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MCL coexpression mm9:770: Difference between revisions

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{{MCL_coexpression_mm9
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splicing;0.000469208992587783;101214,19205,15381!GO:0006397;mRNA processing;0.000469561809974684;101214,19205,15381!GO:0016071;mRNA metabolic process;0.000469561809974684;101214,19205,15381!GO:0006396;RNA processing;0.000893852557727055;101214,19205,15381!GO:0003723;RNA binding;0.00257348900595761;101214,19205,15381!GO:0005634;nucleus;0.0041718075817128;101214,19205,11737,70998,15381!GO:0016070;RNA metabolic process;0.00756204945523937;101214,19205,70998,15381!GO:0010467;gene expression;0.0132872715897345;101214,19205,70998,15381!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0172880752005752;101214,19205,70998,15381!GO:0045120;pronucleus;0.0189441460441609;15381!GO:0016363;nuclear matrix;0.0189441460441609;11737!GO:0043231;intracellular membrane-bound organelle;0.0189441460441609;101214,19205,11737,70998,15381!GO:0043227;membrane-bound organelle;0.0189441460441609;101214,19205,11737,70998,15381!GO:0030529;ribonucleoprotein complex;0.0215939053400419;19205,15381!GO:0043229;intracellular organelle;0.0273558350317909;101214,19205,11737,70998,15381!GO:0043226;organelle;0.0273558350317909;101214,19205,11737,70998,15381!GO:0000166;nucleotide binding;0.0273558350317909;101214,19205,15381!GO:0043283;biopolymer metabolic 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|gostat_on_MCL_coexpression=GO:0008380;RNA splicing;0.000469208992587783;101214,19205,15381!GO:0006397;mRNA processing;0.000469561809974684;101214,19205,15381!GO:0016071;mRNA metabolic process;0.000469561809974684;101214,19205,15381!GO:0006396;RNA processing;0.000893852557727055;101214,19205,15381!GO:0003723;RNA binding;0.00257348900595761;101214,19205,15381!GO:0005634;nucleus;0.0041718075817128;101214,19205,11737,70998,15381!GO:0016070;RNA metabolic process;0.00756204945523937;101214,19205,70998,15381!GO:0010467;gene expression;0.0132872715897345;101214,19205,70998,15381!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0172880752005752;101214,19205,70998,15381!GO:0045120;pronucleus;0.0189441460441609;15381!GO:0016363;nuclear matrix;0.0189441460441609;11737!GO:0043231;intracellular membrane-bound organelle;0.0189441460441609;101214,19205,11737,70998,15381!GO:0043227;membrane-bound organelle;0.0189441460441609;101214,19205,11737,70998,15381!GO:0030529;ribonucleoprotein complex;0.0215939053400419;19205,15381!GO:0043229;intracellular organelle;0.0273558350317909;101214,19205,11737,70998,15381!GO:0043226;organelle;0.0273558350317909;101214,19205,11737,70998,15381!GO:0000166;nucleotide binding;0.0273558350317909;101214,19205,15381!GO:0043283;biopolymer metabolic process;0.0300128468366282;101214,19205,70998,15381!
|ontology_enrichment_celltype=CL:0000542!1.11e-08!13;CL:0000051!1.11e-08!13;CL:0000838!3.75e-08!12;CL:0000084!1.50e-07!11;CL:0000827!1.50e-07!11
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000153!4.06e-09!43;UBERON:0004177!2.57e-07!29;UBERON:0005057!2.57e-07!29;UBERON:0002370!8.74e-07!23;UBERON:0000974!8.74e-07!23;UBERON:0004807!8.74e-07!23;UBERON:0005058!8.74e-07!23;UBERON:0003351!8.74e-07!23;UBERON:0009113!8.74e-07!23;UBERON:0003295!8.74e-07!23;UBERON:0009722!8.74e-07!23;UBERON:0005562!8.74e-07!23;UBERON:0007690!8.74e-07!23
