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MCL coexpression mm9:154: Difference between revisions

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{{MCL_coexpression_mm9
{
|coexpression_dpi_cluster_scores_mean=-

Latest revision as of 14:47, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:58767943..58767961,-p1@ENSMUST00000117558
Mm9::chr13:21808044..21808058,-p3@Hist1h2bf
p3@Hist1h2bj
p3@Hist1h2bl
p3@Hist1h2bn
Mm9::chr13:21808254..21808270,+p1@Hist1h2ab
p1@Hist1h2ac
p1@Hist1h2ad
p1@Hist1h2ae
p1@Hist1h2ag
p1@Hist1h2ah
p1@Hist1h2ai
p1@Hist1h2an
p1@Hist1h2ao
p1@Hist1h2ap
Mm9::chr13:21809495..21809500,+p4@Hist1h3a
p4@Hist1h3g
p4@Hist1h3h
p4@Hist1h3i
Mm9::chr13:21813684..21813736,-p1@ENSMUST00000091710
Mm9::chr13:21813926..21813942,+p1@Hist1h2bm
Mm9::chr13:21845530..21845568,-p@chr13:21845530..21845568
-
Mm9::chr13:21845720..21845737,-p1@Hist1h2ak
Mm9::chr13:21845922..21845930,+p6@Hist1h2bf
p6@Hist1h2bj
p6@Hist1h2bl
p6@Hist1h2bn
Mm9::chr13:21845936..21845952,+p1@Hist1h2bf
p1@Hist1h2bj
p1@Hist1h2bl
p1@Hist1h2bn
Mm9::chr13:21872485..21872501,-p1@Hist1h1b
Mm9::chr13:21875260..21875275,-p1@Hist1h3a
p1@Hist1h3g
p1@Hist1h3h
p1@Hist1h3i
Mm9::chr13:21879110..21879125,-p6@Hist1h2ab
p6@Hist1h2ac
p6@Hist1h2ae
p6@Hist1h2ag
p6@Hist1h2ai
p6@Hist1h2an
p6@Hist1h2ao
p6@Hist1h2ap
p7@Hist1h2ad
p7@Hist1h2ah
Mm9::chr13:21924063..21924067,-p7@Hist1h4c
p7@Hist1h4d
p7@Hist1h4f
p7@Hist1h4h
p7@Hist1h4i
p7@Hist1h4j
p7@Hist1h4k
p7@Hist1h4m
p7@Hist1h4n
p8@Hist1h4a
p8@Hist1h4b
p8@Hist2h4
p8@Hist4h4
Mm9::chr13:22127458..22127475,-p5@Hist1h2ah
Mm9::chr13:22127698..22127717,+p1@Hist1h2bk
Mm9::chr13:22127739..22127743,+p2@Hist1h2bk
Mm9::chr13:22134820..22134847,-p3@Hist1h2ab
p3@Hist1h2ac
p3@Hist1h2ad
p3@Hist1h2ae
p3@Hist1h2ag
p3@Hist1h2ah
p3@Hist1h2ai
p3@Hist1h2an
p3@Hist1h2ao
p3@Hist1h2ap
Mm9::chr13:22135058..22135077,+p4@Hist1h2bf
p4@Hist1h2bj
p4@Hist1h2bl
p4@Hist1h2bn
Mm9::chr13:23622952..23622957,+p3@Hist1h4a
p3@Hist1h4c
p3@Hist1h4d
p3@Hist1h4f
p3@Hist1h4h
p3@Hist1h4i
p3@Hist1h4j
p3@Hist1h4k
p3@Hist1h4m
p3@Hist1h4n
p3@Hist4h4
p4@Hist1h4b
p4@Hist2h4
Mm9::chr13:23625738..23625751,+p1@Hist1h2af
Mm9::chr13:23627280..23627296,+p3@Hist1h3a
p3@Hist1h3g
p3@Hist1h3h
p3@Hist1h3i
Mm9::chr13:23635252..23635271,-p1@Hist1h2bh
Mm9::chr13:23636327..23636345,+p3@Hist1h3e
p3@Hist1h3f
p3@Hist2h3c1
p3@Hist2h3c2-ps
p4@Hist1h3b
p4@Hist1h3c
p4@Hist1h3d
p4@Hist2h3b
Mm9::chr13:23643531..23643541,-p4@Hist1h4a
p4@Hist1h4c
p4@Hist1h4d
p4@Hist1h4f
p4@Hist1h4h
p4@Hist1h4i
p4@Hist1h4j
p4@Hist1h4k
p4@Hist1h4m
p4@Hist1h4n
p4@Hist4h4
p5@Hist1h4b
p5@Hist2h4
Mm9::chr13:23646892..23646908,+p1@Hist1h1d
