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MCL coexpression mm9:735: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001017!4.70e-30!73;UBERON:0001016!1.79e-28!75;UBERON:0002346!3.07e-24!64;UBERON:0003075!3.07e-24!64;UBERON:0007284!3.07e-24!64;UBERON:0004121!2.30e-23!95;UBERON:0000924!2.30e-23!95;UBERON:0006601!2.30e-23!95;UBERON:0000073!8.24e-22!54;UBERON:0001049!7.56e-21!52;UBERON:0005068!7.56e-21!52;UBERON:0006241!7.56e-21!52;UBERON:0007135!7.56e-21!52;UBERON:0010371!1.37e-18!73;UBERON:0003056!4.42e-18!49;UBERON:0000955!4.80e-18!47;UBERON:0006238!4.80e-18!47;UBERON:0002616!8.74e-18!46;UBERON:0010314!1.58e-16!92;UBERON:0003080!5.20e-16!40;UBERON:0002780!8.95e-16!39;UBERON:0001890!8.95e-16!39;UBERON:0006240!8.95e-16!39;UBERON:0002020!1.27e-14!34;UBERON:0003528!7.42e-12!29;UBERON:0002791!7.42e-12!29;UBERON:0001893!7.42e-12!29;UBERON:0000956!1.83e-08!21;UBERON:0001869!1.83e-08!21;UBERON:0000203!1.83e-08!21
|ontology_enrichment_uberon=UBERON:0001017!4.70e-30!73;UBERON:0001016!1.79e-28!75;UBERON:0002346!3.07e-24!64;UBERON:0003075!3.07e-24!64;UBERON:0007284!3.07e-24!64;UBERON:0004121!2.30e-23!95;UBERON:0000924!2.30e-23!95;UBERON:0006601!2.30e-23!95;UBERON:0000073!8.24e-22!54;UBERON:0001049!7.56e-21!52;UBERON:0005068!7.56e-21!52;UBERON:0006241!7.56e-21!52;UBERON:0007135!7.56e-21!52;UBERON:0010371!1.37e-18!73;UBERON:0003056!4.42e-18!49;UBERON:0000955!4.80e-18!47;UBERON:0006238!4.80e-18!47;UBERON:0002616!8.74e-18!46;UBERON:0010314!1.58e-16!92;UBERON:0003080!5.20e-16!40;UBERON:0002780!8.95e-16!39;UBERON:0001890!8.95e-16!39;UBERON:0006240!8.95e-16!39;UBERON:0002020!1.27e-14!34;UBERON:0003528!7.42e-12!29;UBERON:0002791!7.42e-12!29;UBERON:0001893!7.42e-12!29;UBERON:0000956!1.83e-08!21;UBERON:0001869!1.83e-08!21;UBERON:0000203!1.83e-08!21
|tfbs_overrepresentation_for_novel_motifs=0.860199,0.352573,0.297937,0.360062,0.580303,0.373426,1.16061,0.124431,0.131493,2.00078,0.417132,0.447169,1.28029,0.470194,0.214197,0,1.57859,0.19356,0.736624,0.0560853,0.26524,0.60924,0.469335,0.198877,0.304728,0.496413,0.107695,0.392919,0.238759,0.0790295,0.379806,0.754912,1.06562,0.31333,0.614653,0.386349,0.541514,1.12869,0.498354,0.868806,0.196807,0.999982,0.307718,0.215898,1.29974,0.349801,0.578773,0.407653,0.0244624,1.25738,1.54311,1.29662,0.259389,0.894161,0.911367,0.47699,0.249055,0.435119,0.101408,0.47505,0.735292,0.531188,0.854737,0.628155,1.22293,1.60248,1.04613,1.3932,0.730718,1.24673,1.40499,1.3071,0.996746,0.944464,0.659328,0.300089,0.313198,0.567793,0.718494,0.268962,0.80832,0.673009,0.529804,0.764135,0.830765,0.318393,0.0149522,0.271714,0.583509,1.55487,1.11522,1.9501,0.767462,0.205117,0.163126,0.149272,0.388243,0.770215,3.54303,0.50528,0.184103,0.754637,0.87698,0.639679,0.638654,0.999084,1.66347