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MCL coexpression mm9:2824: Difference between revisions

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{{MCL_coexpression_mm9
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copper ion homeostasis;2.00936887370317e-05;19122,26434!GO:0055070;copper ion homeostasis;2.00936887370317e-05;19122,26434!GO:0051260;protein homooligomerization;7.81078619014968e-05;19122,26434!GO:0051259;protein oligomerization;0.000121306222455019;19122,26434!GO:0005507;copper ion binding;0.00031896435691302;19122,26434!GO:0030005;cellular di-, tri-valent inorganic cation homeostasis;0.000700884515879918;19122,26434!GO:0055066;di-, tri-valent inorganic cation homeostasis;0.000700884515879918;19122,26434!GO:0030003;cellular cation homeostasis;0.000700884515879918;19122,26434!GO:0055080;cation homeostasis;0.000700884515879918;19122,26434!GO:0048503;GPI anchor binding;0.000767524049384828;19122,26434!GO:0006461;protein complex assembly;0.000783161993426455;19122,26434!GO:0055082;cellular chemical homeostasis;0.000904389109868064;19122,26434!GO:0006873;cellular ion homeostasis;0.000904389109868064;19122,26434!GO:0035091;phosphoinositide binding;0.00101335011568568;19122,26434!GO:0050801;ion homeostasis;0.00101335011568568;19122,26434!GO:0005543;phospholipid binding;0.0013638582240156;19122,26434!GO:0048878;chemical homeostasis;0.0013638582240156;19122,26434!GO:0019725;cellular homeostasis;0.0013638582240156;19122,26434!GO:0065003;macromolecular complex assembly;0.00287316699102723;19122,26434!GO:0042592;homeostatic process;0.00288700379716113;19122,26434!GO:0008289;lipid binding;0.00331646094962967;19122,26434!GO:0022607;cellular component assembly;0.00343658938090558;19122,26434!GO:0065008;regulation of biological quality;0.00881725972057049;19122,26434!GO:0043169;cation binding;0.0133554956062523;19122,26434,105298!GO:0045121;lipid raft;0.0138335019063751;19122!GO:0046872;metal ion binding;0.0157706284997856;19122,26434,105298!GO:0043167;ion binding;0.0161504046373676;19122,26434,105298!GO:0006979;response to oxidative stress;0.0163375068120297;19122!GO:0007160;cell-matrix 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|gostat_on_MCL_coexpression=GO:0006878;cellular copper ion homeostasis;2.00936887370317e-05;19122,26434!GO:0055070;copper ion homeostasis;2.00936887370317e-05;19122,26434!GO:0051260;protein homooligomerization;7.81078619014968e-05;19122,26434!GO:0051259;protein oligomerization;0.000121306222455019;19122,26434!GO:0005507;copper ion binding;0.00031896435691302;19122,26434!GO:0030005;cellular di-, tri-valent inorganic cation homeostasis;0.000700884515879918;19122,26434!GO:0055066;di-, tri-valent inorganic cation homeostasis;0.000700884515879918;19122,26434!GO:0030003;cellular cation homeostasis;0.000700884515879918;19122,26434!GO:0055080;cation homeostasis;0.000700884515879918;19122,26434!GO:0048503;GPI anchor binding;0.000767524049384828;19122,26434!GO:0006461;protein complex assembly;0.000783161993426455;19122,26434!GO:0055082;cellular chemical homeostasis;0.000904389109868064;19122,26434!GO:0006873;cellular ion homeostasis;0.000904389109868064;19122,26434!GO:0035091;phosphoinositide binding;0.00101335011568568;19122,26434!GO:0050801;ion homeostasis;0.00101335011568568;19122,26434!GO:0005543;phospholipid binding;0.0013638582240156;19122,26434!GO:0048878;chemical homeostasis;0.0013638582240156;19122,26434!GO:0019725;cellular homeostasis;0.0013638582240156;19122,26434!GO:0065003;macromolecular complex assembly;0.00287316699102723;19122,26434!GO:0042592;homeostatic process;0.00288700379716113;19122,26434!GO:0008289;lipid binding;0.00331646094962967;19122,26434!GO:0022607;cellular