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MCL coexpression mm9:2733: Difference between revisions

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{{MCL_coexpression_mm9
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complex;0.000121865652926932;235661,68097!GO:0003777;microtubule motor activity;0.000312168174985246;235661,68097!GO:0005875;microtubule associated complex;0.000515377650432372;235661,68097!GO:0007017;microtubule-based process;0.00108928683367448;235661,68097!GO:0005874;microtubule;0.00108928683367448;235661,68097!GO:0015630;microtubule cytoskeleton;0.00203884839287239;235661,68097!GO:0007010;cytoskeleton organization and biogenesis;0.00427434558388796;235661,68097!GO:0044430;cytoskeletal part;0.00506297758804196;235661,68097!GO:0046907;intracellular transport;0.0053704932565731;235661,68097!GO:0005868;cytoplasmic dynein complex;0.00547720074331084;235661!GO:0051649;establishment of cellular localization;0.00651053243215824;235661,68097!GO:0051641;cellular localization;0.00651053243215824;235661,68097!GO:0005856;cytoskeleton;0.00850868390029496;235661,68097!GO:0006996;organelle organization and biogenesis;0.0129359189935112;235661,68097!GO:0016459;myosin complex;0.0188828728078335;68097!GO:0043232;intracellular non-membrane-bound organelle;0.0188828728078335;235661,68097!GO:0043228;non-membrane-bound organelle;0.0188828728078335;235661,68097!GO:0043234;protein complex;0.0202259463645369;235661,68097!GO:0007018;microtubule-based movement;0.0238788590423317;235661!GO:0030705;cytoskeleton-dependent intracellular transport;0.026773568778255;235661!GO:0032991;macromolecular complex;0.0275248713861544;235661,68097!GO:0006810;transport;0.0310556537513799;235661,68097!GO:0044446;intracellular organelle part;0.0310556537513799;235661,68097!GO:0044422;organelle part;0.0310556537513799;235661,68097!GO:0016043;cellular component organization and biogenesis;0.0310556537513799;235661,68097!GO:0051234;establishment of localization;0.0310556537513799;235661,68097!GO:0051179;localization;0.0369834062872931;235661,68097!GO:0015629;actin 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|gostat_on_MCL_coexpression=GO:0030286;dynein complex;0.000121865652926932;235661,68097!GO:0003777;microtubule motor activity;0.000312168174985246;235661,68097!GO:0005875;microtubule associated complex;0.000515377650432372;235661,68097!GO:0007017;microtubule-based process;0.00108928683367448;235661,68097!GO:0005874;microtubule;0.00108928683367448;235661,68097!GO:0015630;microtubule cytoskeleton;0.00203884839287239;235661,68097!GO:0007010;cytoskeleton organization and biogenesis;0.00427434558388796;235661,68097!GO:0044430;cytoskeletal part;0.00506297758804196;235661,68097!GO:0046907;intracellular transport;0.0053704932565731;235661,68097!GO:0005868;cytoplasmic dynein complex;0.00547720074331084;235661!GO:0051649;establishment of cellular localization;0.00651053243215824;235661,68097!GO:0051641;cellular localization;0.00651053243215824;235661,68097!GO:0005856;cytoskeleton;0.00850868390029496;235661,68097!GO:0006996;organelle organization and biogenesis;0.0129359189935112;235661,68097!GO:0016459;myosin complex;0.0188828728078335;68097!GO:0043232;intracellular non-membrane-bound organelle;0.0188828728078335;235661,68097!GO:0043228;non-membrane-bound organelle;0.0188828728078335;235661,68097!GO:0043234;protein complex;0.0202259463645369;235661,68097!GO:0007018;microtubule-based movement;0.0238788590423317;235661!GO:0030705;cytoskeleton-dependent intracellular transport;0.026773568778255;235661!GO:0032991;macromolecular complex;0.0275248713861544;235661,68097!GO:0006810;transport;0.0310556537513799;235661,68097!GO:0044446;intracellular organelle part;0.0310556537513799;235661,68097!GO:0044422;organelle part;0.0310556537513799;235661,68097!GO:0016043;cellular component organization and biogenesis;0.0310556537513799;235661,68097!GO:0051234;establishment of localization;0.0310556537513799;235661,68097!GO:0051179;localization;0.0369834062872931;235661,68097!GO:0015629;actin cytoskeleton;0.0369834062872931;68097!
|ontology_enrichment_celltype=CL:0000117!8.38e-11!23;CL:0000337!8.38e-11!23;CL:0000540!4.32e-10!33;CL:0000047!4.32e-10!33;CL:0000031!4.32e-10!33;CL:0000404!4.32e-10!33;CL:0002321!4.97e-10!70;CL:0000221!1.01e-08!44;CL:0000133!1.01e-08!44;CL:0002319!1.47e-08!43;CL:0000393!1.01e-07!39;CL:0000211!1.01e-07!39;CL:0000055!8.18e-07!49
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0010314!1.84e-21!92;UBERON:0001016!8.10e-20!75;UBERON:0001017!2.21e-19!73;UBERON:0004121!2.23e-19!95;UBERON:0000924!2.23e-19!95;UBERON:0006601!2.23e-19!95;UBERON:0000073!4.94e-19!54;UBERON:0002346!1.16e-18!64;UBERON:0003075!1.16e-18!64;UBERON:0007284!1.16e-18!64;UBERON:0001049!1.45e-17!52;UBERON:0005068!1.45e-17!52;UBERON:0006241!1.45e-17!52;UBERON:0007135!1.45e-17!52;UBERON:0010371!1.49e-17!73;UBERON:0000955!2.36e-14!47;UBERON:0006238!2.36e-14!47;UBERON:0002616!5.10e-14!46;UBERON:0002020!1.86e-13!34;UBERON:0003056!2.94e-13!49;UBERON:0003080!2.92e-12!40;UBERON:0002780!8.40e-12!39;UBERON:0001890!8.40e-12!39;UBERON:0006240!8.40e-12!39;UBERON:0003528!1.86e-10!29;UBERON:0002791!1.86e-10!29;UBERON:0001893!1.86e-10!29;UBERON:0000477!1.62e-08!244;UBERON:0000025!1.56e-07!114;UBERON:0004111!1.74e-07!122;UBERON:0000956!5.21e-07!21;UBERON:0001869!5.21e-07!21;UBERON:0000203!5.21e-07!21;UBERON:0002619!6.99e-07!17
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.193418,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,1.23467,2.0216,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,1.38557,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,1.55113,0.380786,0.825437,1.24901,0.575271,0.411696,0.608816,0.872889,0.563758,0.902078,0.536514,1.24975,0.582863,0.831295,1.33334,0.610669,0.922882,0.788421,1.05665,0.859154,0.663409,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,2.16101,1.22795,1.00308,0.494668,2.51236,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,1.6706,0.474956,0.284975,1.44925,2.81128,0.402065,1.05896,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,1.62246,0.195254,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,1.94011,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,0.609576,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,1.44008,0.999018,2.0485,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,3.52716,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,0.421338
}}