|tfbs_overrepresentation_for_novel_motifs=0.93395,0.433653,0.330161,0.394491,0.227651,0.40827,0.495658,0.146465,0.154135,0.904288,1.1491,1.21524,0.449446,0.507558,0.24249,0,1.66303,0.22065,0.419123,0.247067,0.802917,0.047629,1.26371,0.226287,0.337218,2.27409,0.128175,0.428336,0.268347,0.656973,1.06602,0.796599,1.82817,0.113369,0.681042,0.482999,2.5174,0.480503,0.191662,0.167387,0.637027,0.419787,0.163087,0.244285,0.317317,0.998423,0.618203,0.443479,0.133514,0.745859,0.679429,1.37808,0.0915709,0.937018,0.954342,0.514504,0.279148,0.471658,0.384731,0.512521,0.776777,0.569793,0.163832,0.668331,1.30341,0.708248,1.08987,1.43807,1.81937,1.29123,1.51902,0.460931,1.60811,0.987652,1.7889,0.349958,0.113315,0.607043,0.759798,0.299972,0.152219,0.713779,0.568383,0.436063,0.873141,0.651261,0.714965,0.319367,0.623015,1.60001,1.15927,0.878077,0.809272,0.232894,1.66008,0.17334,0.444003,0.812053,0.618454,0.585565,0.210602,0.796322,0.919715,0.680015,0.678976,1.07585,1.74861,0.439611,1.48974,0.297733,0.348012,0.921485,0.301014,1.15983,1.16629,0.222515,0.795864,0.398075,0.697928,0.207304,0.993019,1.56109,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.235546,0.90286,0.387557,1.05894,0.527782,1.18781,0.0467191,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,0.621266,1.92834,0.364791,1.88479,0.665499,2.48799,0.938577,0.178329,0.526881,1.01974,0.561556,0.705025,0.352329,0.362302,1.1483,0.872292,0.763895,0.345891,0.669337,0.519673,0.602679,0.482466,0.254444
|tfbs_overrepresentation_jaspar=MA0003.1;0.294637,MA0004.1;1.02263,MA0006.1;1.24699,MA0007.1;0.991467,MA0009.1;0.82278,MA0014.1;0.961396,MA0017.1;0.26239,MA0019.1;0.642876,MA0024.1;1.83441,MA0025.1;1.05446,MA0027.1;2.46647,MA0028.1;0.692501,MA0029.1;0.757957,MA0030.1;0.764448,MA0031.1;0.729293,MA0038.1;1.32237,MA0040.1;0.835181,MA0041.1;0.323687,MA0042.1;0.311486,MA0043.1;0.918718,MA0046.1;0.858391,MA0048.1;0.993388,MA0050.1;0.431976,MA0051.1;0.542972,MA0052.1;0.84317,MA0055.1;0.0882028,MA0056.1;0,MA0057.1;0.549903,MA0058.1;0.823526,MA0059.1;0.316585,MA0060.1;5.5158,MA0061.1;0.194456,MA0063.1;0,MA0066.1;0.523573,MA0067.1;1.16502,MA0068.1;0.563625,MA0069.1;0.843506,MA0070.1;0.833895,MA0071.1;0.431174,MA0072.1;0.825495,MA0073.1;0.00108891,MA0074.1;0.488775,MA0076.1;0.279739,MA0077.1;0.804033,MA0078.1;0.575205,MA0081.1;0.338098,MA0083.1;0.917931,MA0084.1;1.49188,MA0087.1;0.87515,MA0088.1;0.0492918,MA0089.1;0,MA0090.1;0.362551,MA0091.1;0.407455,MA0092.1;0.95209,MA0093.1;1.30984,MA0095.1;0,MA0098.1;0,MA0100.1;1.20151,MA0101.1;0.324888,MA0103.1;0.272167,MA0105.1;0.109964,MA0106.1;1.42499,MA0107.1;0.266586,MA0108.2;2.6976,MA0109.1;0,MA0111.1;0.980871,MA0113.1;0.555251,MA0114.1;0.561811,MA0115.1;0.921497,MA0116.1;0.670446,MA0117.1;0.88947,MA0119.1;0.325434,MA0122.1;0.909168,MA0124.1;1.11203,MA0125.1;2.36402,MA0130.1;0,MA0131.1;0.638414,MA0132.1;0,MA0133.1;0,MA0135.1;0.954884,MA0136.1;0.508047,MA0139.1;0.143341,MA0140.1;0.477483,MA0141.1;0.29014,MA0142.1;0.714976,MA0143.1;0.571221,MA0144.1;0.195095,MA0145.1;0.200183,MA0146.1;0.148686,MA0147.1;1.75741,MA0148.1;0.410398,MA0149.1;0.330018,MA0062.2;0.738221,MA0035.2;0.482026,MA0039.2;0.436553,MA0138.2;0.630612,MA0002.2;0.447007,MA0137.2;0.287486,MA0104.2;1.48162,MA0047.2;0.533516,MA0112.2;0.200175,MA0065.2;0.44341,MA0150.1;0.380623,MA0151.1;0,MA0152.1;0.53362,MA0153.1;0.971406,MA0154.1;0.0809407,MA0155.1;0.0631765,MA0156.1;0.278949,MA0157.1;0.683365,MA0158.1;0,MA0159.1;1.80557,MA0160.1;0.413266,MA0161.1;0,MA0162.1;0.582797,MA0163.1;1.15194,MA0164.1;0.508398,MA0080.2;0.267388,MA0018.2;1.28741,MA0099.2;0.624421,MA0079.2;1.14022,MA0102.2;1.5442,MA0258.1;0.180934,MA0259.1;1.08444,MA0442.1;0
}}

