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MCL coexpression mm9:268: Difference between revisions

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{{MCL_coexpression_mm9
{
|coexpression_dpi_cluster_scores_mean=0

Latest revision as of 15:00, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:7387304..7387356,+p1@Nup43
Mm9::chr11:101303754..101303782,+p1@Gm6341
p1@Rpl27
Mm9::chr11:45768967..45768993,-p1@Thg1l
Mm9::chr12:36883334..36883363,-p1@Bzw2
Mm9::chr12:36883368..36883402,-p2@Bzw2
Mm9::chr12:81744786..81744844,-p1@Erh
p1@Gm10131
p1@Gm6941
Mm9::chr13:100894805..100894841,+p1@Smn1
Mm9::chr13:58503810..58503833,-p2@Hnrnpk
Mm9::chr15:34372931..34372959,-p2@Gm6109
p2@Gm7429
p2@Rpl30-ps10
p2@Rpl30
Mm9::chr16:18248704..18248785,-p1@Ranbp1
Mm9::chr16:91647151..91647205,-p1@Gart
Mm9::chr17:31795674..31795711,-p1@U2af1
Mm9::chr18:10617766..10617843,+p1@Gm14277
p1@Snrpd1
Mm9::chr18:31948774..31948825,+p1@Polr2d
Mm9::chr1:71603742..71603814,+p1@Atic
Mm9::chr2:31526234..31526261,+p1@Exosc2
Mm9::chr2:41844369..41844391,-p1@ENSMUST00000167476
Mm9::chr3:54538923..54539000,-p1@Exosc8
Mm9::chr4:107552350..107552401,+p1@Magoh
Mm9::chr4:45333452..45333506,-p1@Exosc3
Mm9::chr5:114580397..114580453,+p2@Ung
Mm9::chr5:129526068..129526128,+p1@LOC100045999
p1@Ran
Mm9::chr6:117856773..117856819,+p1@Hnrnpf
Mm9::chr6:131243205..131243266,-p1@Magohb
Mm9::chr6:88415411..88415476,+p1@Ruvbl1
Mm9::chr7:19735159..19735193,+p1@Snrpd2
Mm9::chr7:28954709..28954762,+p1@Fbl
p1@LOC100044829
Mm9::chr7:73205414..73205483,+p1@Snrpa1
Mm9::chr8:96560907..96560927,-p1@Nudt21
Mm9::chr9:72961254..72961261,+p1@Rsl24d1
Mm9::chrX:102275103..102275142,+p1@2610029G23Rik


