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MCL coexpression mm9:741: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0005509;calcium ion binding;0.00373182711349774;65945,12314,12315!}}
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expression=GO:0005509;calcium 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binding;0.00373182711349774;65945,12314,12315!|ontology_enrichment_celltype=CL:0000055!1.36e-15!49;CL:0000221!6.53e-14!44;CL:0000133!6.53e-14!44;CL:0002319!9.63e-14!43;CL:0000117!1.28e-13!23;CL:0000337!1.28e-13!23;CL:0000393!7.41e-12!39;CL:0000211!7.41e-12!39;CL:0002321!1.27e-10!70;CL:0000540!4.14e-10!33;CL:0000047!4.14e-10!33;CL:0000031!4.14e-10!33;CL:0000404!4.14e-10!33|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0001017!1.01e-26!73;UBERON:0001016!1.52e-26!75;UBERON:0000073!1.06e-24!54;UBERON:0001049!3.56e-23!52;UBERON:0005068!3.56e-23!52;UBERON:0006241!3.56e-23!52;UBERON:0007135!3.56e-23!52;UBERON:0002346!4.53e-20!64;UBERON:0003075!4.53e-20!64;UBERON:0007284!4.53e-20!64;UBERON:0000955!1.63e-19!47;UBERON:0006238!1.63e-19!47;UBERON:0002616!3.71e-19!46;UBERON:0002020!6.65e-19!34;UBERON:0010314!2.32e-17!92;UBERON:0003080!1.69e-16!40;UBERON:0004121!1.96e-16!95;UBERON:0000924!1.96e-16!95;UBERON:0006601!1.96e-16!95;UBERON:0002780!4.30e-16!39;UBERON:0001890!4.30e-16!39;UBERON:0006240!4.30e-16!39;UBERON:0003528!1.60e-15!29;UBERON:0002791!1.60e-15!29;UBERON:0001893!1.60e-15!29;UBERON:0010371!2.07e-14!73;UBERON:0003056!2.97e-14!49;UBERON:0000956!7.02e-12!21;UBERON:0001869!7.02e-12!21;UBERON:0000203!7.02e-12!21;UBERON:0002619!2.60e-10!17;UBERON:0002021!9.88e-08!10;UBERON:0000411!9.88e-08!10;UBERON:0001950!9.88e-08!10;UBERON:0003076!2.27e-07!12;UBERON:0003057!2.27e-07!12|tfbs_overrepresentation_for_novel_motifs=0.321524,1.23178,0.297937,0.360062,0.200163,0.373426,1.16061,0.392928,0.411053,0.255527,0.417132,0.447169,0.124608,0.470194,0.613681,0,0.656089,0.19356,0.364803,0.205418,0.26524,0.60924,0.469335,1.094,0.822446,0.496413,0.709649,0.392919,0.238759,0.572447,0.379806,0.754912,0.191698,0.646834,0.614653,0.102262,0.184038,1.12869,0.166348,2.01695,0.196807,0.38461,0.130272,0.215898,0.434259,0.349801,0.578773,0.407653,0.0244624,0.677281,0.639101,0.522137,0.259389,0.894161,0.911367,0.47699,0.249055,1.11002,1.12723,0.47505,0.735292,0.531188,1.37954,0.628155,0.487593,0.667546,1.04613,1.3932,0.730718,1.24673,1.40499,0.80439,0.03967,0.944464,0.0968968,0.0893951,1.07748,0.567793,0.718494,0.268962,0.406536,0.673009,0.529804,0.764135,0.830765,0.0593483,0.0149522,0.0791202,0.583509,1.55487,1.11522,0.835661,0.767462,1.75421,0.163126,0.892226,0.388243,0.770215,0.57902,3.01552,0.184103,0.754637,0.87698,0.639679,0.638654,0.3842,0.696857,1.04215,0.273261,0.736223,0.315128,0.878738,0.26996,0.421988,1.12221,0.5687,0.409202,0.363536,0.657356,0.181004,0.949798,0.607824,1.24551,0.566919,1.17594,0.722