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MCL coexpression mm9:525: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0030144;alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity;0.0256382161274507;268510!}}
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6-beta-N-acetylglucosaminyltransferase activity;0.0256382161274507;268510!|ontology_enrichment_celltype=CL:0000117!1.97e-24!23;CL:0000337!1.97e-24!23;CL:0000540!2.77e-20!33;CL:0000047!2.77e-20!33;CL:0000031!2.77e-20!33;CL:0000404!2.77e-20!33;CL:0002319!8.21e-18!43;CL:0000221!3.66e-17!44;CL:0000133!3.66e-17!44;CL:0000393!1.15e-15!39;CL:0000211!1.15e-15!39;CL:0000055!2.45e-14!49;CL:0002321!3.62e-07!70|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0001017!1.87e-39!73;UBERON:0001016!3.85e-39!75;UBERON:0000073!3.13e-35!54;UBERON:0002346!8.35e-35!64;UBERON:0003075!8.35e-35!64;UBERON:0007284!8.35e-35!64;UBERON:0004121!6.42e-34!95;UBERON:0000924!6.42e-34!95;UBERON:0006601!6.42e-34!95;UBERON:0001049!7.46e-33!52;UBERON:0005068!7.46e-33!52;UBERON:0006241!7.46e-33!52;UBERON:0007135!7.46e-33!52;UBERON:0002020!1.01e-31!34;UBERON:0010371!2.44e-28!73;UBERON:0000955!2.98e-27!47;UBERON:0006238!2.98e-27!47;UBERON:0002616!2.35e-26!46;UBERON:0003528!5.94e-26!29;UBERON:0002791!5.94e-26!29;UBERON:0001893!5.94e-26!29;UBERON:0003056!1.25e-25!49;UBERON:0003080!1.35e-24!40;UBERON:0002780!8.60e-24!39;UBERON:0001890!8.60e-24!39;UBERON:0006240!8.60e-24!39;UBERON:0010314!7.98e-21!92;UBERON:0000956!1.42e-17!21;UBERON:0001869!1.42e-17!21;UBERON:0000203!1.42e-17!21;UBERON:0002619!5.53e-14!17;UBERON:0002021!1.99e-12!10;UBERON:0000411!1.99e-12!10;UBERON:0001950!1.99e-12!10;UBERON:0002420!1.66e-09!8;UBERON:0007245!1.66e-09!8;UBERON:0010009!1.66e-09!8;UBERON:0010011!1.66e-09!8;UBERON:0000454!1.66e-09!8;UBERON:0003076!1.73e-08!12;UBERON:0003057!1.73e-08!12;UBERON:0002240!1.35e-07!6;UBERON:0005174!1.35e-07!6;UBERON:0001137!1.35e-07!6;UBERON:0000025!2.69e-07!114;UBERON:0001948!7.21e-07!5;UBERON:0002315!7.21e-07!5|tfbs_overrepresentation_for_novel_motifs=0.224466,0.284621,1.11498,0.716126,0.123731,0.269875,0.346405,0.875434,0.0719629,0.0394224,0.308886,0.336042,0.237599,0.357027,0.419678,0,0.530547,2.44767,0.215337,0.465097,0.176628,0.165365,0.356242,0.122718,0.210021,0.381085,0.203385,0.287195,0.915208,0.145734,0.275529,0.624931,1.2318,0.176308,0.420513,0.61925,0.111136,0.332941,0.322338,0.581324,0.384293,0.279796,0.504634,0.136236,0.0109479,0.24907,0.457618,0.300372,0.647158,0.156829,0.514446,0.404841,0.321327,0.759566,0.776306,0.363247,0.490599,0.325117,0.424359,0.36147,0.606104,0.413233,0.0784106,0.504093,0.372973,0.541429,0.908031,1.25063,1.46477,1.10561,0.189925,0.246154,0.0145353,0.808562,0.181606,0.0433214,0.702638,0.447339,0.590017,1.61198,0.247973,0.546623,1.05972,0.493111,0.69807,0.00290338,0.290012,0.0368325,1.16814,1.41118,0.975915,0.702809,0.636995,0.401201,0.0951738,0.0848579,0.503836,1.54424,0.457849,0.119684,1.19301,1.51291,0.742871,1.28142,0.514023,0.279432,0.569344,0.804983,1.03226,0.177945,0.62491,0.744577,0.533113,0.313258,0.982794,0.381263,0.00519761,0.26114,0.53175,0.352143,3.16643,0.484912,0.382687,1.13466,1.03573,1.44745,0.931332,0.630607,0.906557,0.807921,0.726634,0.252176,0.877862,0.979261,1.0039,0.546308,0.231086,0.768569,0.955897,1.77738,1.3796,0.91261,0.393303,0.634793,0.508066,0.280171,0.460443,1