,0.403887,0.750985,1.35258,0.845852,0.878738,0.743427,1.08155,1.12221,0.195318,0.993542,0.363536,0.657356,1.02287,0.949798,0.607824,0.498153,0.566919,1.17594,1.71587,0.466292,1.79596,1.04463,1.12828,0.86025,0.931072,1.01535,0.48999,1.14365,1.35158,0.329172,0.385921,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,1.00091,0.581788,1.88287,0.331322,0.201635,0.275954,2.76704,0.895708,0.153911,0.489108,0.976367,0.523103,0.224422,0.319291,1.57707,1.1043,0.829923,0.722546,0.841258,0.629147,0.482049,0.53929,0.445669,0.19482
|tfbs_overrepresentation_for_novel_motifs=0.860199,0.352573,0.297937,0.360062,0.580303,0.373426,1.16061,0.124431,0.131493,2.00078,0.417132,0.447169,1.28029,0.470194,0.214197,0,1.57859,0.19356,0.736624,0.0560853,0.26524,0.60924,0.469335,0.198877,0.304728,0.496413,0.107695,0.392919,0.238759,0.0790295,0.379806,0.754912,1.06562,0.31333,0.614653,0.386349,0.541514,1.12869,0.498354,0.868806,0.196807,0.999982,0.307718,0.215898,1.29974,0.349801,0.578773,0.407653,0.0244624,1.25738,1.54311,1.29662,0.259389,0.894161,0.911367,0.47699,0.249055,0.435119,0.101408,0.47505,0.735292,0.531188,0.854737,0.628155,1.22293,1.60248,1.04613,1.3932,0.730718,1.24673,1.40499,1.3071,0.996746,0.944464,0.659328,0.300089,0.313198,0.567793,0.718494,0.268962,0.80832,0.673009,0.529804,0.764135,0.830765,0.318393,0.0149522,0.271714,0.583509,1.55487,1.11522,1.9501,0.767462,0.205117,0.163126,0.149272,0.388243,0.770215,3.54303,0.50528,0.184103,0.754637,0.87698,0.639679,0.638654,0.999084,1.66347,0.403887,0.750985,1.35258,0.845852,0.878738,0.743427,1.08155,1.12221,0.195318,0.993542,0.363536,0.657356,1.02287,0.949798,0.607824,0.498153,0.566919,1.17594,1.71587,0.466292,1.79596,1.04463,1.12828,0.86025,0.931072,1.01535,0.48999,1.14365,1.35158,0.329172,0.385921,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,1.00091,0.581788,1.88287,0.331322,0.201635,0.275954,2.76704,0.895708,0.153911,0.489108,0.976367,0.523103,0.224422,0.319291,1.57707,1.1043,0.829923,0.722546,0.841258,0.629147,0.482049,0.53929,0.445669,0.19482
|tfbs_overrepresentation_jaspar=MA0003.1;1.23085,MA0004.1;0.946922,MA0006.1;1.13936,MA0007.1;0.916416,MA0009.1;0.780842,MA0014.1;1.43076,MA0017.1;0.233089,MA0019.1;0.603066,MA0024.1;1.74864,MA0025.1;1.01089,MA0027.1;2.42079,MA0028.1;1.83149,MA0029.1;0.716673,MA0030.1;0.723093,MA0031.1;0.688336,MA0038.1;0.496338,MA0040.1;0.79313,MA0041.1;0.291712,MA0042.1;0.279998,MA0043.1;0.875991,MA0046.1;0.816137,MA0048.1;1.31676,MA0050.1;0.396459,MA0051.1;0.504875,MA0052.1;0.801048,MA0055.1;0.17385,MA0056.1;0,MA0057.1;0.817159,MA0058.1;1.37894,MA0059.1;0.777514,MA0060.1;3.47915,MA0061.1;0.504772,MA0063.1;0,MA0066.1;0.485868,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;0.175635,MA0074.1;0.451832,MA0076.1;1.28862