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MCL coexpression mm9:747: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0001016!3.62e-38!75;UBERON:0001017!1.03e-37!73;UBERON:0004121!8.84e-34!95;UBERON:0000924!8.84e-34!95;UBERON:0006601!8.84e-34!95;UBERON:0000073!5.04e-30!54;UBERON:0002346!3.74e-29!64;UBERON:0003075!3.74e-29!64;UBERON:0007284!3.74e-29!64;UBERON:0001049!2.71e-28!52;UBERON:0005068!2.71e-28!52;UBERON:0006241!2.71e-28!52;UBERON:0007135!2.71e-28!52;UBERON:0010371!1.92e-25!73;UBERON:0000955!1.97e-24!47;UBERON:0006238!1.97e-24!47;UBERON:0002616!8.86e-24!46;UBERON:0003056!3.03e-21!49;UBERON:0002020!1.50e-20!34;UBERON:0003080!3.15e-20!40;UBERON:0002780!1.39e-19!39;UBERON:0001890!1.39e-19!39;UBERON:0006240!1.39e-19!39;UBERON:0010314!7.08e-19!92;UBERON:0003528!5.68e-17!29;UBERON:0002791!5.68e-17!29;UBERON:0001893!5.68e-17!29;UBERON:0000956!3.99e-12!21;UBERON:0001869!3.99e-12!21;UBERON:0000203!3.99e-12!21;UBERON:0002619!3.19e-10!17;UBERON:0003076!1.58e-08!12;UBERON:0003057!1.58e-08!12;UBERON:0002021!5.17e-07!10;UBERON:0000411!5.17e-07!10;UBERON:0001950!5.17e-07!10
|tfbs_overrepresentation_for_novel_motifs=0.321524,0.883225,1.46622,0.360062,0.200163,0.373426,0.458558,0.785038,0.131493,1.53832,0.417132,0.447169,1.28029,1.18563,0.214197,0,0.656089,0.564478,0.113609,0.0560853,0.26524,0.60924,0.469335,0.198877,0.304728,0.496413,0.349241,0.392919,3.56634,0.0790295,0.379806,0.754912,0.560002,0.646834,0.214608,12.9553,2.32607,0.443753,0.498354,11.0913,0.196807,1.7717,0.0320468,0.617704,0.119503,0.349801,0.578773,0.407653,0.255625,0.677281,0.639101,0.522137,0.550735,0.894161,0.911367,1.20022,0.249055,0.435119,0.332535,0.47505,0.735292,0.531188,0.140453,0.628155,0.487593,0.667546,1.04613,1.3932,0.730718,1.24673,2.99507,0.128829,4.30526,0.944464,1.61595,1.54557,0.0942164,0.567793,0.718494,0.268962,0.406536,0.673009,0.529804,0.119727,1.94005,5.91308,2.09215,1.44534,0.583509,1.55487,1.11522,0.835661,0.767462,0.205117,9.4177,0.149272,0.122617,0.770215,0.57902,0.234357,0.184103,0.754637,0.87698,0.639679,0.638654,0.3842,0.696857,0.403887,3.84891,0.266818,0.315128,0.878738,0.26996,0.421988,1.12221,0.195318,1.37115,0.363536,0.657356,1.02287,0.949798,0.607824,0.498153,0.566919,1.17594,0.722111,0.466292,0.760818,1.04463,0.207624,0.86025,0.353344,1.01535,0.48999,1.14365,0.0358067,0.877308,0.385921,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,0.385031,0.581788,1.88287,0.882109,1.10485,0.97987,3.35582,0.895708,0.153911,0.489108,0.976367,0.523103,0.224422,0.319291,0.328917,1.1043,0.829923,0.722546,0.313083,0.629147,0.482049,0.53929,0.445669,8.73489