Latest revision as of 19:00, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:87800997..87801014,-p1@Dynll2
Mm9::chr9:114597969..114597983,+p3@Dync1li1
Mm9::chr9:114597984..114597995,+p5@Dync1li1


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:0030286dynein complex0.000121865652926932
GO:0003777microtubule motor activity0.000312168174985246
GO:0005875microtubule associated complex0.000515377650432372
GO:0007017microtubule-based process0.00108928683367448
GO:0005874microtubule0.00108928683367448
GO:0015630microtubule cytoskeleton0.00203884839287239
GO:0007010cytoskeleton organization and biogenesis0.00427434558388796
GO:0044430cytoskeletal part0.00506297758804196
GO:0046907intracellular transport0.0053704932565731
GO:0005868cytoplasmic dynein complex0.00547720074331084
GO:0051649establishment of cellular localization0.00651053243215824
GO:0051641cellular localization0.00651053243215824
GO:0005856cytoskeleton0.00850868390029496
GO:0006996organelle organization and biogenesis0.0129359189935112
GO:0016459myosin complex0.0188828728078335
GO:0043232intracellular non-membrane-bound organelle0.0188828728078335
GO:0043228non-membrane-bound organelle0.0188828728078335
GO:0043234protein complex0.0202259463645369
GO:0007018microtubule-based movement0.0238788590423317
GO:0030705cytoskeleton-dependent intracellular transport0.026773568778255
GO:0032991macromolecular complex0.0275248713861544
GO:0006810transport0.0310556537513799
GO:0044446intracellular organelle part0.0310556537513799
GO:0044422organelle part0.0310556537513799
GO:0016043cellular component organization and biogenesis0.0310556537513799
GO:0051234establishment of localization0.0310556537513799
GO:0051179localization0.0369834062872931
GO:0015629actin cytoskeleton0.0369834062872931



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
structure with developmental contribution from neural crest1.84e-2192
nervous system8.10e-2075
central nervous system2.21e-1973
ectoderm-derived structure2.23e-1995
ectoderm2.23e-1995
presumptive ectoderm2.23e-1995
regional part of nervous system4.94e-1954
neurectoderm1.16e-1864
neural plate1.16e-1864
presumptive neural plate1.16e-1864
neural tube1.45e-1752
neural rod1.45e-1752
future spinal cord1.45e-1752
neural keel1.45e-1752
ecto-epithelium1.49e-1773
brain2.36e-1447
future brain2.36e-1447
regional part of brain5.10e-1446
gray matter1.86e-1334
pre-chordal neural plate2.94e-1349
anterior neural tube2.92e-1240
regional part of forebrain8.40e-1239
forebrain8.40e-1239
future forebrain8.40e-1239
brain grey matter1.86e-1029
regional part of telencephalon1.86e-1029
telencephalon1.86e-1029
anatomical cluster1.62e-08244
tube1.56e-07114
anatomical conduit1.74e-07122
cerebral cortex5.21e-0721
cerebral hemisphere5.21e-0721
pallium5.21e-0721
regional part of cerebral cortex6.99e-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)
MA0003.13.09356
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.12.60474
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
MA0048.11.66457
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.12.37331
MA0056.10
MA0057.10.337566
MA0058.10.690848
MA0059.10.705317
MA0060.10.502699
MA0061.10.5406
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.908538
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.971751
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
MA0146.12.07553
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
MA0104.21.21648
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
MA0162.13.72632
MA0163.10.477233
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.23.96489
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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