,MA0077.1;0.762273,MA0078.1;0.536502,MA0081.1;0.305576,MA0083.1;0.875209,MA0084.1;1.44691,MA0087.1;0.832758,MA0088.1;0.34573,MA0089.1;0,MA0090.1;0.329158,MA0091.1;0.372635,MA0092.1;0.329444,MA0093.1;1.20057,MA0095.1;0,MA0098.1;0,MA0100.1;1.12255,MA0101.1;0.292867,MA0103.1;0.242398,MA0105.1;0.0911942,MA0106.1;0.543967,MA0107.1;0.237082,MA0108.2;0.625209,MA0109.1;0,MA0111.1;0.342068,MA0113.1;1.28551,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;1.45836,MA0132.1;0,MA0133.1;0,MA0135.1;0.911905,MA0136.1;0.470672,MA0139.1;0.121562,MA0140.1;0.440804,MA0141.1;0.259554,MA0142.1;0.674191,MA0143.1;0.53259,MA0144.1;0.169559,MA0145.1;0.371997,MA0146.1;1.62155,MA0147.1;1.6106,MA0148.1;0.375491,MA0149.1;0.2978,MA0062.2;1.08157,MA0035.2;0.44524,MA0039.2;0.468563,MA0138.2;0.590987,MA0002.2;0.123715,MA0137.2;0.257017,MA0104.2;1.34242,MA0047.2;0.495607,MA0112.2;0.163154,MA0065.2;0.665832,MA0150.1;0.346631,MA0151.1;0,MA0152.1;0.495709,MA0153.1;0.92832,MA0154.1;0.501928,MA0155.1;0.732931,MA0156.1;0.694831,MA0157.1;0.642984,MA0158.1;0,MA0159.1;0.550545,MA0160.1;0.378276,MA0161.1;0,MA0162.1;2.70539,MA0163.1;0.121321,MA0164.1;0.471016,MA0080.2;0.237846,MA0018.2;0.480226,MA0099.2;0.584892,MA0079.2;0.937792,MA0102.2;1.49914,MA0258.1;0.156336,MA0259.1;1.56071,MA0442.1;0
}}
}}

Revision as of 12:14, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr15:78004456..78004519,-p1@Ift27
Mm9::chr15:78004520..78004539,-p4@Ift27
Mm9::chr1:75139208..75139299,-p1@1810031K17Rik
Mm9::chr2:164860321..164860359,-p2@Ncoa5
Mm9::chr5:121902471..121902527,-p2@Erp29
Mm9::chr6:113327781..113327849,-p1@Tada3
Mm9::chr6:113327860..113327871,-p7@Tada3
Mm9::chr7:13623550..13623656,-p2@Ube2m
Mm9::chr8:73118260..73118271,+p2@Isyna1
Mm9::chr8:73993125..73993157,+p2@Dda1


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:0016872intramolecular lyase activity0.015118730944159
GO:0004512inositol-3-phosphate synthase activity0.015118730944159
GO:0006021inositol biosynthetic process0.015118730944159
GO:0015234thiamin transmembrane transporter activity0.015118730944159
GO:0015888thiamin transport0.015118730944159
GO:0008518reduced folate carrier activity0.0188932370255071
GO:0051180vitamin transport0.0188932370255071
GO:0008517folic acid transporter activity0.0188932370255071
GO:0051183vitamin transporter activity0.0274660192782756
GO:0051184cofactor transporter activity0.0274660192782756
GO:0005788endoplasmic reticulum lumen0.0274660192782756
GO:0006020inositol metabolic process0.0283204530089576
GO:0005542folic acid binding0.029042640209335



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 system4.70e-3073
nervous system1.79e-2875
neurectoderm3.07e-2464
neural plate3.07e-2464
presumptive neural plate3.07e-2464