Mm9::chr13:23647420..23647454,-p@chr13:23647420..23647454
-
Mm9::chr13:23654245..23654261,-p1@Hist1h3c
p1@Hist1h3d
p1@Hist1h3e
p1@Hist1h3f
p1@Hist2h3b
p1@Hist2h3c1
p1@Hist2h3c2-ps
p2@Hist1h3b
Mm9::chr13:23663020..23663039,-p2@Hist1h2ab
p2@Hist1h2ac
p2@Hist1h2ad
p2@Hist1h2ae
p2@Hist1h2ag
p2@Hist1h2ah
p2@Hist1h2ai
p2@Hist1h2an
p2@Hist1h2ao
p2@Hist1h2ap
Mm9::chr13:23663251..23663261,+p1@Hist1h2bc
p1@Hist1h2be
p1@Hist1h2bg
p2@Hist2h2bb
Mm9::chr13:23666068..23666098,-p2@Hist1h2bf
p2@Hist1h2bj
p2@Hist1h2bl
p2@Hist1h2bn
Mm9::chr13:23666303..23666318,+p2@Hist1h3d
p5@Hist1h2ad
Mm9::chr13:23667622..23667642,+p2@Hist1h3e
p2@Hist1h3f
p2@Hist2h3c1
p2@Hist2h3c2-ps
p3@Hist1h3b
p3@Hist1h3c
p3@Hist1h3d
p3@Hist2h3b
Mm9::chr13:23667651..23667662,+p5@Hist1h3d
Mm9::chr13:23673432..23673438,+p1@Hist1h4a
p1@Hist1h4b
p1@Hist1h4c
p1@Hist1h4d
p1@Hist1h4f
p1@Hist1h4h
p1@Hist1h4i
p1@Hist1h4j
p1@Hist1h4k
p1@Hist1h4m
p1@Hist1h4n
p1@Hist2h4
p1@Hist4h4
Mm9::chr13:23677839..23677850,-p@chr13:23677839..23677850
-
Mm9::chr13:23677852..23677864,-p@chr13:23677852..23677864
-
Mm9::chr13:23713806..23713858,-p@chr13:23713806..23713858
-
Mm9::chr13:23713864..23713920,+p@chr13:23713864..23713920
+
Mm9::chr13:23713886..23713975,-p@chr13:23713886..23713975
-
Mm9::chr13:23714417..23714432,-p1@Hist1h1e
Mm9::chr13:23775810..23775836,-p5@Hist1h2ab
p5@Hist1h2ac
p5@Hist1h2ae
p5@Hist1h2ag
p5@Hist1h2ai
p5@Hist1h2an
p5@Hist1h2ao
p5@Hist1h2ap
p6@Hist1h2ad
p6@Hist1h2ah
Mm9::chr13:23776061..23776077,+p2@Hist1h2bc
p2@Hist1h2be
p2@Hist1h2bg
p3@Hist2h2bb
Mm9::chr13:23790324..23790329,-p2@Hist1h4a
p2@Hist1h4c
p2@Hist1h4d
p2@Hist1h4f
p2@Hist1h4h
p2@Hist1h4i
p2@Hist1h4j
p2@Hist1h4k
p2@Hist1h4m
p2@Hist1h4n
p2@Hist4h4
p3@Hist1h4b
p3@Hist2h4
Mm9::chr13:23830673..23830678,+p1@Hist1h1c
Mm9::chr13:23837380..23837395,-p2@Hist1h3c
Mm9::chr13:23838365..23838391,-p1@ENSMUST00000118168
Mm9::chr13:23838614..23838632,+p1@Hist1h2bb
Mm9::chr13:23842938..23842955,+p4@Hist1h2ab
p4@Hist1h2ac
p4@Hist1h2ad
p4@Hist1h2ae
p4@Hist1h2ag
p4@Hist1h2ah
p4@Hist1h2ai
p4@Hist1h2an
p4@Hist1h2ao
p4@Hist1h2ap
Mm9::chr13:23842976..23842987,+p7@Hist1h2ab
p7@Hist1h2ac
p7@Hist1h2ae
p7@Hist1h2ag
p7@Hist1h2ai
p7@Hist1h2an
p7@Hist1h2ao
p8@Hist1h2ad
p8@Hist1h2ah
p8@Hist1h2ap
Mm9::chr13:23844210..23844220,+p1@Hist1h3b
Mm9::chr13:23848853..23848864,+p2@Hist1h4b
Mm9::chr13:23853036..23853057,-p5@Hist1h4a
Mm9::chr13:23854231..23854233,-p5@Hist1h3a
p5@Hist1h3g
p5@Hist1h3h
p5@Hist1h3i
Mm9::chr13:23854247..23854260,-p2@Hist1h3a
p2@Hist1h3g
p2@Hist1h3h
p2@Hist1h3i
Mm9::chr13:23855529..23855543,+p1@Hist1h1a
Mm9::chr17:27054056..27054104,+p1@Kifc5b
Mm9::chr17:35183484..35183504,-p2@Msh5