111,0.466292,0.760818,1.04463,0.59809,0.86025,0.353344,1.01535,0.48999,1.14365,0.33206,0.329172,2.66642,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,0.385031,0.581788,1.88287,0.882109,0.201635,0.97987,0.129005,0.895708,0.153911,0.489108,0.976367,0.523103,0.224422,0.319291,0.328917,1.1043,0.829923,0.722546,0.313083,0.629147,0.482049,0.18312,0.445669,0.0896551|tfbs_overrepresentation_jaspar=MA0003.1;0.0214004,MA0004.1;0.360508,MA0006.1;0.210471,MA0007.1;0.346734,MA0009.1;0.780842,MA0014.1;1.092,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;0.79301,MA0042.1;0.76637,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;0.0139872,MA0056.1;0,MA0057.1;0.471918,MA0058.1;0.273976,MA0059.1;0.28489,MA0060.1;0.145297,MA0061.1;0.16896,MA0063.1;0,MA0066.1;0.485868,MA0067.1;1.12095,MA0068.1;0.484739,MA0069.1;0.801381,MA0070.1;1.85999,MA0071.1;0.395679,MA0072.1;0.783532,MA0073.1;0.0215953,MA0074.1;0.451832,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;0.623059,MA0089.1;0,MA0090.1;0.877277,MA0091.1;0.973668,MA0092.1;1.57894,MA0093.1;0.226349,MA0095.1;0,MA0098.1;0,MA0100.1;0.440912,MA0101.1;0.292867,MA0103.1;0.242398,MA0105.1;0.632131,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;1.13868,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;0.772315,MA0140.1;0.440804,MA0141.1;1.32567,MA0142.1;0.674191,MA0143.1;0.53259,MA0144.1;0.169559,MA0145.1;0.664015,MA0146.1;0.412111,MA0147.1;0.530496,MA0148.1;0.375491,MA0149.1;0.2978,MA0062.2;0.0948004,MA0035.2;0.44524,MA0039.2;0.11913,MA0138.2;0.590987,MA0002.2;0.123715,MA0137.2;1.31624,MA0104.2;0.418613,MA0047.2;0.495607,MA0112.2;0.371983,MA0065.2;0.665832,MA0150.1;0.346631,MA0151.1;0,MA0152.1;0.495709,MA0153.1;0.92832,MA0154.1;0.862467,MA0155.1;0.732931,MA0156.1;0.248865,MA0157.1;0.642984,MA0158.1;0,MA0159.1;0.550545,MA0160.1;0.378276,MA0161.1;0,MA0162.1;0.0488928,MA0163.1;0.679942,MA0164.1;0.471016,MA0080.2;0.669221,MA0018.2;0.480226,MA0099.2;0.584892,MA0079.2;0.195216,MA0102.2;1.49914,MA0258.1;0.473611,MA0259.1;0.170828,MA0442.1;0}}

Latest revision as of 15:48, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr19:6235665..6235679,-p2@Ppp2r5b
Mm9::chr4:149001393..149001405,+p5@Clstn1
Mm9::chr6:95982989..95983016,+p@chr6:95982989..95983016
+
Mm9::chr7:17500809..17500825,-p@chr7:17500809..17500825
-
Mm9::chr7:17501357..17501384,-p@chr7:17501357..17501384
-
Mm9::chr7:17501389..17501409,-p@chr7:17501389..17501409
-
Mm9::chr7:17502533..17502561,-p5@Calm2
p6@Calm3
p7@Calm1
Mm9::chr7:17502981..17502996,-p10@Calm3
p11@Calm1
p9@Calm2
Mm9::chr7:17503029..17503048,-p7@Calm2
p8@Calm3
p9@Calm1
Mm9::chr7:17503062..17503077,-p@chr7:17503062..17503077
-


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:0005509calcium ion binding0.00373182711349774



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 system1.01e-2673
nervous system1.52e-2675