|tfbs_overrepresentation_jaspar=MA0003.1;3.94305,MA0004.1;0.360508,MA0006.1;0.604851,MA0007.1;0.346734,MA0009.1;0.780842,MA0014.1;1.80909,MA0017.1;0.233089,MA0019.1;0.603066,MA0024.1;0.737933,MA0025.1;1.01089,MA0027.1;2.42079,MA0028.1;0.625707,MA0029.1;0.716673,MA0030.1;0.723093,MA0031.1;0.688336,MA0038.1;0.496338,MA0040.1;0.79313,MA0041.1;4.99231,MA0042.1;2.98799,MA0043.1;0.875991,MA0046.1;0.816137,MA0048.1;0.236433,MA0050.1;0.396459,MA0051.1;0.504875,MA0052.1;0.801048,MA0055.1;0.344,MA0056.1;0,MA0057.1;0.471918,MA0058.1;0.273976,MA0059.1;0.28489,MA0060.1;0.446031,MA0061.1;0.504772,MA0063.1;0,MA0066.1;1.21924,MA0067.1;1.12095,MA0068.1;0.0621035,MA0069.1;0.801381,MA0070.1;0.791856,MA0071.1;0.395679,MA0072.1;0.783532,MA0073.1;7.68794,MA0074.1;2.00038,MA0076.1;0.249619,MA0077.1;0.762273,MA0078.1;0.536502,MA0081.1;0.824359,MA0083.1;0.875209,MA0084.1;1.44691,MA0087.1;0.832758,MA0088.1;1.86507,MA0089.1;0,MA0090.1;0.329158,MA0091.1;0.372635,MA0092.1;0.329444,MA0093.1;0.226349,MA0095.1;0,MA0098.1;0,MA0100.1;0.440912,MA0101.1;0.292867,MA0103.1;0.242398,MA0105.1;1.56265,MA0106.1;0.543967,MA0107.1;0.237082,MA0108.2;0.625209,MA0109.1;0,MA0111.1;0.342068,MA0113.1;0.516916,MA0114.1;0.500166,MA0115.1;0.878749,MA0116.1;0.604438,MA0117.1;0.846964,MA0119.1;0.293392,MA0122.1;0.866511,MA0124.1;1.06819,MA0125.1;0.994853,MA0130.1;0,MA0131.1;0.598671,MA0132.1;0,MA0133.1;0,MA0135.1;0.911905,MA0136.1;0.470672,MA0139.1;1.26076,MA0140.1;0.440804,MA0141.1;0.259554,MA0142.1;0.674191,MA0143.1;0.53259,MA0144.1;0.169559,MA0145.1;0.664015,MA0146.1;1.62155,MA0147.1;0.530496,MA0148.1;0.375491,MA0149.1;2.2387,MA0062.2;0.314778,MA0035.2;0.44524,MA0039.2;3.94506,MA0138.2;0.590987,MA0002.2;0.123715,MA0137.2;0.257017,MA0104.2;0.418613,MA0047.2;0.495607,MA0112.2;0.163154,MA0065.2;3.09719,MA0150.1;0.346631,MA0151.1;0,MA0152.1;0.495709,MA0153.1;0.92832,MA0154.1;1.3022,MA0155.1;1.58565,MA0156.1;0.248865,MA0157.1;0.642984,MA0158.1;0,MA0159.1;0.187774,MA0160.1;0.378276,MA0161.1;0,MA0162.1;9.08041,MA0163.1;7.35073,MA0164.1;0.471016,MA0080.2;0.237846,MA0018.2;1.20715,MA0099.2;0.584892,MA0079.2;29.5854,MA0102.2;1.49914,MA0258.1;0.156336,MA0259.1;0.50935,MA0442.1;0
}}