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:0006396RNA processing2.84575510558761e-13
GO:0003723RNA binding9.04964770713806e-10
GO:0010467gene expression6.58462118452629e-09
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process2.4425123101148e-08
GO:0022613ribonucleoprotein complex biogenesis and assembly9.6640159363622e-08
GO:0006397mRNA processing2.87880327723895e-07
GO:0016071mRNA metabolic process5.36733190548972e-07
GO:0008380RNA splicing1.71344843459706e-06
GO:0000178exosome (RNase complex)5.70283950895519e-06
GO:0016070RNA metabolic process5.87107282851618e-06
GO:0016072rRNA metabolic process1.05109240237543e-05
GO:0006364rRNA processing1.05109240237543e-05
GO:0044238primary metabolic process1.11171430359242e-05
GO:0030529ribonucleoprotein complex1.11171430359242e-05
GO:0044237cellular metabolic process1.11171430359242e-05
GO:0005681spliceosome1.11171430359242e-05
GO:0043170macromolecule metabolic process3.74004777176496e-05
GO:0005634nucleus5.47837026515738e-05
GO:0032991macromolecular complex7.35848035621704e-05
GO:0042254ribosome biogenesis and assembly0.000186471419281264
GO:0016742hydroxymethyl-, formyl- and related transferase activity0.000186471419281264
GO:0003676nucleic acid binding0.000222696387637151
GO:0004527exonuclease activity0.000256765118792631
GO:0004372glycine hydroxymethyltransferase activity0.000342140868387165
GO:0043283biopolymer metabolic process0.000401000647743775
GO:0022618protein-RNA complex assembly0.000859282418816777
GO:0044428nuclear part0.00105556349000239
GO:0016043cellular component organization and biogenesis0.00160364658245473
GO:0000245spliceosome assembly0.0028027044199249
GO:0044424intracellular part0.00329603599130794
GO:0043229intracellular organelle0.00385128503489917
GO:0043226organelle0.00385128503489917
GO:0004518nuclease activity0.00451318536050928
GO:0005622intracellular0.00523634913168027
GO:0008168methyltransferase activity0.00682189229167808
GO:0016741transferase activity, transferring one-carbon groups0.00682189229167808
GO:0000377RNA splicing, via transesterification reactions with bulged adenosine as nucleophile0.00682189229167808
GO:0000398nuclear mRNA splicing, via spliceosome0.00682189229167808
GO:0000375RNA splicing, via transesterification reactions0.00682189229167808
GO:0009113purine base biosynthetic process0.00682189229167808
GO:0046607positive regulation of centrosome cycle0.00682189229167808
GO:0004641phosphoribosylformylglycinamidine cyclo-ligase activity0.00682189229167808
GO:0046602regulation of mitotic centrosome separation0.00682189229167808
GO:0046605regulation of centrosome cycle0.00682189229167808
GO:0045437uridine nucleosidase activity0.00682189229167808
GO:0016074snoRNA metabolic process0.00682189229167808
GO:0004644phosphoribosylglycinamide formyltransferase activity0.00682189229167808
GO:0003937IMP cyclohydrolase activity0.00682189229167808
GO:0004643phosphoribosylaminoimidazolecarboxamide formyltransferase activity0.00682189229167808
GO:0046604positive regulation of mitotic centrosome separation0.00682189229167808
GO:0051028mRNA transport0.00800341206382138
GO:0006996organelle organization and biogenesis0.00800341206382138
GO:0043231intracellular membrane-bound organelle0.00800341206382138
GO:0043227membrane-bound organelle0.00800341206382138
GO:0051236establishment of RNA localization0.00800341206382138
GO:0050657nucleic acid transport0.00800341206382138
GO:0050658RNA transport0.00800341206382138
GO:0006403RNA localization0.00818292632174482
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.00934457117399923
GO:0004844uracil DNA N-glycosylase activity0.0100264232315109
GO:0046040IMP metabolic process0.0100264232315109
GO:0006189'de novo' IMP biosynthetic process0.0100264232315109
GO:0006188IMP biosynthetic process0.0100264232315109
GO:0030515snoRNA binding0.0100264232315109
GO:0051299centrosome separation0.0100264232315109
GO:0007100mitotic centrosome separation0.0100264232315109
GO:0004637phosphoribosylamine-glycine ligase activity0.0100264232315109
GO:0006164purine nucleotide biosynthetic process0.0112988392980572
GO:0006310DNA recombination0.0140014647333496
GO:0006163purine nucleotide metabolic process0.0140014647333496
GO:0016882cyclo-ligase activity0.0140014647333496
GO:0006379mRNA cleavage0.0140014647333496
GO:0044446intracellular organelle part0.0144112696167113
GO:0044422organelle part0.0145353275771984
GO:0019238cyclohydrolase activity0.017921387915388
GO:0046112nucleobase biosynthetic process0.0220980893118266
GO:0065003macromolecular complex assembly0.0223042678357786
GO:0016779nucleotidyltransferase activity0.0256271454173277
GO:0005730nucleolus0.0257701017514945
GO:0016787hydrolase activity0.0272455153924382
GO:0015030Cajal body0.0279933635356416
GO:0007098centrosome cycle0.0279933635356416
GO:0006144purine base metabolic process0.0279933635356416
GO:0009165nucleotide biosynthetic process0.0302783473221256
GO:0051297centrosome organization and biogenesis0.0302783473221256
GO:0002566somatic diversification of immune receptors via somatic mutation0.0302783473221256
GO:0016446somatic hypermutation of immunoglobulin genes0.0302783473221256
GO:0022607cellular component assembly0.0302783473221256
GO:0031023microtubule organizing center organization and biogenesis0.0328576281770539
GO:00001753'-5'-exoribonuclease activity0.0328576281770539
GO:0019104DNA N-glycosylase activity0.0328576281770539
GO:0009168purine ribonucleoside monophosphate biosynthetic process0.0357193414185093
GO:0009127purine nucleoside monophosphate biosynthetic process0.0357193414185093
GO:0009167purine ribonucleoside monophosphate metabolic process0.0384590397326422
GO:0009126purine nucleoside monophosphate metabolic process0.0384590397326422
GO:0006412translation0.039978205275709
GO:0031202RNA splicing factor activity, transesterification mechanism0.0402705752914268
GO:0004532exoribonuclease activity0.0423436693409843
GO:0016896exoribonuclease activity, producing 5'-phosphomonoesters0.0423436693409843
GO:0009156ribonucleoside monophosphate biosynthetic process0.0423436693409843
GO:0009161ribonucleoside monophosphate metabolic process0.0446020580687409
GO:0007051spindle organization and biogenesis0.0446020580687409
GO:0044249cellular biosynthetic process0.0446020580687409
GO:0005732small nucleolar ribonucleoprotein complex0.0457243882494226
GO:00084083'-5' exonuclease activity0.0457243882494226
GO:0009124nucleoside monophosphate biosynthetic process0.0457243882494226
GO:0009112nucleobase metabolic process0.0457243882494226
GO:0016799hydrolase activity, hydrolyzing N-glycosyl compounds0.0478819462112155
GO:0009123nucleoside monophosphate metabolic process0.0478819462112155
GO:0009117nucleotide metabolic process0.0492322474392219
GO:0006284base-excision repair0.049961101762453



