0.191143,0.766158,0.860721,0.683831,1.43157,0.234079,0.975762,0.860101,0.438297,0.382372,0.126724,1.70931,0.466602,0.326286,0.0834993,0.980484,0.283915,0.293566,0.512146,0.34807,0.337012,0.19345,0.570705,0.457464,0.736781,0.82076,0.837732,0.414119,0.581069,0.37415,0.535132,0.412262,0.664611,0.46618,0.104381,0.560059,0.424276,0.598412,0.970969,1.3158,0.660133,1.17005,0.229771,0.313987,1.11546,0.870406,0.51601,0.483805,0.233965,0.50152,0.648171,1.82802,0.316038,0.60374,0.464847,0.293128,0.758319,0.580776,0.237482,0.198381,0.516731,1.47691,1.03946,0.763136,0.696137,0.16091,0.782777,0.11194,0.622881,0.698838,0.512384,0.67526,0.862562,0.683562,0.803823,0.571268,0.57027,0.3259,0.627019,0.344504,0.222586,0.216685,0.261228,0.805555,0.626352,0.361667,1.04639,0.152197,0.136172,0.306448,0.58848,0.139554,0.875675,0.540309,0.434408,0.500675,1.09972,0.651709,1.04215,0.689622,0.969481,0.49047,0.787341,0.296885,0.940498,0.426575,1.06766,0.231689,0.274293,0.327523,1.01927,1.84381,1.44523,0.975592,0.445463,0.693891,0.564145,0.326684,0.515065,1.80426,0.276297,0.477267,0.445509,0.663851,0.822286,0.115938,0.425729,0.901933,0.458393,0.178202,0.265096,0.274055,1.02862,0.757491,0.652135,0.25933,0.561023,1.07498,0.141416,1.77028,0.00224839
|tfbs_overrepresentation_jaspar=MA0003.1;0.112759,MA0004.1;0.303605,MA0006.1;0.496735,MA0007.1;0.290695,MA0009.1;0.709264,MA0014.1;0.212509,MA0017.1;0.186015,MA0019.1;0.535691,MA0024.1;0.667197,MA0025.1;0.936082,MA0027.1;2.34178,MA0028.1;0.173587,MA0029.1;0.64639,MA0030.1;0.65267,MA0031.1;0.618697,MA0038.1;0.432665,MA0040.1;0.721328,MA0041.1;0.239557,MA0042.1;0.228771,MA0043.1;0.802848,MA0046.1;0.743934,MA0048.1;0.168666,MA0050.1;0.337476,MA0051.1;0.440863,MA0052.1;0.729105,MA0055.1;0.226387,MA0056.1;0,MA0057.1;0.151898,MA0058.1;0.635024,MA0059.1;0.658541,MA0060.1;0.108526,MA0061.1;0.129002,MA0063.1;0,MA0066.1;0.422624,MA0067.1;1.04514,MA0068.1;0.0405002,MA0069.1;1.73105,MA0070.1;0.720077,MA0071.1;0.336739,MA0072.1;0.711905,MA0073.1;0.010504,MA0074.1;0.390075,MA0076.1;0.200996,MA0077.1;0.691048,MA0078.1;0.471303,MA0081.1;0.702944,MA0083.1;0.802078,MA0084.1;1.3693,MA0087.1;0.760279,MA0088.1;0.742898,MA0089.1;0,MA0090.1;0.27428,MA0091.1;0.315003,MA0092.1;0.274547,MA0093.1;0.179936,MA0095.1;0,MA0098.1;0,MA0100.1;0.379666,MA0101.1;0.240622,MA0103.1;0.19444,MA0105.1;0.0633795,MA0106.1;0.478503,MA0107.1;0.189625,MA0108.2;0.557195,MA0109.1;0,MA0111.1;1.42413,MA0113.1;0.452439,MA0114.1;0.797973,MA0115.1;0.805567,MA0116.1;0.496352,MA0117.1;0.774259,MA0119.1;0.241106,MA0122.1;0.793507,MA0124.1;0.992825,MA0125.1;0.920215,MA0130.1;0,MA0131.1;0.531427,MA0132.1;0,MA0133.1;0,MA0135.1;0.838263,MA0136.1;0.408073,MA0139.1;0.61859,MA0140.1;0.379562,MA0141.1;0.210047,MA0142.1;0.604892,MA0143.1;0.467531,MA0144.1;0.129525,MA0145.1;0.0257706,MA0146.1;0.00325174,MA0147.1;0.428193,MA0148.1;0.317692,MA0149.1;0.245177,MA0062.2;0.235333,MA0035.2;0.383789,MA0039.2;0.0528941,MA0138.2;1.30053,MA0002.2;0.302282,MA0137.2;0.207733,MA0104.2;0.670538,MA0047.2;0.431964,MA0112.2;0.494696,MA0065.2;0.265926,MA0150.1;0.790482,MA0151.1;0,MA0152.1;0.432062,MA0153.1;0.854464,MA0154.1;0.16541,MA0155.1;0.0312913,MA0156.1;0.200311,MA0157.1;0.574484,MA0158.1;0,MA0159.1;0.145521,MA0160.1;0.320315,MA0161.1;0,MA0162.1;0.00450899,MA0163.1;0.0220786,MA0164.1;0.408402,MA0080.2;0.556674,MA0018.2;0.417217,MA0099.2;0.518072,MA0079.2;0.0826333,MA0102.2;1.42135,MA0258.1;0.118033,MA0259.1;0.130633,MA0442.1;0
}}