component assembly;0.00343658938090558;19122,26434!GO:0065008;regulation of biological quality;0.00881725972057049;19122,26434!GO:0043169;cation binding;0.0133554956062523;19122,26434,105298!GO:0045121;lipid raft;0.0138335019063751;19122!GO:0046872;metal ion binding;0.0157706284997856;19122,26434,105298!GO:0043167;ion binding;0.0161504046373676;19122,26434,105298!GO:0006979;response to oxidative stress;0.0163375068120297;19122!GO:0007160;cell-matrix adhesion;0.0220620126922838;105298!GO:0031589;cell-substrate adhesion;0.0226757069710698;105298!
|ontology_enrichment_celltype=CL:0000055!3.88e-13!49;CL:0000221!3.90e-11!44;CL:0000133!3.90e-11!44;CL:0002319!8.13e-11!43;CL:0000393!1.85e-08!39;CL:0000211!1.85e-08!39
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004121!5.26e-25!95;UBERON:0000924!5.26e-25!95;UBERON:0006601!5.26e-25!95;UBERON:0001016!4.58e-24!75;UBERON:0001017!2.00e-23!73;UBERON:0010314!4.92e-19!92;UBERON:0010371!4.25e-17!73;UBERON:0000073!9.67e-17!54;UBERON:0001049!1.10e-15!52;UBERON:0005068!1.10e-15!52;UBERON:0006241!1.10e-15!52;UBERON:0007135!1.10e-15!52;UBERON:0002346!2.03e-15!64;UBERON:0003075!2.03e-15!64;UBERON:0007284!2.03e-15!64;UBERON:0000955!3.31e-15!47;UBERON:0006238!3.31e-15!47;UBERON:0002616!1.20e-14!46;UBERON:0004111!6.65e-12!122;UBERON:0003080!1.72e-11!40;UBERON:0000025!5.74e-11!114;UBERON:0002780!6.92e-11!39;UBERON:0001890!6.92e-11!39;UBERON:0006240!6.92e-11!39;UBERON:0002020!1.45e-10!34;UBERON:0003056!1.66e-10!49;UBERON:0003528!2.67e-10!29;UBERON:0002791!2.67e-10!29;UBERON:0001893!2.67e-10!29;UBERON:0000956!1.37e-07!21;UBERON:0001869!1.37e-07!21;UBERON:0000203!1.37e-07!21;UBERON:0002619!2.53e-07!17
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.193418,0.722405,0.801166,0.587814,0.81763,2.12177,0.467321,0.479531,0.66329,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,1.38557,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,1.55113,0.380786,0.825437,1.24901,0.575271,0.411696,2.51624,0.144706,0.563758,0.902078,0.536514,1.24975,0.582863,0.831295,0.261619,0.610669,0.922882,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.284975,1.44925,0.416814,1.03818,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,0.181575,0.195254,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,1.98904,1.649,2.74838,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,1.79445,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,3.34259,0.955954,1.65529,0.751419,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.38417,0.260379,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,2.09085,1.34909
|tfbs_overrepresentation_jaspar=MA0003.1;0.0699972,MA0004.1;0.801718,MA0006.1;0.60285,MA0007.1;0.784593,MA0009.1;1.27673,MA0014.1;0.133574,MA0017.1;0.635031,MA0019.1;1.08369,MA0024.1;1.23079,MA0025.1;3.33329,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;0.353763,MA0050.1;1.97065,MA0051.1;2.23119,MA0052.1;1.29825,MA0055.1;0.190475,MA0056.1;0,MA0057.1;0.337566,MA0058.1;0.690848,MA0059.1;0.705317,MA0060.1;1.25521,MA0061.1;0.5406,MA0063.1;0,MA0066.1;0.951196,MA0067.1;1.63197,MA0068.1;2.46203,MA0069.1;1.29861,MA0070.1;1.28847,MA0071.1;0.844726,MA0072.1;1.2796,MA0073.1;6.00139,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;1.80015,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;2.21145,MA0146.1;1.44443,MA0147.1;0.556853,MA0148.1;0.820161,MA0149.1;0.722227,MA0062.2;0.412742,MA0035.2;0.903829,MA0039.2;2.6396,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;0.964824,MA0163.1;0.477233,MA0164.1;0.933981,MA0080.2;0.64167,MA0018.2;0.944669,MA0099.2;1.06348,MA0079.2;3.48353,MA0102.2;2.01714,MA0258.1;0.520639,MA0259.1;0.543506,MA0442.1;0
}}