.73788,0.232952,0.124893,0.0377782,0.0106906,0.761071,0.0882878,0.374365,0.839715,0.405736,0.143092,0.222538,0.230865,0.96517,0.697256,0.593895,0.620756,0.50503,0.367885,0.356446,0.8896,0.0249603|tfbs_overrepresentation_jaspar=MA0003.1;0.0100854,MA0004.1;0.258473,MA0006.1;0.817804,MA0007.1;0.246385,MA0009.1;1.56562,MA0014.1;0.023905,MA0017.1;0.150118,MA0019.1;0.480432,MA0024.1;0.608636,MA0025.1;0.873493,MA0027.1;2.275,MA0028.1;0.138956,MA0029.1;1.4365,MA0030.1;2.46973,MA0031.1;0.561217,MA0038.1;0.381016,MA0040.1;0.661716,MA0041.1;0.198922,MA0042.1;0.189008,MA0043.1;0.74191,MA0046.1;0.683926,MA0048.1;0.121113,MA0050.1;0.789929,MA0051.1;2.68041,MA0052.1;0.669354,MA0055.1;0.0652519,MA0056.1;0,MA0057.1;0.261486,MA0058.1;0.183941,MA0059.1;0.19314,MA0060.1;0.0819399,MA0061.1;0.32765,MA0063.1;0,MA0066.1;0.970926,MA0067.1;0.981551,MA0068.1;1.17375,MA0069.1;0.669676,MA0070.1;0.660488,MA0071.1;0.289658,MA0072.1;0.652465,MA0073.1;0.0850495,MA0074.1;0.340281,MA0076.1;0.163664,MA0077.1;0.632005,MA0078.1;0.418168,MA0081.1;0.210747,MA0083.1;0.741151,MA0084.1;1.30392,MA0087.1;0.699999,MA0088.1;0.339729,MA0089.1;0,MA0090.1;0.231074,MA0091.1;0.269175,MA0092.1;1.21955,MA0093.1;0.144649,MA0095.1;0,MA0098.1;0,MA0100.1;0.330364,MA0101.1;0.199903,MA0103.1;0.477056,MA0105.1;0.684733,MA0106.1;1.91018,MA0107.1;0.153373,MA0108.2;0.50131,MA0109.1;0,MA0111.1;1.26116,MA0113.1;1.03368,MA0114.1;0.0981613,MA0115.1;0.744589,MA0116.1;1.91953,MA0117.1;0.713754,MA0119.1;0.200349,MA0122.1;0.732707,MA0124.1;0.929684,MA0125.1;0.857794,MA0130.1;0,MA0131.1;0.476296,MA0132.1;0,MA0133.1;0,MA0135.1;0.77683,MA0136.1;0.357464,MA0139.1;0.0649474,MA0140.1;0.330266,MA0141.1;0.511953,MA0142.1;0.547747,MA0143.1;0.414534,MA0144.1;0.674112,MA0145.1;0.370377,MA0146.1;0.0854135,MA0147.1;0.107632,MA0148.1;1.37059,MA0149.1;0.204102,MA0062.2;0.046824,MA0035.2;0.33429,MA0039.2;0.0846004,MA0138.2;0.469076,MA0002.2;0.5079,MA0137.2;0.506794,MA0104.2;0.0740839,MA0047.2;0.990617,MA0112.2;0.189423,MA0065.2;0.3717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Latest revision as of 15:27, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:116828045..116828049,+p5@Mgat5b
Mm9::chr11:16954693..16954700,+p@chr11:16954693..16954700
+
Mm9::chr12:73313141..73313164,-p@chr12:73313141..73313164
-
Mm9::chr12:73313178..73313189,-p@chr12:73313178..73313189
-
Mm9::chr12:73313399..73313409,-p@chr12:73313399..73313409
-
Mm9::chr12:73313502..73313511,-p@chr12:73313502..73313511
-
Mm9::chr12:73313514..73313529,-p@chr12:73313514..73313529
-
Mm9::chr19:8913125..8913139,-p@chr19:8913125..8913139
-
Mm9::chr1:160621435..160621446,+p@chr1:160621435..160621446
+
Mm9::chr1:175266941..175266951,-p@chr1:175266941..175266951
-
Mm9::chr1:175275934..175275941,-p@chr1:175275934..175275941
-
Mm9::chr1:94972820..94972832,-p@chr1:94972820..94972832
-
Mm9::chr6:71759404..71759428,+p@chr6:71759404..71759428
+
Mm9::chr8:96487383..96487399,+p@chr8:96487383..96487399
+


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:0030144alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity0.0256382161274507



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>

Uber Anatomy
Ontology termp-valuen
central nervous system1.87e-3973
nervous system3.85e-3975
regional part of nervous system3.13e-3554
neurectoderm8.35e-3564
neural plate8.35e-3564
presumptive neural plate8.35e-3564
