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MCL coexpression mm9:704: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!4.30e-18!73;UBERON:0001016!2.28e-17!75;UBERON:0002346!1.01e-16!64;UBERON:0003075!1.01e-16!64;UBERON:0007284!1.01e-16!64;UBERON:0000073!1.41e-16!54;UBERON:0010314!2.32e-16!92;UBERON:0001049!1.92e-15!52;UBERON:0005068!1.92e-15!52;UBERON:0006241!1.92e-15!52;UBERON:0007135!1.92e-15!52;UBERON:0004121!6.47e-15!95;UBERON:0000924!6.47e-15!95;UBERON:0006601!6.47e-15!95;UBERON:0010371!1.26e-13!73;UBERON:0000955!2.65e-13!47;UBERON:0006238!2.65e-13!47;UBERON:0002616!7.31e-13!46;UBERON:0003056!9.11e-12!49;UBERON:0002020!2.46e-11!34;UBERON:0003080!6.51e-11!40;UBERON:0000025!9.37e-11!114;UBERON:0002780!2.53e-10!39;UBERON:0001890!2.53e-10!39;UBERON:0006240!2.53e-10!39;UBERON:0004111!3.38e-10!122;UBERON:0003528!1.80e-09!29;UBERON:0002791!1.80e-09!29;UBERON:0001893!1.80e-09!29;UBERON:0000468!1.05e-07!333;UBERON:0000956!6.29e-07!21;UBERON:0001869!6.29e-07!21;UBERON:0000203!6.29e-07!21
|tfbs_overrepresentation_for_novel_motifs=0.860199,0.178895,0.297937,0.360062,0.580303,0.373426,1.16061,0.124431,0.411053,0.255527,0.417132,0.447169,1.28029,0.470194,0.613681,0,0.656089,0.19356,0.113609,0.451901,0.26524,0.336916,0.469335,0.577226,1.4907,0.496413,0.349241,0.392919,0.67135,0.967915,0.379806,1.78376,0.191698,0.31333,1.1554,0.386349,1.03506,1.12869,0.963289,0.442131,0.196807,0.38461,0.307718,0.215898,1.29974,0.349801,0.578773,1.05036,0.104497,0.241306,0.639101,0.522137,0.935589,0.894161,0.911367,0.47699,0.249055,0.435119,1.12723,0.47505,0.735292,1.31585,0.433822,0.628155,0.487593,1.60248,1.04613,1.3932,0.730718,1.24673,0.281085,0.404236,0.356247,0.944464,0.659328,0.0893951,0.313198,0.567793,0.718494,0.268962,0.406536,0.673009,0.529804,0.764135,0.830765,0.81514,0.0697823,0.96859,0.583509,1.55487,1.11522,0.835661,0.767462,1.11849,0.163126,0.149272,0.388243,0.770215,0.57902,0.0659594,0.184103,0.754637,0.87698,0.639679,0.638654,0.999084,0.696857,0.403887,0.750985,1.35258,1.52799,0.878738,0.26996,0.421988,2.53424,0.195318,0.993542,0.953611,0.657356,0.534159,0.949798,0.607824,0.498153,0.566919,1.17594,0.722111,0.466292,0.760818,1.04463,0.207624,0.86025,0.353344,1.01535,0.48999,1.14365,0.142597,0.329172,0.385921,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,0.385031,0.581788,1.88287,0.882109,1.10485,0.275954,0.884616,0.895708,0.153911,0.489108,0.976367,0.523103,0.224422,0.319291,0.328917,1.1043,0.829923,0.722546,0.313083,0.629147,0.482049,0.53929,0.445669,0.809881
|tfbs_overrepresentation_jaspar=MA0003.1;0.958381,MA0004.1;0.360508,MA0006.1;0.210471,MA0007.1;0.346734,MA0009.1;0.780842,MA0014.1;2.22426,MA0017.1;0.233089,MA0019.1;0.603066,MA0024.1;0.737933,MA0025.1;1.01089,MA0027.1;2.42079,MA0028.1;1.17347,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;0.279998,MA0043.1;0.875991,MA0046.1;0.816137,MA0048.1;1.82935,MA0050.1;0.396459,MA0051.1;0.504875,MA0052.1;0.801048,MA0055.1;0.866263,MA0056.1;0,MA0057.1;2.2848,MA0058.1;0.273976,MA0059.1;0.28489,MA0060.1;0.446031,MA0061.1;0.973999,MA0063.1;0,MA0066.1;0.485868,MA0067.1;1.12095,MA0068.1;0.836551,MA0069.1;0.801381,MA0070.1;0.791856,MA0071.1;0.395679,MA0072.1;0.783532,MA0073.1;3.93533,MA0074.1;0.451832,MA0076.1;1.99258,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;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;1.0562,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;1.44977,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;1.96326,MA0141.1;0.259554,MA0142.1;0.674191,MA0143.1;0.53259,MA0144.1;0.169559,MA0145.1;0.664015,MA0146.1;1.25057,MA0147.1;0.179496,MA0148.1;0.375491,MA0149.1;0.806798,MA0062.2;1.08157,MA0035.2;1.1319,MA0039.2;3.09333,MA0138.2;0.590987,MA0002.2;0.391079,MA0137.2;0.713675,MA0104.2;0.134457,MA0047.2;0.495607,MA0112.2;0.663994,MA0065.2;0.373167,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;0.694831,MA0157.1;0.642984,MA0158.1;0,MA0159.1;1.6576,MA0160.1;0.378276,MA0161.1;0,MA0162.1;1.0367,MA0163.1;2.5777,MA0164.1;0.471016,MA0080.2;0.237846,MA0018.2;0.480226,MA0099.2;0.584892,MA0079.2;9.77299,MA0102.2;1.49914,MA0258.1;0.156336,MA0259.1;0.170828,MA0442.1;0
}}

Latest revision as of 15:45, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:121296262..121296301,+p1@Fn3k
Mm9::chr11:31770901..31770923,+p1@Cpeb4
Mm9::chr11:61770282..61770293,+p3@Specc1
Mm9::chr11:74433096..74433145,+p1@E130309D14Rik
Mm9::chr16:58670619..58670668,+p@chr16:58670619..58670668
+
Mm9::chr2:84574207..84574264,+p1@Ypel4
Mm9::chr2:84578292..84578295,+p@chr2:84578292..84578295
+
Mm9::chr6:72047555..72047624,+p1@St3gal5
Mm9::chr8:63433523..63433587,-p2@Clcn3
Mm9::chr9:44096214..44096236,-p3@Abcg4


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:0030389fructosamine metabolic process0.0241056264723607
GO:0030387fructosamine-3-kinase activity0.0241056264723607
GO:0004109coproporphyrinogen oxidase activity0.032134671976103



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
neuron3.48e-0733
neuronal stem cell3.48e-0733
neuroblast3.48e-0733
electrically signaling cell3.48e-0733

Uber Anatomy
Ontology termp-valuen
central nervous system4.30e-1873
nervous system2.28e-1775
neurectoderm1.01e-1664
neural plate1.01e-1664
presumptive neural plate1.01e-1664
regional part of nervous system1.41e-1654
structure with developmental contribution from neural crest2.32e-1692
neural tube1.92e-1552
neural rod1.92e-1552
future spinal cord1.92e-1552
neural keel1.92e-1552
ectoderm-derived structure6.47e-1595
ectoderm6.47e-1595
presumptive ectoderm6.47e-1595
ecto-epithelium1.26e-1373
brain2.65e-1347
future brain2.65e-1347
regional part of brain7.31e-1346
pre-chordal neural plate9.11e-1249
gray matter2.46e-1134
anterior neural tube6.51e-1140
tube9.37e-11114
regional part of forebrain2.53e-1039
forebrain2.53e-1039
future forebrain2.53e-1039
anatomical conduit3.38e-10122
brain grey matter1.80e-0929
regional part of telencephalon1.80e-0929
telencephalon1.80e-0929
multi-cellular organism1.05e-07333
cerebral cortex6.29e-0721
cerebral hemisphere6.29e-0721
pallium6.29e-0721


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)
MA0003.10.958381
MA0004.10.360508
MA0006.10.210471
MA0007.10.346734
MA0009.10.780842
MA0014.12.22426
MA0017.10.233089
MA0019.10.603066
MA0024.10.737933
MA0025.11.01089
MA0027.12.42079
MA0028.11.17347
MA0029.10.716673
MA0030.10.723093
MA0031.10.688336
MA0038.10.496338
MA0040.10.79313
MA0041.10.79301
MA0042.10.279998
MA0043.10.875991
MA0046.10.816137
MA0048.11.82935
MA0050.10.396459
MA0051.10.504875
MA0052.10.801048
MA0055.10.866263
MA0056.10
MA0057.12.2848
MA0058.10.273976
MA0059.10.28489
MA0060.10.446031
MA0061.10.973999
MA0063.10
MA0066.10.485868
MA0067.11.12095
MA0068.10.836551
MA0069.10.801381
MA0070.10.791856
MA0071.10.395679
MA0072.10.783532
MA0073.13.93533
MA0074.10.451832
MA0076.11.99258
MA0077.10.762273
MA0078.10.536502
MA0081.10.305576
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
MA0105.11.0562
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
MA0119.11.44977
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
MA0140.11.96326
MA0141.10.259554
MA0142.10.674191
MA0143.10.53259
MA0144.10.169559
MA0145.10.664015
MA0146.11.25057
MA0147.10.179496
MA0148.10.375491
MA0149.10.806798
MA0062.21.08157
MA0035.21.1319
MA0039.23.09333
MA0138.20.590987
MA0002.20.391079
MA0137.20.713675
MA0104.20.134457
MA0047.20.495607
MA0112.20.663994
MA0065.20.373167
MA0150.10.346631
MA0151.10
MA0152.10.495709
MA0153.10.92832
MA0154.10.862467
MA0155.10.732931
MA0156.10.694831
MA0157.10.642984
MA0158.10
MA0159.11.6576
MA0160.10.378276
MA0161.10
MA0162.11.0367
MA0163.12.5777
MA0164.10.471016
MA0080.20.237846
MA0018.20.480226
MA0099.20.584892
MA0079.29.77299
MA0102.21.49914
MA0258.10.156336
MA0259.10.170828
MA0442.10
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