Latest revision as of 15:49, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr3:8667033..8667046,-p3@Hey1
Mm9::chr4:41587002..41587016,-p1@Enho
Mm9::chr4:41587133..41587170,-p2@Enho
Mm9::chr5:136108551..136108564,+p3@Rhbdd2
Mm9::chr7:25266999..25267006,+p2@Cadm4
Mm9::chr7:25267010..25267095,+p1@Cadm4
Mm9::chr7:25284618..25284623,+p@chr7:25284618..25284623
+
Mm9::chr7:25286643..25286656,+p@chr7:25286643..25286656
+
Mm9::chr7:51684213..51684237,+p6@Lrrc4b
Mm9::chr7:51684308..51684349,+p4@Lrrc4b


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

no results for this coexpression

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
nervous system3.62e-3875
central nervous system1.03e-3773
ectoderm-derived structure8.84e-3495
ectoderm8.84e-3495
presumptive ectoderm8.84e-3495
regional part of nervous system5.04e-3054
neurectoderm3.74e-2964
neural plate3.74e-2964
presumptive neural plate3.74e-2964
neural tube2.71e-2852
neural rod2.71e-2852
future spinal cord2.71e-2852
neural keel2.71e-2852
ecto-epithelium1.92e-2573
brain1.97e-2447
future brain1.97e-2447
regional part of brain8.86e-2446
pre-chordal neural plate3.03e-2149
gray matter1.50e-2034
anterior neural tube3.15e-2040
regional part of forebrain1.39e-1939
forebrain1.39e-1939
future forebrain1.39e-1939
structure with developmental contribution from neural crest7.08e-1992
brain grey matter5.68e-1729
regional part of telencephalon5.68e-1729
telencephalon5.68e-1729
cerebral cortex3.99e-1221
cerebral hemisphere3.99e-1221
pallium3.99e-1221
regional part of cerebral cortex3.19e-1017
posterior neural tube1.58e-0812
chordal neural plate1.58e-0812
occipital lobe5.17e-0710
visual cortex5.17e-0710
neocortex5.17e-0710


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)
MA0003.13.94305
MA0004.10.360508
MA0006.10.604851
MA0007.10.346734
MA0009.10.780842
MA0014.11.80909
MA0017.10.233089
MA0019.10.603066
MA0024.10.737933
MA0025.11.01089
MA0027.12.42079
MA0028.10.625707
MA0029.10.716673
MA0030.10.723093
MA0031.10.688336
MA0038.10.496338
MA0040.10.79313
MA0041.14.99231
MA0042.12.98799
MA0043.10.875991
MA0046.10.816137
MA0048.10.236433
MA0050.10.396459
MA0051.10.504875
MA0052.10.801048
MA0055.10.344
MA0056.10
MA0057.10.471918
MA0058.10.273976
MA0059.10.28489
MA0060.10.446031
MA0061.10.504772
MA0063.10
MA0066.11.21924
MA0067.11.12095
MA0068.10.0621035
MA0069.10.801381
MA0070.10.791856
MA0071.10.395679
MA0072.10.783532
MA0073.17.68794
MA0074.12.00038
MA0076.10.249619
MA0077.10.762273
MA0078.10.536502
MA0081.10.824359
MA0083.10.875209
MA0084.11.44691
MA0087.10.832758
MA0088.11.86507
MA0089.10
MA0090.10.329158
MA0091.10.372635
MA0092.10.329444
MA0093.10.226349
MA0095.10
MA0098.10
MA0100.10.440912
MA0101.10.292867
MA0103.10.242398
MA0105.11.56265
MA0106.10.543967
MA0107.10.237082
MA0108.20.625209
MA0109.10
MA0111.10.342068
MA0113.10.516916
MA0114.10.500166
MA0115.10.878749
MA0116.10.604438
MA0117.10.846964
MA0119.10.293392
MA0122.10.866511
MA0124.11.06819
MA0125.10.994853
MA0130.10
MA0131.10.598671
MA0132.10
MA0133.10
MA0135.10.911905
MA0136.10.470672
MA0139.11.26076
MA0140.10.440804
MA0141.10.259554
MA0142.10.674191
MA0143.10.53259
MA0144.10.169559
MA0145.10.664015
MA0146.11.62155
MA0147.10.530496
MA0148.10.375491
MA0149.12.2387
MA0062.20.314778
MA0035.20.44524
MA0039.23.94506
MA0138.20.590987
MA0002.20.123715
MA0137.20.257017
MA0104.20.418613
MA0047.20.495607
MA0112.20.163154
MA0065.23.09719
MA0150.10.346631
MA0151.10
MA0152.10.495709
MA0153.10.92832
MA0154.11.3022
MA0155.11.58565
MA0156.10.248865
MA0157.10.642984
MA0158.10
MA0159.10.187774
MA0160.10.378276
MA0161.10
MA0162.19.08041
MA0163.17.35073
MA0164.10.471016
MA0080.20.237846
MA0018.21.20715
MA0099.20.584892
MA0079.229.5854
MA0102.21.49914
MA0258.10.156336
MA0259.10.50935
MA0442.10
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