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MCL coexpression mm9:733: Difference between revisions

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{{MCL_coexpression_mm9
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complex;0.0370123163137112;13626!GO:0006349;genetic imprinting;0.0370123163137112;13626!GO:0035097;histone methyltransferase complex;0.0370123163137112;13626!GO:0005634;nucleus;0.0370123163137112;13626,53886,231986,269704!GO:0017053;transcriptional repressor complex;0.0370123163137112;231986!GO:0031519;PcG protein complex;0.0370123163137112;13626!GO:0043283;biopolymer metabolic process;0.0370123163137112;13626,53886,231986,269704!GO:0001739;sex chromatin;0.0370123163137112;13626!GO:0000803;sex chromosome;0.0370123163137112;13626!GO:0045120;pronucleus;0.0370123163137112;13626!GO:0016571;histone methylation;0.0370123163137112;13626!GO:0044451;nucleoplasm part;0.0383916747404711;13626,231986!GO:0010468;regulation of gene expression;0.0383916747404711;13626,231986,269704!GO:0005720;nuclear heterochromatin;0.0383916747404711;13626!GO:0005654;nucleoplasm;0.0383916747404711;13626,231986!GO:0042054;histone methyltransferase activity;0.0383916747404711;13626!GO:0008213;protein amino acid alkylation;0.0383916747404711;13626!GO:0006479;protein amino acid methylation;0.0383916747404711;13626!GO:0004693;cyclin-dependent protein kinase activity;0.0383916747404711;53886!GO:0000790;nuclear chromatin;0.0383916747404711;13626!GO:0008276;protein methyltransferase activity;0.0383916747404711;13626!GO:0031981;nuclear lumen;0.0383916747404711;13626,231986!GO:0043170;macromolecule metabolic process;0.0383916747404711;13626,53886,231986,269704!GO:0016570;histone modification;0.0383916747404711;13626!GO:0000792;heterochromatin;0.0385558823317547;13626!GO:0016569;covalent chromatin modification;0.0385558823317547;13626!GO:0031974;membrane-enclosed lumen;0.038814610994547;13626,231986!GO:0043233;organelle lumen;0.038814610994547;13626,231986!GO:0043414;biopolymer methylation;0.038814610994547;13626!GO:0040029;regulation of gene expression, epigenetic;0.038814610994547;13626!GO:0032259;methylation;0.0393031576574954;13626!GO:0010467;gene expression;0.0423687115763379;13626,231986,269704!GO:0003714;transcription corepressor activity;0.0449295376650605;231986!GO:0044238;primary metabolic process;0.0449295376650605;13626,53886,231986,269704!GO:0044237;cellular metabolic process;0.0449295376650605;13626,53886,231986,269704!GO:0043231;intracellular membrane-bound organelle;0.0449295376650605;13626,53886,231986,269704!GO:0043227;membrane-bound organelle;0.0449295376650605;13626,53886,231986,269704!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0464302673569337;13626,231986,269704!GO:0044454;nuclear chromosome part;0.0464302673569337;13626!GO:0044428;nuclear 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|ontology_enrichment_celltype=CL:0000540!5.31e-09!33;CL:0000047!5.31e-09!33;CL:0000031!5.31e-09!33;CL:0000404!5.31e-09!33;CL:0000117!6.73e-09!23;CL:0000337!6.73e-09!23
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002346!5.96e-23!64;UBERON:0003075!5.96e-23!64;UBERON:0007284!5.96e-23!64;UBERON:0001017!8.53e-22!73;UBERON:0000073!3.31e-21!54;UBERON:0010371!8.95e-21!73;UBERON:0004121!1.10e-20!95;UBERON:0000924!1.10e-20!95;UBERON:0006601!1.10e-20!95;UBERON:0001016!3.93e-20!75;UBERON:0001049!5.77e-20!52;UBERON:0005068!5.77e-20!52;UBERON:0006241!5.77e-20!52;UBERON:0007135!5.77e-20!52;UBERON:0003056!1.10e-18!49;UBERON:0000955!2.00e-17!47;UBERON:0006238!2.00e-17!47;UBERON:0010314!6.62e-17!92;UBERON:0002616!8.40e-17!46;UBERON:0003080!3.92e-16!40;UBERON:0002780!1.46e-15!39;UBERON:0001890!1.46e-15!39;UBERON:0006240!1.46e-15!39;UBERON:0002020!1.69e-14!34;UBERON:0003528!4.85e-12!29;UBERON:0002791!4.85e-12!29;UBERON:0001893!4.85e-12!29;UBERON:0000956!6.80e-09!21;UBERON:0001869!6.80e-09!21;UBERON:0000203!6.80e-09!21;UBERON:0002619!4.34e-08!17;UBERON:0002021!6.41e-08!10;UBERON:0000411!6.41e-08!10;UBERON:0001950!6.41e-08!10;UBERON:0000025!2.09e-07!114;UBERON:0004111!3.41e-07!122;UBERON:0000468!4.03e-07!333
|tfbs_overrepresentation_for_novel_motifs=0.321524,0.178895,0.297937,0.945937,0.200163,0.373426,0.458558,0.124431,0.411053,0.255527,0.417132,0.447169,0.124608,0.470194,0.214197,0,0.656089,0.564478,0.113609,0.451901,0.26524,0.336916,0.469335,0.577226,0.304728,0.496413,0.349241,0.392919,0.238759,0.271461,0.989437,0.754912,0.560002,0.31333,1.1554,0.218093,1.63646,0.443753,0.166348,0.143746,0.196807,0.38461,0.56316,0.215898,0.249283,0.349801,0.578773,0.407653,0.772185,0.241306,0.639101,0.522137,0.259389,0.894161,0.911367,0.47699,0.249055,0.435119,0.101408,0.47505,0.735292,0.531188,0.433822,0.628155,0.487593,0.667546,1.04613,1.3932,0.730718,1.24673,0.281085,0.80439,0.639498,0.944464,2.20686,0.300089,0.313198,0.567793,0.718494,0.74114,0.406536,0.673009,0.529804,0.764135,0.830765,0.158895,0.0697823,0.0791202,0.583509,1.55487,1.11522,0.835661,0.767462,1.11849,0.163126,0.455999,0.777003,0.770215,0.57902,0.0659594,0.184103,0.754637,0.87698,0.639679,0.638654,0.999084,1.66347,0.403887,0.750985,0.266818,0.315128,0.878738,0.26996,0.421988,1.12221,0.195318,1.79896,0.363536,0.657356,0.181004,0.949798,0.607824,0.498153,0.566919,1.17594,0.722111,0.466292,0.760818,1.04463,0.207624,0.86025,0.353344,1.01535,1.22806,1.14365,0.33206,0.877308,0.385921,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,0.385031,0.581788,1.88287,0.882109,0.58382,0.0806411,0.559158,0.895708,0.911723,1.22617,0.976367,0.523103,0.224422,0.319291,0.328917,1.1043,0.829923,0.722546,0.313083,0.629147,0.482049,0.53929,0.445669,0.19482
}}