Latest revision as of 15:37, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr17:17539647..17539735,+p1@Lix1
Mm9::chr1:136763197..136763205,-p@chr1:136763197..136763205
-
Mm9::chr2:26998050..26998076,-p3@Fam163b
Mm9::chr3:117278186..117278200,+p6@4833424O15Rik
Mm9::chr6:5736930..5736933,+p@chr6:5736930..5736933
+
Mm9::chr6:5739540..5739543,+p@chr6:5739540..5739543
+
Mm9::chr7:133906383..133906396,+p7@Mapk3
Mm9::chr7:133906398..133906414,+p8@Mapk3
Mm9::chr7:151424595..151424610,+p@chr7:151424595..151424610
+
Mm9::chr7:151424623..151424635,+p@chr7:151424623..151424635
+
Mm9::chr9:104471931..104471961,+p3@Cpne4
Mm9::chr9:112138015..112138040,-p11@Arpp21


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:0008599protein phosphatase type 1 regulator activity0.0403056258892532
GO:0001784phosphotyrosine binding0.0403056258892532
GO:0045309protein phosphorylated amino acid binding0.0403056258892532
GO:0043330response to exogenous dsRNA0.0403056258892532
GO:0031663lipopolysaccharide-mediated signaling pathway0.0403056258892532
GO:0032496response to lipopolysaccharide0.0403056258892532
GO:0051219phosphoprotein binding0.0403056258892532
GO:0004707MAP kinase activity0.0403056258892532
GO:0043331response to dsRNA0.0403056258892532
GO:0002237response to molecule of bacterial origin0.0474158328063201



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)1.77e-1623
neuroblast (sensu Vertebrata)1.77e-1623
neuron9.96e-1033
neuronal stem cell9.96e-1033
neuroblast9.96e-1033
electrically signaling cell9.96e-1033
electrically responsive cell4.52e-0739
electrically active cell4.52e-0739

Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.59e-2954
neural tube2.00e-2752
neural rod2.00e-2752
future spinal cord2.00e-2752
neural keel2.00e-2752
neurectoderm1.80e-2664
neural plate1.80e-2664
presumptive neural plate1.80e-2664
gray matter1.12e-2434
ecto-epithelium2.98e-2473
brain4.61e-2447
future brain4.61e-2447
central nervous system5.87e-2473
nervous system1.23e-2375
pre-chordal neural plate2.42e-2349
regional part of brain5.07e-2346
ectoderm-derived structure2.07e-2295
ectoderm2.07e-2295
presumptive ectoderm2.07e-2295
anterior neural tube2.62e-2240
regional part of forebrain2.03e-2139
forebrain2.03e-2139
future forebrain2.03e-2139
brain grey matter6.33e-2129
regional part of telencephalon6.33e-2129
telencephalon6.33e-2129
structure with developmental contribution from neural crest5.30e-1692
cerebral cortex9.50e-1621
cerebral hemisphere9.50e-1621
pallium9.50e-1621
regional part of cerebral cortex5.05e-1317
occipital lobe3.45e-1110
visual cortex3.45e-1110
neocortex3.45e-1110


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)
MA0003.10.112759
MA0004.10.303605
MA0006.10.496735
MA0007.10.290695
MA0009.10.709264
MA0014.10.212509
MA0017.10.186015
MA0019.10.535691
MA0024.10.667197
MA0025.10.936082
MA0027.12.34178
MA0028.10.173587
MA0029.10.64639
MA0030.10.65267
MA0031.10.618697
MA0038.10.432665
MA0040.10.721328
MA0041.10.239557
MA0042.10.228771
MA0043.10.802848
MA0046.10.743934
MA0048.10.168666
MA0050.10.337476
MA0051.10.440863
MA0052.10.729105
MA0055.10.226387
MA0056.10
MA0057.10.151898
MA0058.10.635024
MA0059.10.658541
MA0060.10.108526
MA0061.10.129002
MA0063.10
MA0066.10.422624
MA0067.11.04514
MA0068.10.0405002
MA0069.11.73105
MA0070.10.720077
MA0071.10.336739
MA0072.10.711905
MA0073.10.010504
MA0074.10.390075
MA0076.10.200996
MA0077.10.691048
MA0078.10.471303
MA0081.10.702944
MA0083.10.802078
MA0084.11.3693
MA0087.10.760279
MA0088.10.742898
MA0089.10
MA0090.10.27428
MA0091.10.315003
MA0092.10.274547
MA0093.10.179936
MA0095.10
MA0098.10
MA0100.10.379666
MA0101.10.240622
MA0103.10.19444
MA0105.10.0633795
MA0106.10.478503
MA0107.10.189625
MA0108.20.557195
MA0109.10
MA0111.11.42413
MA0113.10.452439
MA0114.10.797973
MA0115.10.805567
MA0116.10.496352
MA0117.10.774259
MA0119.10.241106
MA0122.10.793507
MA0124.10.992825
MA0125.10.920215
MA0130.10
MA0131.10.531427
MA0132.10
MA0133.10
MA0135.10.838263
MA0136.10.408073
MA0139.10.61859
MA0140.10.379562
MA0141.10.210047
MA0142.10.604892
MA0143.10.467531
MA0144.10.129525
MA0145.10.0257706
MA0146.10.00325174
MA0147.10.428193
MA0148.10.317692
MA0149.10.245177
MA0062.20.235333
MA0035.20.383789
MA0039.20.0528941
MA0138.21.30053
MA0002.20.302282
MA0137.20.207733
MA0104.20.670538
MA0047.20.431964
MA0112.20.494696
MA0065.20.265926
MA0150.10.790482
MA0151.10
MA0152.10.432062
MA0153.10.854464
MA0154.10.16541
MA0155.10.0312913
MA0156.10.200311
MA0157.10.574484
MA0158.10
MA0159.10.145521
MA0160.10.320315
MA0161.10
MA0162.10.00450899
MA0163.10.0220786
MA0164.10.408402
MA0080.20.556674
MA0018.20.417217
MA0099.20.518072
MA0079.20.0826333
MA0102.21.42135
MA0258.10.118033
MA0259.10.130633
MA0442.10
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