ectoderm-derived structure6.42e-3495
ectoderm6.42e-3495
presumptive ectoderm6.42e-3495
neural tube7.46e-3352
neural rod7.46e-3352
future spinal cord7.46e-3352
neural keel7.46e-3352
gray matter1.01e-3134
ecto-epithelium2.44e-2873
brain2.98e-2747
future brain2.98e-2747
regional part of brain2.35e-2646
brain grey matter5.94e-2629
regional part of telencephalon5.94e-2629
telencephalon5.94e-2629
pre-chordal neural plate1.25e-2549
anterior neural tube1.35e-2440
regional part of forebrain8.60e-2439
forebrain8.60e-2439
future forebrain8.60e-2439
structure with developmental contribution from neural crest7.98e-2192
cerebral cortex1.42e-1721
cerebral hemisphere1.42e-1721
pallium1.42e-1721
regional part of cerebral cortex5.53e-1417
occipital lobe1.99e-1210
visual cortex1.99e-1210
neocortex1.99e-1210
basal ganglion1.66e-098
nuclear complex of neuraxis1.66e-098
aggregate regional part of brain1.66e-098
collection of basal ganglia1.66e-098
cerebral subcortex1.66e-098
posterior neural tube1.73e-0812
chordal neural plate1.73e-0812
spinal cord1.35e-076
dorsal region element1.35e-076
dorsum1.35e-076
tube2.69e-07114
regional part of spinal cord7.21e-075
gray matter of spinal cord7.21e-075


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)
MA0003.10.0100854
MA0004.10.258473
MA0006.10.817804
MA0007.10.246385
MA0009.11.56562
MA0014.10.023905
MA0017.10.150118
MA0019.10.480432
MA0024.10.608636
MA0025.10.873493
MA0027.12.275
MA0028.10.138956
MA0029.11.4365
MA0030.12.46973
MA0031.10.561217
MA0038.10.381016
MA0040.10.661716
MA0041.10.198922
MA0042.10.189008
MA0043.10.74191
MA0046.10.683926
MA0048.10.121113
MA0050.10.789929
MA0051.12.68041
MA0052.10.669354
MA0055.10.0652519
MA0056.10
MA0057.10.261486
MA0058.10.183941
MA0059.10.19314
MA0060.10.0819399
MA0061.10.32765
MA0063.10
MA0066.10.970926
MA0067.10.981551
MA0068.11.17375
MA0069.10.669676
MA0070.10.660488
MA0071.10.289658
MA0072.10.652465
MA0073.10.0850495
MA0074.10.340281
MA0076.10.163664
MA0077.10.632005
MA0078.10.418168
MA0081.10.210747
MA0083.10.741151
MA0084.11.30392
MA0087.10.699999
MA0088.10.339729
MA0089.10
MA0090.10.231074
MA0091.10.269175
MA0092.11.21955
MA0093.10.144649
MA0095.10
MA0098.10
MA0100.10.330364
MA0101.10.199903
MA0103.10.477056
MA0105.10.684733
MA0106.11.91018
MA0107.10.153373
MA0108.20.50131
MA0109.10
MA0111.11.26116
MA0113.11.03368
MA0114.10.0981613
MA0115.10.744589
MA0116.11.91953
MA0117.10.713754
MA0119.10.200349
MA0122.10.732707
MA0124.10.929684
MA0125.10.857794
MA0130.10
MA0131.10.476296
MA0132.10
MA0133.10
MA0135.10.77683
MA0136.10.357464
MA0139.10.0649474
MA0140.10.330266
MA0141.10.511953
MA0142.10.547747
MA0143.10.414534
MA0144.10.674112
MA0145.10.370377
MA0146.10.0854135
MA0147.10.107632
MA0148.11.37059
MA0149.10.204102
MA0062.20.046824
MA0035.20.33429
MA0039.20.0846004
MA0138.20.469076
MA0002.20.5079
MA0137.20.506794
MA0104.20.0740839
MA0047.20.990617
MA0112.20.189423
MA0065.20.371748
MA0150.10.246295
MA0151.10
MA0152.10.380437
MA0153.10.792819
MA0154.10.837005
MA0155.10.22104
MA0156.10.163042
MA0157.10.518122
MA0158.10
MA0159.10.114033
MA0160.10.274172
MA0161.10
MA0162.10.21028
MA0163.10.70702
MA0164.10.357779
MA0080.20.153997
MA0018.20.366212
MA0099.20.463355
MA0079.20.176062
MA0102.21.35579
MA0258.10.0900907
MA0259.10.331447
MA0442.10
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