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MCL coexpression mm9:3042: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000117!1.79e-11!23;CL:0000337!1.79e-11!23;CL:0000540!1.10e-07!33;CL:0000047!1.10e-07!33;CL:0000031!1.10e-07!33;CL:0000404!1.10e-07!33
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002346!5.64e-14!64;UBERON:0003075!5.64e-14!64;UBERON:0007284!5.64e-14!64;UBERON:0010371!9.29e-13!73;UBERON:0000073!2.16e-12!54;UBERON:0001049!2.60e-12!52;UBERON:0005068!2.60e-12!52;UBERON:0006241!2.60e-12!52;UBERON:0007135!2.60e-12!52;UBERON:0004121!9.01e-12!95;UBERON:0000924!9.01e-12!95;UBERON:0006601!9.01e-12!95;UBERON:0010314!1.01e-11!92;UBERON:0003056!1.82e-11!49;UBERON:0001017!2.43e-11!73;UBERON:0000468!7.03e-11!333;UBERON:0001016!1.54e-10!75;UBERON:0000955!3.81e-10!47;UBERON:0006238!3.81e-10!47;UBERON:0002020!3.97e-10!34;UBERON:0002616!9.88e-10!46;UBERON:0000991!2.76e-09!18;UBERON:0005564!2.76e-09!18;UBERON:0003080!4.60e-09!40;UBERON:0002780!9.16e-09!39;UBERON:0001890!9.16e-09!39;UBERON:0006240!9.16e-09!39;UBERON:0004176!9.21e-09!17;UBERON:0009196!9.21e-09!17;UBERON:0009117!9.21e-09!17;UBERON:0000922!3.59e-08!320;UBERON:0000473!7.56e-08!14;UBERON:0003528!9.71e-08!29;UBERON:0002791!9.71e-08!29;UBERON:0001893!9.71e-08!29;UBERON:0003133!1.38e-07!24;UBERON:0003135!2.30e-07!15;UBERON:0005156!5.50e-07!26;UBERON:0000990!5.50e-07!26
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.193418,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.66329,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.876292,0.679146,0.275782,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,1.55113,0.99159,0.825437,1.24901,1.40911,1.05917,0.608816,2.7168,1.38481,0.902078,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,1.47707,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.777706,1.44925,0.416814,0.402065,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,0.535545,0.568545,1.75916,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,0.609576,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.38417,0.260379,1.39822,1.28513,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,1.38188,0.904334,0.421338
|tfbs_overrepresentation_jaspar=MA0003.1;0.526413,MA0004.1;0.801718,MA0006.1;0.60285,MA0007.1;0.784593,MA0009.1;1.27673,MA0014.1;1.93445,MA0017.1;0.635031,MA0019.1;1.08369,MA0024.1;1.23079,MA0025.1;1.51835,MA0027.1;2.9431,MA0028.1;0.61552,MA0029.1;1.20789,MA0030.1;1.21482,MA0031.1;1.17722,MA0038.1;0.963265,MA0040.1;1.28983,MA0041.1;0.714279,MA0042.1;0.69885,MA0043.1;1.3775,MA0046.1;1.31428,MA0048.1;0.932001,MA0050.1;0.845669,MA0051.1;0.973068,MA0052.1;1.29825,MA0055.1;0.557057,MA0056.1;0,MA0057.1;0.337566,MA0058.1;0.690848,MA0059.1;0.705317,MA0060.1;0.502699,MA0061.1;0.5406,MA0063.1;0,MA0066.1;2.18658,MA0067.1;1.63197,MA0068.1;5.46058,MA0069.1;1.29861,MA0070.1;1.28847,MA0071.1;0.844726,MA0072.1;1.2796,MA0073.1;2.11706,MA0074.1;0.911576,MA0076.1;0.657929,MA0077.1;1.2569,MA0078.1;1.0091,MA0081.1;0.732313,MA0083.1;1.37668,MA0084.1;1.96428,MA0087.1;1.33189,MA0088.1;0.766354,MA0089.1;0,MA0090.1;0.762482,MA0091.1;0.816659,MA0092.1;0.762845,MA0093.1;0.62555,MA0095.1;0,MA0098.1;0,MA0100.1;0.89873,MA0101.1;0.71579,MA0103.1;0.647985,MA0105.1;0.405648,MA0106.1;1.01755,MA0107.1;0.640607,MA0108.2;1.10817,MA0109.1;0,MA0111.1;0.778753,MA0113.1;0.986839,MA0114.1;0.537669,MA0115.1;1.38041,MA0116.1;0.602598,MA0117.1;1.34691,MA0119.1;0.716476,MA0122.1;1.36752,MA0124.1;1.57762,MA0125.1;1.5017,MA0130.1;0,MA0131.1;1.07881,MA0132.1;0,MA0133.1;0,MA0135.1;1.4152,MA0136.1;0.933582,MA0139.1;0.462282,MA0140.1;0.898603,MA0141.1;0.671467,MA0142.1;1.16183,MA0143.1;1.00467,MA0144.1;0.541532,MA0145.1;0.292366,MA0146.1;0.151124,MA0147.1;0.556853,MA0148.1;0.820161,MA0149.1;0.722227,MA0062.2;0.412742,MA0035.2;0.903829,MA0039.2;0.181475,MA0138.2;1.07027,MA0002.2;0.466067,MA0137.2;0.668025,MA0104.2;0.48458,MA0047.2;0.962424,MA0112.2;0.29236,MA0065.2;0.292912,MA0150.1;0.784464,MA0151.1;0,MA0152.1;0.962542,MA0153.1;1.43238,MA0154.1;0.35067,MA0155.1;0.840842,MA0156.1;0.656895,MA0157.1;1.12772,MA0158.1;0,MA0159.1;0.569393,MA0160.1;0.823568,MA0161.1;0,MA0162.1;0.499274,MA0163.1;0.477233,MA0164.1;0.933981,MA0080.2;0.64167,MA0018.2;0.944669,MA0099.2;1.06348,MA0079.2;3.0269,MA0102.2;2.01714,MA0258.1;1.29343,MA0259.1;0.543506,MA0442.1;0
}}