Latest revision as of 15:48, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr15:26291955..26291956,+p@chr15:26291955..26291956
+
Mm9::chr4:110256532..110256536,+p@chr4:110256532..110256536
+
Mm9::chr4:110262019..110262022,+p@chr4:110262019..110262022
+
Mm9::chr4:110325225..110325231,+p@chr4:110325225..110325231
+
Mm9::chr4:151401911..151401934,+p@chr4:151401911..151401934
+
Mm9::chr5:125342568..125342602,+p2@Zfp664
Mm9::chr5:92444356..92444360,-p@chr5:92444356..92444360
-
Mm9::chr5:92471656..92471727,-p1@Cdkl2
Mm9::chr6:53018556..53018650,-p1@Jazf1
Mm9::chr7:97129757..97129776,+p@chr7:97129757..97129776
+


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:0035098ESC/E(Z) complex0.0370123163137112
GO:0006349genetic imprinting0.0370123163137112
GO:0035097histone methyltransferase complex0.0370123163137112
GO:0005634nucleus0.0370123163137112
GO:0017053transcriptional repressor complex0.0370123163137112
GO:0031519PcG protein complex0.0370123163137112
GO:0043283biopolymer metabolic process0.0370123163137112
GO:0001739sex chromatin0.0370123163137112
GO:0000803sex chromosome0.0370123163137112
GO:0045120pronucleus0.0370123163137112
GO:0016571histone methylation0.0370123163137112
GO:0044451nucleoplasm part0.0383916747404711
GO:0010468regulation of gene expression0.0383916747404711
GO:0005720nuclear heterochromatin0.0383916747404711
GO:0005654nucleoplasm0.0383916747404711
GO:0042054histone methyltransferase activity0.0383916747404711
GO:0008213protein amino acid alkylation0.0383916747404711
GO:0006479protein amino acid methylation0.0383916747404711
GO:0004693cyclin-dependent protein kinase activity0.0383916747404711
GO:0000790nuclear chromatin0.0383916747404711
GO:0008276protein methyltransferase activity0.0383916747404711
GO:0031981nuclear lumen0.0383916747404711
GO:0043170macromolecule metabolic process0.0383916747404711
GO:0016570histone modification0.0383916747404711
GO:0000792heterochromatin0.0385558823317547
GO:0016569covalent chromatin modification0.0385558823317547
GO:0031974membrane-enclosed lumen0.038814610994547
GO:0043233organelle lumen0.038814610994547
GO:0043414biopolymer methylation0.038814610994547
GO:0040029regulation of gene expression, epigenetic0.038814610994547
GO:0032259methylation0.0393031576574954
GO:0010467gene expression0.0423687115763379
GO:0003714transcription corepressor activity0.0449295376650605
GO:0044238primary metabolic process0.0449295376650605
GO:0044237cellular metabolic process0.0449295376650605
GO:0043231intracellular membrane-bound organelle0.0449295376650605
GO:0043227membrane-bound organelle0.0449295376650605
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0464302673569337
GO:0044454nuclear chromosome part0.0464302673569337
GO:0044428nuclear part0.0491307095045673