Mm9::chr18:34911425..34911440,+p1@ENSMUST00000142855
p1@uc008elg.1
p1@uc008elh.1
Mm9::chr18:39820862..39820868,-p@chr18:39820862..39820868
-
Mm9::chr19:7397574..7397577,-p@chr19:7397574..7397577
-
Mm9::chr3:96023800..96023823,+p1@Hist2h2ab
Mm9::chr3:96024804..96024822,-p1@Hist2h2ac
Mm9::chr3:96067248..96067263,-p2@Hist2h4
Mm9::chr3:96072594..96072606,+p2@Hist2h3b
Mm9::chr3:96073618..96073626,+p1@Hist2h2bb
Mm9::chr4:119193561..119193562,+p1@ENSMUST00000117835
Mm9::chr4:132019788..132019844,-p1@Med18
Mm9::chr6:136752935..136752940,-p5@Hist4h4
Mm9::chr7:16894727..16894739,-p@chr7:16894727..16894739
-
Mm9::chr8:27834958..27834963,+p@chr8:27834958..27834963
+
Mm9::chr9:44142768..44142787,+p1@H2afx
Mm9::chrX:7651846..7651862,-p3@Suv39h1


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:0000786nucleosome4.54534776411056e-73
GO:0031497chromatin assembly1.6443385904071e-72
GO:0006334nucleosome assembly1.55291372217991e-71
GO:0006333chromatin assembly or disassembly3.84735263021232e-69
GO:0065004protein-DNA complex assembly1.37082163787034e-67
GO:0000785chromatin6.72255786138519e-66
GO:0044427chromosomal part9.72870346254215e-59
GO:0006325establishment and/or maintenance of chromatin architecture7.49415962637564e-58
GO:0006323DNA packaging1.93957964602179e-57
GO:0005694chromosome3.40194152934528e-56
GO:0022607cellular component assembly7.24117528139616e-53
GO:0065003macromolecular complex assembly8.36159776093012e-53
GO:0051276chromosome organization and biogenesis1.18999538032754e-52
GO:0006259DNA metabolic process2.09201323573024e-45
GO:0006996organelle organization and biogenesis9.86082158379068e-39
GO:0043234protein complex7.55926030174304e-38
GO:0043232intracellular non-membrane-bound organelle1.39736564136237e-36
GO:0043228non-membrane-bound organelle1.39736564136237e-36
GO:0003676nucleic acid binding5.39129430141821e-36
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process2.82082999332525e-35
GO:0032991macromolecular complex3.17633767599368e-34
GO:0044446intracellular organelle part8.89553220045201e-32
GO:0044422organelle part9.68752112028437e-32
GO:0003677DNA binding4.1094927496173e-29
GO:0005634nucleus3.58203478191734e-28
GO:0016043cellular component organization and biogenesis1.25575804814168e-27
GO:0043283biopolymer metabolic process1.6312109650786e-23
GO:0043170macromolecule metabolic process3.95596705266027e-16
GO:0043231intracellular membrane-bound organelle3.94251030695156e-15
GO:0043227membrane-bound organelle3.97527661505878e-15
GO:0044238primary metabolic process5.12879898984438e-13
GO:0044237cellular metabolic process5.92628857074674e-13
GO:0043229intracellular organelle1.58141775139402e-12
