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MCL coexpression mm9:709: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004121!5.03e-26!95;UBERON:0000924!5.03e-26!95;UBERON:0006601!5.03e-26!95;UBERON:0002346!1.94e-25!64;UBERON:0003075!1.94e-25!64;UBERON:0007284!1.94e-25!64;UBERON:0010371!8.81e-25!73;UBERON:0000073!2.52e-24!54;UBERON:0001017!7.98e-24!73;UBERON:0001016!1.08e-23!75;UBERON:0001049!6.57e-23!52;UBERON:0005068!6.57e-23!52;UBERON:0006241!6.57e-23!52;UBERON:0007135!6.57e-23!52;UBERON:0003056!2.55e-20!49;UBERON:0000955!6.03e-20!47;UBERON:0006238!6.03e-20!47;UBERON:0002616!2.71e-19!46;UBERON:0010314!5.52e-19!92;UBERON:0003080!1.27e-16!40;UBERON:0002780!5.81e-16!39;UBERON:0001890!5.81e-16!39;UBERON:0006240!5.81e-16!39;UBERON:0002020!1.95e-14!34;UBERON:0003528!8.27e-12!29;UBERON:0002791!8.27e-12!29;UBERON:0001893!8.27e-12!29;UBERON:0000956!1.81e-08!21;UBERON:0001869!1.81e-08!21;UBERON:0000203!1.81e-08!21;UBERON:0002619!1.92e-07!17;UBERON:0003076!5.81e-07!12;UBERON:0003057!5.81e-07!12
|tfbs_overrepresentation_for_novel_motifs=0.860199,0.178895,0.807108,0.360062,0.200163,0.373426,1.16061,0.392928,0.411053,1.12691,0.417132,0.447169,0.785818,0.470194,0.214197,0,0.656089,0.19356,1.209,0.0560853,0.732601,0.60924,0.469335,0.198877,0.304728,3.17554,0.349241,1.01819,0.67135,0.0790295,0.989437,0.754912,0.191698,0.31333,1.1554,1.55204,0.541514,0.443753,0.166348,0.442131,0.196807,1.7717,0.130272,0.215898,1.68044,0.923221,0.578773,0.407653,0.0244624,0.241306,0.639101,3.29098,0.0747297,0.894161,0.911367,0.47699,0.249055,0.435119,0.101408,2.07809,1.74318,0.531188,0.140453,0.628155,0.487593,0.667546,1.04613,1.3932,0.730718,1.24673,1.40499,0.128829,5.00531,0.944464,5.96462,0.300089,0.0942164,0.567793,0.718494,0.268962,0.129727,0.673009,0.529804,0.119727,0.830765,2.41237,0.596492,0.0791202,2.4344,1.55487,1.11522,1.9501,0.767462,0.205117,0.950022,0.149272,1.84308,0.770215,0.57902,0.234357,1.03532,0.754637,0.87698,0.639679,0.638654,0.999084,0.696857,0.403887,0.750985,0.736223,0.315128,0.878738,1.36417,0.421988,1.12221,0.195318,3.34205,0.953611,1.58124,0.181004,0.949798,0.607824,0.498153,0.566919,1.17594,0.722111,1.17725,5.74851,1.04463,1.76799,0.86025,0.353344,1.01535,0.48999,1.14365,0.33206,1.57798,0.385921,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,1.529,0.385031,0.581788,1.88287,0.331322,1.10485,0.275954,6.07363,0.895708,0.46758,0.489108,0.976367,0.523103,1.19319,0.319291,0.876739,1.1043,0.829923,0.722546,0.313083,0.629147,0.482049,0.18312,0.445669,2.70658
|tfbs_overrepresentation_jaspar=MA0003.1;2.62288,MA0004.1;0.360508,MA0006.1;3.32509,MA0007.1;0.346734,MA0009.1;0.780842,MA0014.1;5.36608,MA0017.1;0.233089,MA0019.1;0.603066,MA0024.1;0.737933,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;2.40257,MA0050.1;0.396459,MA0051.1;0.504875,MA0052.1;0.801048,MA0055.1;0.0660514,MA0056.1;0,MA0057.1;1.73264,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;0.836551,MA0069.1;0.801381,MA0070.1;0.791856,MA0071.1;0.395679,MA0072.1;0.783532,MA0073.1;1.31405,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;1.39028,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;1.12255,MA0101.1;0.292867,MA0103.1;1.26149,MA0105.1;0.304995,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;1.53894,MA0115.1;0.878749,MA0116.1;0.210297,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;0.385513,MA0140.1;0.440804,MA0141.1;0.259554,MA0142.1;0.674191,MA0143.1;0.53259,MA0144.1;0.506239,MA0145.1;0.371997,MA0146.1;0.923066,MA0147.1;1.6106,MA0148.1;0.375491,MA0149.1;0.2978,MA0062.2;1.5965,MA0035.2;0.44524,MA0039.2;5.88263,MA0138.2;1.44221,MA0002.2;0.391079,MA0137.2;0.713675,MA0104.2;1.34242,MA0047.2;0.495607,MA0112.2;1.95537,MA0065.2;1.9594,MA0150.1;0.346631,MA0151.1;0,MA0152.1;0.495709,MA0153.1;0.92832,MA0154.1;0.232525,MA0155.1;0.186607,MA0156.1;0.694831,MA0157.1;0.642984,MA0158.1;0,MA0159.1;0.550545,MA0160.1;0.378276,MA0161.1;0,MA0162.1;1.39091,MA0163.1;0.679942,MA0164.1;0.471016,MA0080.2;0.669221,MA0018.2;0.480226,MA0099.2;0.584892,MA0079.2;2.58709,MA0102.2;1.49914,MA0258.1;0.921856,MA0259.1;2.96805,MA0442.1;0
}}

