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MCL coexpression mm9:1036: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0044249;cellular biosynthetic process;0.00253564774886875;27367,69895,270685!GO:0009257;10-formyltetrahydrofolate biosynthetic process;0.00253564774886875;270685!GO:0003735;structural constituent of ribosome;0.00253564774886875;27367,69895!GO:0005840;ribosome;0.00253564774886875;27367,69895!GO:0009058;biosynthetic process;0.00253564774886875;27367,69895,270685!GO:0009256;10-formyltetrahydrofolate metabolic process;0.00253564774886875;270685!GO:0004329;formate-tetrahydrofolate ligase activity;0.00253564774886875;270685!GO:0009396;folic acid and derivative biosynthetic process;0.00776329406794076;270685!GO:0006412;translation;0.00887039156264768;27367,69895!GO:0030529;ribonucleoprotein complex;0.00887039156264768;27367,69895!GO:0006760;folic acid and derivative metabolic process;0.00887039156264768;270685!GO:0009059;macromolecule biosynthetic process;0.0161856074324591;27367,69895!GO:0044444;cytoplasmic part;0.0195166510969675;27367,69895,270685!GO:0006752;group transfer coenzyme metabolic process;0.0341338087604507;270685!GO:0046483;heterocycle metabolic process;0.0389122065212837;270685!GO:0006730;one-carbon compound metabolic process;0.0425345502092769;270685!GO:0009108;coenzyme biosynthetic process;0.0431377310490122;270685!GO:0051188;cofactor biosynthetic process;0.0470887349534143;270685!GO:0043232;intracellular non-membrane-bound organelle;0.0474648560494127;27367,69895!GO:0043228;non-membrane-bound organelle;0.0474648560494127;27367,69895!GO:0006725;aromatic compound metabolic process;0.0474648560494127;270685!}}
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biosynthetic process;0.00253564774886875;27367,69895,270685!GO:0009257;10-formyltetrahydrofolate biosynthetic process;0.00253564774886875;270685!GO:0003735;structural constituent of ribosome;0.00253564774886875;27367,69895!GO:0005840;ribosome;0.00253564774886875;27367,69895!GO:0009058;biosynthetic process;0.00253564774886875;27367,69895,270685!GO:0009256;10-formyltetrahydrofolate metabolic process;0.00253564774886875;270685!GO:0004329;formate-tetrahydrofolate ligase activity;0.00253564774886875;270685!GO:0009396;folic acid and derivative biosynthetic process;0.00776329406794076;270685!GO:0006412;translation;0.00887039156264768;27367,69895!GO:0030529;ribonucleoprotein complex;0.00887039156264768;27367,69895!GO:0006760;folic acid and derivative metabolic process;0.00887039156264768;270685!GO:0009059;macromolecule biosynthetic process;0.0161856074324591;27367,69895!GO:0044444;cytoplasmic part;0.0195166510969675;27367,69895,270685!GO:0006752;group transfer coenzyme metabolic process;0.0341338087604507;270685!GO:0046483;heterocycle metabolic process;0.0389122065212837;270685!GO:0006730;one-carbon compound metabolic process;0.0425345502092769;270685!GO:0009108;coenzyme biosynthetic process;0.0431377310490122;270685!GO:0051188;cofactor biosynthetic process;0.0470887349534143;270685!GO:0043232;intracellular non-membrane-bound organelle;0.0474648560494127;27367,69895!GO:0043228;non-membrane-bound organelle;0.0474648560494127;27367,69895!GO:0006725;aromatic compound metabolic process;0.0474648560494127;270685!|ontology_enrichment_celltype=CL:0000988!1.78e-14!32;CL:0002032!1.78e-14!32;CL:0000037!1.78e-14!32;CL:0000566!1.78e-14!32;CL:0000837!1.78e-14!32;CL:0002242!7.43e-11!16;CL:0002031!2.02e-10!25;CL:0002320!3.62e-09!46;CL:0000134!3.62e-09!46;CL:0000542!9.19e-09!13;CL:0000051!9.19e-09!13;CL:0000838!2.15e-08!12;CL:0000084!7.10e-08!11;CL:0000827!7.10e-08!11;CL:0000049!3.44e-07!19;CL:0000219!5.54e-07!54;CL:0000791!6.80e-07!9;CL:0000789!6.80e-07!9;CL:0002420!6.80e-07!9;CL:0002419!6.80e-07!9;CL:0000790!6.80e-07!9|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0002390!4.35e-10!45;UBERON:0003061!4.35e-10!45;UBERON:0002193!1.48e-09!48;UBERON:0002405!1.48e-09!48;UBERON:0002384!3.62e-09!46;UBERON:0004177!7.74e-09!29;UBERON:0005057!7.74e-09!29;UBERON:0000072!2.88e-07!27;UBERON:0000077!7.23e-07!35|tfbs_overrepresentation_for_novel_motifs=0.438063,0.0418382,0.411716,0.480627,0.299217,0.495263,1.43443,0.206208,0.215218,0.478312,1.34037,0.575086,0.206435,1.46059,0.315771,0,0.795315,0.291368,0.561256,0.361892,0.374752,0.27937,0.598814,0.80655,0.419327,0.62766,0.184473,0.516511,0.911169,0.446946,0.50223,0.897561,0.289148,0.498917,0.848378,0.0235321,2.14888,0.57142,0.717242,0.230656,0.295233,0.507468,0.0742755,1.53741,0.515031,0.469348,0.714592,0.532496,0.219744,0.347313,0.777641,0.654933,0.431711,1.04034,1.0579,0.606984,0.356236,0.56214,0.176152,0.604914,0.877332,0.664501,0.226529,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,1.52206,1.09164,0.97874,0.482617,0.166511,0.703064,0.859987,0.378988,0.610783,0.812889,0.663039,0.200155,0.975495,1.37268,0.164297,0.447265,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,1.30733,0.237542,0.203879,0.913319,0.71485,0.127063,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,1.30996,0.383871,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.796976,0.418498,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,1.26636,0.717753,2.03691,0.448938,0.300961,0.452587,1.38961,1.04192,0.243291,0.619892,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,1.09603,0.767269,0.612377,0.278874,1.40533,0.433127|tfbs_overrepresentation_jaspar=MA0003.1;0.339775,MA0004.1;1.20906,MA0006.1;0.837454,MA0007.1;0.465969,MA0009.1;0.92425,MA0014.1;0.0886247,MA0017.1;0.337808,MA0019.1;0.740036,MA0024.1;0.880057,MA0025.1;1.15921,MA0027.1;2.57545,MA0028.1;1.55156,MA0029.1;0.858105,MA0030.1;0.864739,MA0031.1;0.828781,MA0038.1;0.62758,MA0040.1;0.936879,MA0041.1;0.404721,MA0042.1;0.391504,MA0043.1;1.02178,MA0046.1;0.960497,MA0048.1;0.128106,MA0050.1;0.520357,MA0051.1;0.636645,MA0052.1;0.945011,MA0055.1;0.157978,MA0056.1;0,MA0057.1;0.117936,MA0058.1;1.77195,MA0059.1;0.397033,MA0060.1;1.22438,MA0061.1;1.33382,MA0063.1;0,MA0066.1;0.616444,MA0067.1;1.27078,MA0068.1;0.121435,MA0069.1;0.945354,MA0070.1;0.93557,MA0071.1;0.519509,MA0072.1;0.927016,MA0073.1;0.0004304,MA0074.1;0.580087,MA0076.1;0.938908,MA0077.1;0.905143,MA0078.1;0.670113,MA0081.1;0.420276,MA0083.1;1.02098,MA0084.1;1.59945,MA0087.1;0.977537,MA0088.1;0.0841779,MA0089.1;0,MA0090.1;1.1347,MA0091.1;0.494398,MA0092.1;0.446857,MA0093.1;1.58083,MA0095.1;0,MA0098.1;0,MA0100.1;0.568369,MA0101.1;1.0468,MA0103.1;0.348572,MA0105.1;0.162418,MA0106.1;0.677988,MA0107.1;0.906859,MA0108.2;4.33655,MA0109.1;0,MA0111.1;0.460823,MA0113.1;0.649407,MA0114.1;0.719313,MA0115.1;1.0246,MA0116.1;1.51389,MA0117.1;0.992087,MA0119.1;1.04809,MA0122.1;1.01209,MA0124.1;1.21735,MA0125.1;1.14291,MA0130.1;0,MA0131.1;1.74348,MA0132.1;0,MA0133.1;0,MA0135.1;1.05845,MA0136.1;0.600242,MA0139.1;0.202522,MA0140.1;0.568252,MA0141.1;0.368264,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;0.262477,MA0145.1;0.0910975,MA0146.1;0.0256827,MA0147.1;0.753844,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;2.20069,MA0035.2;0.573016,MA0039.2;1.37408,MA0138.2;0.727395,MA0002.2;0.592533,MA0137.2;0.365364,MA0104.2;0.624968,MA0047.2;0.626803,MA0112.2;0.0910939,MA0065.2;0.305574,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;0.397336,MA0155.1;0.102995,MA0156.1;0.936991,MA0157.1;0.781683,MA0158.1;0,MA0159.1;0.776527,MA0160.1;0.50056,MA0161.1;0,MA0162.1;1.26636,MA0163.1;0.116706,MA0164.1;0.600609,MA0080.2;0.908823,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;0.065018,MA0102.2;1.65195,MA0258.1;0.246285,MA0259.1;1.34223,MA0442.1;0}}

Latest revision as of 16:17, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:6373383..6373454,-p1@Mthfd1l
Mm9::chr14:52817186..52817193,+p1@ENSMUST00000143086
p1@uc007tos.1