ectoderm-derived structure2.30e-2395
ectoderm2.30e-2395
presumptive ectoderm2.30e-2395
regional part of nervous system8.24e-2254
neural tube7.56e-2152
neural rod7.56e-2152
future spinal cord7.56e-2152
neural keel7.56e-2152
ecto-epithelium1.37e-1873
pre-chordal neural plate4.42e-1849
brain4.80e-1847
future brain4.80e-1847
regional part of brain8.74e-1846
structure with developmental contribution from neural crest1.58e-1692
anterior neural tube5.20e-1640
regional part of forebrain8.95e-1639
forebrain8.95e-1639
future forebrain8.95e-1639
gray matter1.27e-1434
brain grey matter7.42e-1229
regional part of telencephalon7.42e-1229
telencephalon7.42e-1229
cerebral cortex1.83e-0821
cerebral hemisphere1.83e-0821
pallium1.83e-0821


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)
MA0003.11.23085
MA0004.10.946922
MA0006.11.13936
MA0007.10.916416
MA0009.10.780842
MA0014.11.43076
MA0017.10.233089
MA0019.10.603066
MA0024.11.74864
MA0025.11.01089
MA0027.12.42079
MA0028.11.83149
MA0029.10.716673
MA0030.10.723093
MA0031.10.688336
MA0038.10.496338
MA0040.10.79313
MA0041.10.291712
MA0042.10.279998
MA0043.10.875991
MA0046.10.816137
MA0048.11.31676
MA0050.10.396459
MA0051.10.504875
MA0052.10.801048
MA0055.10.17385
MA0056.10
MA0057.10.817159
MA0058.11.37894
MA0059.10.777514
MA0060.13.47915
MA0061.10.504772
MA0063.10
MA0066.10.485868
MA0067.11.12095
MA0068.10.0621035
MA0069.10.801381
MA0070.10.791856
MA0071.10.395679
MA0072.10.783532
MA0073.10.175635
MA0074.10.451832
MA0076.11.28862
MA0077.10.762273
MA0078.10.536502
MA0081.10.305576
MA0083.10.875209
MA0084.11.44691
MA0087.10.832758
MA0088.10.34573
MA0089.10
MA0090.10.329158
MA0091.10.372635
MA0092.10.329444
MA0093.11.20057
MA0095.10
MA0098.10
MA0100.11.12255
MA0101.10.292867
MA0103.10.242398
MA0105.10.0911942
MA0106.10.543967
MA0107.10.237082
MA0108.20.625209
MA0109.10
MA0111.10.342068
MA0113.11.28551
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
MA0131.11.45836
MA0132.10
MA0133.10
MA0135.10.911905
MA0136.10.470672
MA0139.10.121562
MA0140.10.440804
MA0141.10.259554
MA0142.10.674191
MA0143.10.53259
MA0144.10.169559
MA0145.10.371997
MA0146.11.62155
MA0147.11.6106
MA0148.10.375491
MA0149.10.2978
MA0062.21.08157
MA0035.20.44524
MA0039.20.468563
MA0138.20.590987
MA0002.20.123715
MA0137.20.257017
MA0104.21.34242
MA0047.20.495607
MA0112.20.163154
MA0065.20.665832
MA0150.10.346631
MA0151.10
MA0152.10.495709
MA0153.10.92832
MA0154.10.501928
MA0155.10.732931
MA0156.10.694831
MA0157.10.642984
MA0158.10
MA0159.10.550545
MA0160.10.378276
MA0161.10
MA0162.12.70539
MA0163.10.121321
MA0164.10.471016
MA0080.20.237846
MA0018.20.480226
MA0099.20.584892
MA0079.20.937792
MA0102.21.49914
MA0258.10.156336
MA0259.11.56071
MA0442.10
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