GO:0043226organelle1.58641878619199e-12
GO:0044424intracellular part3.25300988646215e-09
GO:0005622intracellular1.16522856491793e-08
GO:0016584nucleosome positioning4.04974076280158e-08
GO:0044464cell part0.0118588142169974
GO:0005623cell0.0118588142169974
GO:0007283spermatogenesis0.0329786730350195
GO:0048232male gamete generation0.0329786730350195
GO:0051567histone H3-K9 methylation0.0347530180865507



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)
MA0003.10.000359213
MA0004.10.00669008
MA0006.10.0831859
MA0007.10.0911657
MA0009.10.419157
MA0014.10.00193741
MA0017.10.00530614
MA0019.11.21058
MA0024.110.1875
MA0025.11.39381
MA0027.11.56266
MA0028.10.0436039
MA0029.10.102863
MA0030.10.105861
MA0031.10.0901414
MA0038.14.42201
MA0040.10.435748
MA0041.10.0492954
MA0042.10.199482
MA0043.11.66378
MA0046.10.467411
MA0048.10.119724
MA0050.10.492665
MA0051.10.120308
MA0052.12.03102
MA0055.10.413713
MA0056.10
MA0057.10.00337324
MA0058.10.0017002
MA0059.10.0020842
MA0060.132.2529
MA0061.10.0156422
MA0063.10
MA0066.10.0248976
MA0067.10.359458
MA0068.10.0192699
MA0069.10.145688
MA0070.10.855067
MA0071.10.0102889
MA0072.10.136091
MA0073.18.81395e-14
MA0074.10.082784
MA0076.10.142482
MA0077.10.394526
MA0078.10.036898
MA0081.10.0181624
MA0083.10.552043
MA0084.10.632114
MA0087.10.490752
MA0088.10.000421552
MA0089.10
MA0090.10.0248245
MA0091.10.424302
MA0092.10.0764441
MA0093.10.000605019
MA0095.10
MA0098.10
MA0100.10.195572
MA0101.10.118095
MA0103.10.00639465
MA0105.10.00813351
MA0106.12.41626
MA0107.10.0578828
MA0108.210.3345
MA0109.10
MA0111.10.00520674
MA0113.10.129842
MA0114.10.0770914
MA0115.10.190558
MA0116.10.0131635
MA0117.10.511001
MA0119.10.0152349
MA0122.10.183122
MA0124.11.54383
MA0125.10.266765
MA0130.10
MA0131.13.44378
MA0132.10
MA0133.10
MA0135.10.211304
MA0136.10.0952642
MA0139.10.0106275
MA0140.10.0759194
MA0141.11.13805
MA0142.11.49459
MA0143.10.142797
MA0144.10.0392729
MA0145.10.00949492
MA0146.10.02615
MA0147.10.0200551
MA0148.10.432296
MA0149.10.00261706
MA0062.20.0430191
MA0035.20.643688
MA0039.20.000143737
MA0138.20.0530361
MA0002.20.0271057
MA0137.20.0302968
MA0104.20.0057879
MA0047.20.113222
MA0112.22.29812e-07
MA0065.20.000230385
MA0150.10.00554966
MA0151.10
MA0152.10.508687
MA0153.11.18347
MA0154.12.95683e-05
MA0155.10.0537848
MA0156.10.141186
MA0157.10.534484
MA0158.10
MA0159.10.00795707
MA0160.10.0432094
MA0161.10
MA0162.10.0349847
MA0163.15.34836e-10
MA0164.11.07003
MA0080.20.0221514
MA0018.21.51873
MA0099.20.0510638
MA0079.20
MA0102.20.678885
MA0258.10.000681795
MA0259.10.0403555
MA0442.10
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