Mm9::chr15:79913772..79913789,-p1@Gm12816
p1@LOC674810
p1@Rpl3
Mm9::chr17:24665188..24665209,+p1@2610019E17Rik
Mm9::chr17:24856834..24856861,-p1@Snhg9
Mm9::chr3:123211248..123211259,-p1@Snhg8
Mm9::chr9:88417714..88417733,-p1@ENSMUST00000034997
p1@uc009qys.1


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:0044249cellular biosynthetic process0.00253564774886875
GO:000925710-formyltetrahydrofolate biosynthetic process0.00253564774886875
GO:0003735structural constituent of ribosome0.00253564774886875
GO:0005840ribosome0.00253564774886875
GO:0009058biosynthetic process0.00253564774886875
GO:000925610-formyltetrahydrofolate metabolic process0.00253564774886875
GO:0004329formate-tetrahydrofolate ligase activity0.00253564774886875
GO:0009396folic acid and derivative biosynthetic process0.00776329406794076
GO:0006412translation0.00887039156264768
GO:0030529ribonucleoprotein complex0.00887039156264768
GO:0006760folic acid and derivative metabolic process0.00887039156264768
GO:0009059macromolecule biosynthetic process0.0161856074324591
GO:0044444cytoplasmic part0.0195166510969675
GO:0006752group transfer coenzyme metabolic process0.0341338087604507
GO:0046483heterocycle metabolic process0.0389122065212837
GO:0006730one-carbon compound metabolic process0.0425345502092769
GO:0009108coenzyme biosynthetic process0.0431377310490122
GO:0051188cofactor biosynthetic process0.0470887349534143
GO:0043232intracellular non-membrane-bound organelle0.0474648560494127
GO:0043228non-membrane-bound organelle0.0474648560494127
GO:0006725aromatic compound metabolic process0.0474648560494127



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
hematopoietic system4.35e-1045
blood island4.35e-1045
hemolymphoid system1.48e-0948
immune system1.48e-0948
connective tissue3.62e-0946
hemopoietic organ7.74e-0929
immune organ7.74e-0929
segment of respiratory tract2.88e-0727
mixed endoderm/mesoderm-derived structure7.23e-0735


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)
MA0003.10.339775
MA0004.11.20906
MA0006.10.837454
MA0007.10.465969
MA0009.10.92425
MA0014.10.0886247
MA0017.10.337808
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.11.55156
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.11.02178
MA0046.10.960497
MA0048.10.128106
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.157978
MA0056.10
MA0057.10.117936
MA0058.11.77195
MA0059.10.397033
MA0060.11.22438
MA0061.11.33382
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.121435
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.10.0004304
MA0074.10.580087
MA0076.10.938908
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.0841779
MA0089.10
MA0090.11.1347
MA0091.10.494398
MA0092.10.446857
MA0093.11.58083
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.11.0468
MA0103.10.348572
MA0105.10.162418
MA0106.10.677988
MA0107.10.906859
MA0108.24.33655
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.719313
MA0115.11.0246
MA0116.11.51389
MA0117.10.992087
MA0119.11.04809
MA0122.11.01209
MA0124.11.21735
MA0125.11.14291
MA0130.10
MA0131.11.74348
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.10.600242
MA0139.10.202522
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.10.0910975
MA0146.10.0256827
MA0147.10.753844
MA0148.10.49752
MA0149.10.411562
MA0062.22.20069
MA0035.20.573016
MA0039.21.37408
MA0138.20.727395
MA0002.20.592533
MA0137.20.365364
MA0104.20.624968
MA0047.20.626803
MA0112.20.0910939
MA0065.20.305574
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.397336
MA0155.10.102995
MA0156.10.936991
MA0157.10.781683
MA0158.10
MA0159.10.776527
MA0160.10.50056
MA0161.10
MA0162.11.26636
MA0163.10.116706
MA0164.10.600609
MA0080.20.908823
MA0018.20.610433
MA0099.20.721008
MA0079.20.065018
MA0102.21.65195
MA0258.10.246285
MA0259.11.34223
MA0442.10
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