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
neuron5.31e-0933
neuronal stem cell5.31e-0933
neuroblast5.31e-0933
electrically signaling cell5.31e-0933
CNS neuron (sensu Vertebrata)6.73e-0923
neuroblast (sensu Vertebrata)6.73e-0923

Uber Anatomy
Ontology termp-valuen
neurectoderm5.96e-2364
neural plate5.96e-2364
presumptive neural plate5.96e-2364
central nervous system8.53e-2273
regional part of nervous system3.31e-2154
ecto-epithelium8.95e-2173
ectoderm-derived structure1.10e-2095
ectoderm1.10e-2095
presumptive ectoderm1.10e-2095
nervous system3.93e-2075
neural tube5.77e-2052
neural rod5.77e-2052
future spinal cord5.77e-2052
neural keel5.77e-2052
pre-chordal neural plate1.10e-1849
brain2.00e-1747
future brain2.00e-1747
structure with developmental contribution from neural crest6.62e-1792
regional part of brain8.40e-1746
anterior neural tube3.92e-1640
regional part of forebrain1.46e-1539
forebrain1.46e-1539
future forebrain1.46e-1539
gray matter1.69e-1434
brain grey matter4.85e-1229
regional part of telencephalon4.85e-1229
telencephalon4.85e-1229
cerebral cortex6.80e-0921
cerebral hemisphere6.80e-0921
pallium6.80e-0921
regional part of cerebral cortex4.34e-0817
occipital lobe6.41e-0810
visual cortex6.41e-0810
neocortex6.41e-0810
tube2.09e-07114
anatomical conduit3.41e-07122
multi-cellular organism4.03e-07333


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)
MA0003.10.347165
MA0004.10.360508
MA0006.10.210471
MA0007.10.346734
MA0009.10.780842
MA0014.10.544988
MA0017.10.233089
MA0019.10.603066
MA0024.10.737933
MA0025.11.01089
MA0027.12.42079
MA0028.10.219287
MA0029.12.86082
MA0030.11.71791
MA0031.11.64576
MA0038.10.496338
MA0040.10.79313
MA0041.10.79301
MA0042.10.279998
MA0043.10.875991
MA0046.10.816137
MA0048.10.236433
MA0050.10.396459
MA0051.10.504875
MA0052.10.801048
MA0055.10.344
MA0056.10
MA0057.10.817159
MA0058.10.273976
MA0059.10.28489
MA0060.10.8754
MA0061.10.16896
MA0063.10
MA0066.10.485868
MA0067.11.12095
MA0068.10.0621035
MA0069.10.801381
MA0070.10.791856
MA0071.10.395679
MA0072.10.783532
MA0073.10.00140273
MA0074.10.451832
MA0076.10.249619
MA0077.10.762273
MA0078.10.536502
MA0081.10.305576
MA0083.10.875209
MA0084.11.44691
MA0087.10.832758
MA0088.10.34573
MA0089.10
MA0090.10.877277
MA0091.10.372635
MA0092.10.329444
MA0093.10.226349
MA0095.10
MA0098.10
MA0100.10.440912
MA0101.10.292867
MA0103.10.67982
MA0105.10.304995
MA0106.11.34295
MA0107.10.237082
MA0108.20.625209
MA0109.10
MA0111.10.90605
MA0113.10.516916
MA0114.10.500166
MA0115.10.878749
MA0116.10.604438
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
MA0139.10.385513
MA0140.10.440804
MA0141.10.259554
MA0142.10.674191
MA0143.10.53259
MA0144.10.169559
MA0145.10.371997
MA0146.10.642452
MA0147.10.179496
MA0148.10.979954
MA0149.10.2978
MA0062.20.0948004
MA0035.20.44524
MA0039.20.321097
MA0138.20.590987
MA0002.20.391079
MA0137.20.257017
MA0104.20.134457
MA0047.21.24007
MA0112.20.371983
MA0065.21.03323
MA0150.10.346631
MA0151.10
MA0152.10.495709
MA0153.10.92832
MA0154.10.232525
MA0155.10.416651
MA0156.10.248865
MA0157.11.55122
MA0158.10
MA0159.10.550545
MA0160.10.378276
MA0161.10
MA0162.10.27679
MA0163.10.121321
MA0164.10.471016
MA0080.20.237846
MA0018.20.480226
MA0099.20.584892
MA0079.20.937792
MA0102.21.49914
MA0258.10.473611
MA0259.10.170828
MA0442.10
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