Latest revision as of 15:45, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:43561465..43561517,-p1@Ttc1
Mm9::chr16:56717559..56717570,-p3@Tfg
Mm9::chr18:38456480..38456491,+p5@Rnf14
Mm9::chr5:125342499..125342518,-p4@Ccdc92
Mm9::chr5:125342530..125342574,-p2@Ccdc92
Mm9::chr5:125342586..125342597,-p8@Ccdc92
Mm9::chr5:125342836..125342853,-p6@Ccdc92
Mm9::chr5:125342855..125342871,-p7@Ccdc92
Mm9::chr9:106367618..106367633,-p@chr9:106367618..106367633
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Mm9::chr9:4309719..4309748,+p2@Kbtbd3


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>

Cell Type
Ontology termp-valuen
CNS neuron (sensu Vertebrata)7.29e-0923
neuroblast (sensu Vertebrata)7.29e-0923
ectodermal cell5.79e-0844
neurectodermal cell5.79e-0844
neural cell1.13e-0743

Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure5.03e-2695
ectoderm5.03e-2695
presumptive ectoderm5.03e-2695
neurectoderm1.94e-2564
neural plate1.94e-2564
presumptive neural plate1.94e-2564
ecto-epithelium8.81e-2573
regional part of nervous system2.52e-2454
central nervous system7.98e-2473
nervous system1.08e-2375
neural tube6.57e-2352
neural rod6.57e-2352
future spinal cord6.57e-2352
neural keel6.57e-2352
pre-chordal neural plate2.55e-2049
brain6.03e-2047
future brain6.03e-2047
regional part of brain2.71e-1946
structure with developmental contribution from neural crest5.52e-1992
anterior neural tube1.27e-1640
regional part of forebrain5.81e-1639
forebrain5.81e-1639
future forebrain5.81e-1639
gray matter1.95e-1434
brain grey matter8.27e-1229
regional part of telencephalon8.27e-1229
telencephalon8.27e-1229
cerebral cortex1.81e-0821
cerebral hemisphere1.81e-0821
pallium1.81e-0821
regional part of cerebral cortex1.92e-0717
posterior neural tube5.81e-0712
chordal neural plate5.81e-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)
MA0003.12.62288
MA0004.10.360508
MA0006.13.32509
MA0007.10.346734
MA0009.10.780842
MA0014.15.36608
MA0017.10.233089
MA0019.10.603066
MA0024.10.737933
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
MA0048.12.40257
MA0050.10.396459
MA0051.10.504875
MA0052.10.801048
MA0055.10.0660514
MA0056.10
MA0057.11.73264
MA0058.10.273976
MA0059.10.28489
MA0060.10.145297
MA0061.10.16896
MA0063.10
MA0066.10.485868
MA0067.11.12095
MA0068.10.836551
MA0069.10.801381
MA0070.10.791856
MA0071.10.395679
MA0072.10.783532
MA0073.11.31405
MA0074.10.451832
MA0076.11.28862
MA0077.10.762273
MA0078.10.536502
MA0081.10.305576
MA0083.10.875209
MA0084.11.44691
MA0087.10.832758
MA0088.11.39028
MA0089.10
MA0090.10.329158
MA0091.10.372635
MA0092.10.329444
MA0093.10.226349
MA0095.10
MA0098.10
MA0100.11.12255
MA0101.10.292867
MA0103.11.26149
MA0105.10.304995
MA0106.10.543967
MA0107.10.237082
MA0108.20.625209
MA0109.10
MA0111.10.342068
MA0113.10.516916
MA0114.11.53894
MA0115.10.878749
MA0116.10.210297
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
MA0139.10.385513
MA0140.10.440804
MA0141.10.259554
MA0142.10.674191
MA0143.10.53259
MA0144.10.506239
MA0145.10.371997
MA0146.10.923066
MA0147.11.6106
MA0148.10.375491
MA0149.10.2978
MA0062.21.5965
MA0035.20.44524
MA0039.25.88263
MA0138.21.44221
MA0002.20.391079
MA0137.20.713675
MA0104.21.34242
MA0047.20.495607
MA0112.21.95537
MA0065.21.9594
MA0150.10.346631
MA0151.10
MA0152.10.495709
MA0153.10.92832
MA0154.10.232525
MA0155.10.186607
MA0156.10.694831
MA0157.10.642984
MA0158.10
MA0159.10.550545
MA0160.10.378276
MA0161.10
MA0162.11.39091
MA0163.10.679942
MA0164.10.471016
MA0080.20.669221
MA0018.20.480226
MA0099.20.584892
MA0079.22.58709
MA0102.21.49914
MA0258.10.921856
MA0259.12.96805
MA0442.10
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