Latest revision as of 19:08, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:19711627..19711680,-p1@Epdr1
Mm9::chr2:131735667..131735684,+p1@Prnp
Mm9::chr2:131735687..131735715,+p1@Prnd


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:0006878cellular copper ion homeostasis2.00936887370317e-05
GO:0055070copper ion homeostasis2.00936887370317e-05
GO:0051260protein homooligomerization7.81078619014968e-05
GO:0051259protein oligomerization0.000121306222455019
GO:0005507copper ion binding0.00031896435691302
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.000700884515879918
GO:0055066di-, tri-valent inorganic cation homeostasis0.000700884515879918
GO:0030003cellular cation homeostasis0.000700884515879918
GO:0055080cation homeostasis0.000700884515879918
GO:0048503GPI anchor binding0.000767524049384828
GO:0006461protein complex assembly0.000783161993426455
GO:0055082cellular chemical homeostasis0.000904389109868064
GO:0006873cellular ion homeostasis0.000904389109868064
GO:0035091phosphoinositide binding0.00101335011568568
GO:0050801ion homeostasis0.00101335011568568
GO:0005543phospholipid binding0.0013638582240156
GO:0048878chemical homeostasis0.0013638582240156
GO:0019725cellular homeostasis0.0013638582240156
GO:0065003macromolecular complex assembly0.00287316699102723
GO:0042592homeostatic process0.00288700379716113
GO:0008289lipid binding0.00331646094962967
GO:0022607cellular component assembly0.00343658938090558
GO:0065008regulation of biological quality0.00881725972057049
GO:0043169cation binding0.0133554956062523
GO:0045121lipid raft0.0138335019063751
GO:0046872metal ion binding0.0157706284997856
GO:0043167ion binding0.0161504046373676
GO:0006979response to oxidative stress0.0163375068120297
GO:0007160cell-matrix adhesion0.0220620126922838
GO:0031589cell-substrate adhesion0.0226757069710698



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
non-terminally differentiated cell3.88e-1349
ectodermal cell3.90e-1144
neurectodermal cell3.90e-1144
neural cell8.13e-1143
electrically responsive cell1.85e-0839
electrically active cell1.85e-0839

Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure5.26e-2595
ectoderm5.26e-2595
presumptive ectoderm5.26e-2595
nervous system4.58e-2475
central nervous system2.00e-2373
structure with developmental contribution from neural crest4.92e-1992
ecto-epithelium4.25e-1773
regional part of nervous system9.67e-1754
neural tube1.10e-1552
neural rod1.10e-1552
future spinal cord1.10e-1552
neural keel1.10e-1552
neurectoderm2.03e-1564
neural plate2.03e-1564
presumptive neural plate2.03e-1564
brain3.31e-1547
future brain3.31e-1547
regional part of brain1.20e-1446
anatomical conduit6.65e-12122
anterior neural tube1.72e-1140
tube5.74e-11114
regional part of forebrain6.92e-1139
forebrain6.92e-1139
future forebrain6.92e-1139
gray matter1.45e-1034
pre-chordal neural plate1.66e-1049
brain grey matter2.67e-1029
regional part of telencephalon2.67e-1029
telencephalon2.67e-1029
cerebral cortex1.37e-0721
cerebral hemisphere1.37e-0721
pallium1.37e-0721
regional part of cerebral cortex2.53e-0717


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)
MA0003.10.0699972
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.10.133574
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.13.33329
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
MA0048.10.353763
MA0050.11.97065
MA0051.12.23119
MA0052.11.29825
MA0055.10.190475
MA0056.10
MA0057.10.337566
MA0058.10.690848
MA0059.10.705317
MA0060.11.25521
MA0061.10.5406
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.12.46203
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.16.00139
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
MA0092.11.80015
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
MA0145.12.21145
MA0146.11.44443
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.22.6396
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
MA0162.10.964824
MA0163.10.477233
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.23.48353
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:2824&oldid=3074823"