Latest revision as of 15:51, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:79317403..79317419,+p1@Ptbp1
Mm9::chr11:116714397..116714413,-p1@Srsf2
Mm9::chr14:52723666..52723686,-p1@Hnrnpc
Mm9::chr14:52723690..52723701,-p2@Hnrnpc
Mm9::chr17:80606639..80606648,-p1@Srsf7
Mm9::chr5:114580714..114580735,-p@chr5:114580714..114580735
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Mm9::chr6:49214013..49214059,-p1@Tra2a
Mm9::chr9:62189896..62189919,+p5@Anp32a
Mm9::chrX:50265409..50265538,+p1@Phf6


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:0008380RNA splicing0.000469208992587783
GO:0006397mRNA processing0.000469561809974684
GO:0016071mRNA metabolic process0.000469561809974684
GO:0006396RNA processing0.000893852557727055
GO:0003723RNA binding0.00257348900595761
GO:0005634nucleus0.0041718075817128
GO:0016070RNA metabolic process0.00756204945523937
GO:0010467gene expression0.0132872715897345
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0172880752005752
GO:0045120pronucleus0.0189441460441609
GO:0016363nuclear matrix0.0189441460441609
GO:0043231intracellular membrane-bound organelle0.0189441460441609
GO:0043227membrane-bound organelle0.0189441460441609
GO:0030529ribonucleoprotein complex0.0215939053400419
GO:0043229intracellular organelle0.0273558350317909
GO:0043226organelle0.0273558350317909
GO:0000166nucleotide binding0.0273558350317909
GO:0043283biopolymer metabolic process0.0300128468366282



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
lymphocyte1.11e-0813
common lymphoid progenitor1.11e-0813
lymphoid lineage restricted progenitor cell3.75e-0812
T cell1.50e-0711
pro-T cell1.50e-0711

Uber Anatomy
Ontology termp-valuen
anterior region of body4.06e-0943
hemopoietic organ2.57e-0729
immune organ2.57e-0729
thymus8.74e-0723
neck8.74e-0723
respiratory system epithelium8.74e-0723
hemolymphoid system gland8.74e-0723
pharyngeal epithelium8.74e-0723
thymic region8.74e-0723
pharyngeal gland8.74e-0723
entire pharyngeal arch endoderm8.74e-0723
thymus primordium8.74e-0723
early pharyngeal endoderm8.74e-0723


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)
MA0003.10.294637
MA0004.11.02263
MA0006.11.24699
MA0007.10.991467
MA0009.10.82278
MA0014.10.961396
MA0017.10.26239
MA0019.10.642876
MA0024.11.83441
MA0025.11.05446
MA0027.12.46647
MA0028.10.692501
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.11.32237
MA0040.10.835181
MA0041.10.323687
MA0042.10.311486
MA0043.10.918718
MA0046.10.858391
MA0048.10.993388
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.10.0882028
MA0056.10
MA0057.10.549903
MA0058.10.823526
MA0059.10.316585
MA0060.15.5158
MA0061.10.194456
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.563625
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.10.00108891
MA0074.10.488775
MA0076.10.279739
MA0077.10.804033
MA0078.10.575205
MA0081.10.338098
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.0492918
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.95209
MA0093.11.30984
MA0095.10
MA0098.10
MA0100.11.20151
MA0101.10.324888
MA0103.10.272167
MA0105.10.109964
MA0106.11.42499
MA0107.10.266586
MA0108.22.6976
MA0109.10
MA0111.10.980871
MA0113.10.555251
MA0114.10.561811
MA0115.10.921497
MA0116.10.670446
MA0117.10.88947
MA0119.10.325434
MA0122.10.909168
MA0124.11.11203
MA0125.12.36402
MA0130.10
MA0131.10.638414
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.143341
MA0140.10.477483
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.10.195095
MA0145.10.200183
MA0146.10.148686
MA0147.11.75741
MA0148.10.410398
MA0149.10.330018
MA0062.20.738221
MA0035.20.482026
MA0039.20.436553
MA0138.20.630612
MA0002.20.447007
MA0137.20.287486
MA0104.21.48162
MA0047.20.533516
MA0112.20.200175
MA0065.20.44341
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.0809407
MA0155.10.0631765
MA0156.10.278949
MA0157.10.683365
MA0158.10
MA0159.11.80557
MA0160.10.413266
MA0161.10
MA0162.10.582797
MA0163.11.15194
MA0164.10.508398
MA0080.20.267388
MA0018.21.28741
MA0099.20.624421
MA0079.21.14022
MA0102.21.5442
MA0258.10.180934
MA0259.11.08444
MA0442.10
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