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><br><br><br>


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)
MA0003.10.592804
MA0004.11.46023
MA0006.11.49695
MA0007.10.93006
MA0009.10.366963
MA0014.10.516538
MA0017.10.535828
MA0019.10.229805
MA0024.11.58912
MA0025.10.564682
MA0027.11.93116
MA0028.17.16535
MA0029.10.315482
MA0030.10.858
MA0031.10.79685
MA0038.10.476304
MA0040.10.377038
MA0041.11.12891
MA0042.11.07306
MA0043.10.446565
MA0046.10.396073
MA0048.10.397143
MA0050.10.326024
MA0051.10.48978
MA0052.10.383564
MA0055.12.46272
MA0056.10
MA0057.10.716364
MA0058.11.48133
MA0059.10.40278
MA0060.10.998423
MA0061.10.0628971
MA0063.10
MA0066.10.150832
MA0067.10.664516
MA0068.10.060674
MA0069.10.383839
MA0070.10.37599
MA0071.10.0985618
MA0072.10.369163
MA0073.18.62259e-06
MA0074.10.810061
MA0076.14.79143
MA0077.10.351866
MA0078.10.540438
MA0081.10.783797
MA0083.10.445897
MA0084.10.971934
MA0087.10.409958
MA0088.10.189004
MA0089.10
MA0090.10.234247
MA0091.10.0866349
MA0092.10.0660496
MA0093.11.61755
MA0095.10
MA0098.10
MA0100.10.391104
MA0101.10.420824
MA0103.10.131431
MA0105.10.231519
MA0106.11.05332
MA0107.10.125829
MA0108.20.245881
MA0109.10
MA0111.10.535827
MA0113.10.508933
MA0114.10.550015
MA0115.11.13985
MA0116.11.49562
MA0117.10.42191
MA0119.10.422018
MA0122.10.438479
MA0124.10.616327
MA0125.10.55037
MA0130.10
MA0131.11.87112
MA0132.10
MA0133.10
MA0135.10.477472
MA0136.10.436338
MA0139.10.353358
MA0140.10.390942
MA0141.10.0381379
MA0142.10.282551
MA0143.10.180984
MA0144.10.0133016
MA0145.10.128216
MA0146.10.537515
MA0147.12.11438
MA0148.10.296488
MA0149.10.0525422
MA0062.29.00954
MA0035.20.126246
MA0039.21.47491
MA0138.20.221177
MA0002.20.362338
MA0137.20.341252
MA0104.22.46551
MA0047.20.475155
MA0112.20.0663097
MA0065.20.496457
MA0150.10.257198
MA0151.10
MA0152.10.157023
MA0153.10.491737
MA0154.10.243616
MA0155.10.591109
MA0156.11.32785
MA0157.10.259017
MA0158.10
MA0159.10.389805
MA0160.10.089496
MA0161.10
MA0162.10.846557
MA0163.10.0173309
MA0164.10.141659
MA0080.20.874029
MA0018.20.451116
MA0099.20.216863
MA0079.20.409427
MA0102.21.0223
MA0258.10.0532628
MA0259.12.01875
MA0442.10
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