regional part of nervous system1.06e-2454
neural tube3.56e-2352
neural rod3.56e-2352
future spinal cord3.56e-2352
neural keel3.56e-2352
neurectoderm4.53e-2064
neural plate4.53e-2064
presumptive neural plate4.53e-2064
brain1.63e-1947
future brain1.63e-1947
regional part of brain3.71e-1946
gray matter6.65e-1934
structure with developmental contribution from neural crest2.32e-1792
anterior neural tube1.69e-1640
ectoderm-derived structure1.96e-1695
ectoderm1.96e-1695
presumptive ectoderm1.96e-1695
regional part of forebrain4.30e-1639
forebrain4.30e-1639
future forebrain4.30e-1639
brain grey matter1.60e-1529
regional part of telencephalon1.60e-1529
telencephalon1.60e-1529
ecto-epithelium2.07e-1473
pre-chordal neural plate2.97e-1449
cerebral cortex7.02e-1221
cerebral hemisphere7.02e-1221
pallium7.02e-1221
regional part of cerebral cortex2.60e-1017
occipital lobe9.88e-0810
visual cortex9.88e-0810
neocortex9.88e-0810
posterior neural tube2.27e-0712
chordal neural plate2.27e-0712


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)
MA0003.10.0214004
MA0004.10.360508
MA0006.10.210471
MA0007.10.346734
MA0009.10.780842
MA0014.11.092
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
MA0041.10.79301
MA0042.10.76637
MA0043.10.875991
MA0046.10.816137
MA0048.10.236433
MA0050.10.396459
MA0051.10.504875
MA0052.10.801048
MA0055.10.0139872
MA0056.10
MA0057.10.471918
MA0058.10.273976
MA0059.10.28489
MA0060.10.145297
MA0061.10.16896
MA0063.10
MA0066.10.485868
MA0067.11.12095
MA0068.10.484739
MA0069.10.801381
MA0070.11.85999
MA0071.10.395679
MA0072.10.783532
MA0073.10.0215953
MA0074.10.451832
MA0076.10.249619
MA0077.10.762273
MA0078.10.536502
MA0081.10.824359
MA0083.10.875209
MA0084.11.44691
MA0087.10.832758
MA0088.10.623059
MA0089.10
MA0090.10.877277
MA0091.10.973668
MA0092.11.57894
MA0093.10.226349
MA0095.10
MA0098.10
MA0100.10.440912
MA0101.10.292867
MA0103.10.242398
MA0105.10.632131
MA0106.10.543967
MA0107.10.237082
MA0108.20.625209
MA0109.10
MA0111.10.342068
MA0113.10.516916
MA0114.10.500166
MA0115.10.878749
MA0116.11.13868
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
MA0139.10.772315
MA0140.10.440804
MA0141.11.32567
MA0142.10.674191
MA0143.10.53259
MA0144.10.169559
MA0145.10.664015
MA0146.10.412111
MA0147.10.530496
MA0148.10.375491
MA0149.10.2978
MA0062.20.0948004
MA0035.20.44524
MA0039.20.11913
MA0138.20.590987
MA0002.20.123715
MA0137.21.31624
MA0104.20.418613
MA0047.20.495607
MA0112.20.371983
MA0065.20.665832
MA0150.10.346631
MA0151.10
MA0152.10.495709
MA0153.10.92832
MA0154.10.862467
MA0155.10.732931
MA0156.10.248865
MA0157.10.642984
MA0158.10
MA0159.10.550545
MA0160.10.378276
MA0161.10
MA0162.10.0488928
MA0163.10.679942
MA0164.10.471016
MA0080.20.669221
MA0018.20.480226
MA0099.20.584892
MA0079.20.195216
MA0102.21.49914
MA0258.10.473611
MA0259.10.170828
MA0442.10
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