Latest revision as of 19:29, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr16:35541361..35541425,+p1@Sema5b
Mm9::chr3:94964371..94964427,+p1@Sema6c
Mm9::chr3:94964891..94964895,+p@chr3:94964891..94964895
+


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:0007399nervous system development0.0217461573508419
GO:0048731system development0.032358021051397
GO:0048869cellular developmental process0.032358021051397
GO:0030154cell differentiation0.032358021051397
GO:0048856anatomical structure development0.032358021051397
GO:0005615extracellular space0.032358021051397
GO:0044421extracellular region part0.032358021051397
GO:0007275multicellular organismal development0.032358021051397
GO:0032502developmental process0.0498043738766139



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)1.79e-1123
neuroblast (sensu Vertebrata)1.79e-1123
neuron1.10e-0733
neuronal stem cell1.10e-0733
neuroblast1.10e-0733
electrically signaling cell1.10e-0733

Uber Anatomy
Ontology termp-valuen
neurectoderm5.64e-1464
neural plate5.64e-1464
presumptive neural plate5.64e-1464
ecto-epithelium9.29e-1373
regional part of nervous system2.16e-1254
neural tube2.60e-1252
neural rod2.60e-1252
future spinal cord2.60e-1252
neural keel2.60e-1252
ectoderm-derived structure9.01e-1295
ectoderm9.01e-1295
presumptive ectoderm9.01e-1295
structure with developmental contribution from neural crest1.01e-1192
pre-chordal neural plate1.82e-1149
central nervous system2.43e-1173
multi-cellular organism7.03e-11333
nervous system1.54e-1075
brain3.81e-1047
future brain3.81e-1047
gray matter3.97e-1034
regional part of brain9.88e-1046
gonad2.76e-0918
gonad primordium2.76e-0918
anterior neural tube4.60e-0940
regional part of forebrain9.16e-0939
forebrain9.16e-0939
future forebrain9.16e-0939
external genitalia9.21e-0917
indifferent external genitalia9.21e-0917
indifferent gonad9.21e-0917
embryo3.59e-08320
testis7.56e-0814
brain grey matter9.71e-0829
regional part of telencephalon9.71e-0829
telencephalon9.71e-0829
reproductive organ1.38e-0724
male reproductive organ2.30e-0715
reproductive structure5.50e-0726
reproductive system5.50e-0726


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)
MA0003.10.526413
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.11.93445
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.10.61552
MA0029.11.20789
MA0030.11.21482
MA0031.11.17722
MA0038.10.963265
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.10.932001
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.557057
MA0056.10
MA0057.10.337566
MA0058.10.690848
MA0059.10.705317
MA0060.10.502699
MA0061.10.5406
MA0063.10
MA0066.12.18658
MA0067.11.63197
MA0068.15.46058
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.12.11706
MA0074.10.911576
MA0076.10.657929
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.766354
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.10.62555
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.10.71579
MA0103.10.647985
MA0105.10.405648
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.10.537669
MA0115.11.38041
MA0116.10.602598
MA0117.11.34691
MA0119.10.716476
MA0122.11.36752
MA0124.11.57762
MA0125.11.5017
MA0130.10
MA0131.11.07881
MA0132.10
MA0133.10
MA0135.11.4152
MA0136.10.933582
MA0139.10.462282
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.10.292366
MA0146.10.151124
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.20.181475
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.20.48458
MA0047.20.962424
MA0112.20.29236
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.10.840842
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.10.499274
MA0163.10.477233
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.23.0269
MA0102.22.01714
MA0258.11.29343
MA0259.10.543506
MA0442.10
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