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MCL coexpression mm9:327: Difference between revisions

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{{MCL_coexpression_mm9
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oexpression=GO:0005634;nucleus;0.00893147018551157;71041,231452,21815,70428,17975,71991,26939,11834,28036,53319,245000,67628!GO:0044424;intracellular part;0.00893147018551157;71041,12469,231452,21815,70428,17975,13627,24030,67738,71991,26939,11834,28036,53319,245000,67628,72831!GO:0003723;RNA binding;0.00893147018551157;28036,11834,53319,17975,72831!GO:0005622;intracellular;0.00893147018551157;71041,12469,231452,21815,70428,17975,13627,24030,67738,71991,26939,11834,28036,53319,245000,67628,72831!GO:0043231;intracellular membrane-bound organelle;0.00893147018551157;71041,231452,21815,70428,17975,24030,71991,26939,11834,28036,53319,245000,67628,72831!GO:0043227;membrane-bound organelle;0.00893147018551157;71041,231452,21815,70428,17975,24030,71991,26939,11834,28036,53319,245000,67628,72831!GO:0010467;gene expression;0.0124184894000314;71041,21815,70428,13627,24030,71991,11834,28036,26939!GO:0003676;nucleic acid binding;0.0124184894000314;21815,70428,17975,13627,11834,28036,53319,245000,72831!GO:0003899;DNA-directed RNA polymerase activity;0.0124184894000314;26939,70428!GO:0000166;nucleotide binding;0.0250303259944819;13627,12469,28036,53319,57815,17975,72831!GO:0043229;intracellular organelle;0.0250303259944819;71041,231452,21815,70428,17975,24030,71991,26939,11834,28036,53319,245000,67628,72831!GO:0043226;organelle;0.0250303259944819;71041,231452,21815,70428,17975,24030,71991,26939,11834,28036,53319,245000,67628,72831!GO:0032405;MutLalpha complex binding;0.0250303259944819;245000!GO:0032407;MutSalpha complex binding;0.0250303259944819;245000!GO:0008432;JUN kinase binding;0.0250303259944819;21815!GO:0032404;mismatch repair complex binding;0.0250303259944819;245000!GO:0042405;nuclear inclusion body;0.0250303259944819;53319!GO:0044428;nuclear part;0.0250303259944819;71991,21815,11834,53319,17975!GO:0000109;nucleotide-excision repair complex;0.034379028864868;71991!GO:0016973;poly(A)+ mRNA export from nucleus;0.0395695407995545;53319!GO:0006283;transcription-coupled nucleotide-excision repair;0.0395695407995545;71991!GO:0016234;inclusion body;0.0395695407995545;53319!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.040060873560071;71041,21815,70428,71991,11834,28036,26939,245000!GO:0016779;nucleotidyltransferase activity;0.0418329151080293;26939,70428!GO:0005528;FK506 binding;0.0418329151080293;67738!GO:0005527;macrolide binding;0.0418329151080293;67738!GO:0043393;regulation of protein binding;0.0464582033755782;245000!GO:0008144;drug binding;0.0464582033755782;67738!GO:0044238;primary metabolic process;0.0464582033755782;71041,12469,21815,70428,13627,24030,67738,71991,11834,28036,26939,245000!GO:0051320;S phase;0.0464582033755782;67628!GO:0000084;S phase of mitotic cell cycle;0.0464582033755782;67628!GO:0044237;cellular metabolic process;0.0464582033755782;71041,12469,21815,70428,13627,24030,67738,71991,11834,28036,26939,245000!GO:0006457;protein folding;0.0464582033755782;12469,67738!GO:0005487;nucleocytoplasmic transporter activity;0.0496520151209464;53319!|ontology_enrichment_celltype=CL:0000988!1.18e-09!32;CL:0002032!1.18e-09!32;CL:0000037!1.18e-09!32;CL:0000566!1.18e-09!32;CL:0000837!1.18e-09!32;CL:0000542!1.84e-08!13;CL:0000051!1.84e-08!13;CL:0002242!3.12e-08!16;CL:0000838!4.86e-08!12;CL:0000084!2.00e-07!11;CL:0000827!2.00e-07!11;CL:0000791!7.23e-07!9;CL:0000789!7.23e-07!9;CL:0002420!7.23e-07!9;CL:0002419!7.23e-07!9;CL:0000790!7.23e-07!9|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0004177!8.87e-08!29;UBERON:0005057!8.87e-08!29;UBERON:0000153!9.04e-08!43|tfbs_overrepresentation_for_novel_motifs=0.687857,0.900159,1.04415,0.126379,0.161423,0.13486,0.5625,0.369064,0.395461,0.778026,1.51966,0.184641,0.369722,1.7321,0.0476623,0,0.915598,0.152896,0.328981,0.402773,0.251591,0.397987,1.72866,0.365428,0.64228,1.17751,0.15247,0.884926,1.23101,0.578277,1.37041,0.430274,0.347532,0.448632,1.10133,0.0286452,0.936427,0.53714,0.285595,0.441656,0.157073,1.38961,0.120149,0.182247,2.02369,1.82075,0.77462,0.476169,0.0377659,0.473837,0.332337,1.25115,0.342929,0.553844,0.569458,0.594337,0.22823,0.176187,0.284434,0.590972,1.06273,1.27712,0.224761,1.55736,1.15233,0.355898,0.693798,1.02539,0.409398,0.883956,0.578753,0.198432,2.13772,0.599674,3.16673,0.0404583,0.124698,0.754851,0.398928,0.0738984,0.200441,0.360462,0.245495,0.35158,1.24289,3.61649,0.705835,0.20538,0.287376,1.18318,0.758722,0.501285,0.44118,0.0437656,0.277879,0.245164,0.18465,0.44358,1.41495,0.160637,0.0352891,0.430036,1.33098,0.332812,0.33197,1.38797,1.75762,0.469886,0.557908,0.540816,0.67046,0.539906,0.258506,0.966414,0.765328,0.155153,1.62558,0.803238,0.347417,0.321151,0.604565,0.306855,0.22163,0.274265,0.816304,0.40202,0.198291,0.4354,0.692394,0.387426,0.523273,0.387123,0.665113,0.616957,0.785621,0.0260273,0.708721,0.44012,0.739526,1.5459,1.15207,0.698162,0.651432,0.439187,0.326804,0.438656,0.286009,1.50665,0.108773,1.9566,0.855374,1.85846,0.555246,0.773127,0.214931,0.629009,0.240389,0.193809,0.101676,1.16738,0.748413,1.24129,1.03889,0.323614,0.324177,0.209743,0.592606,0.183582,1.39213|tfbs_overrepresentation_jaspar=MA0003.1;1.87655,MA0004.1;0.794862,MA0006.1;0.394627,MA0007.1;1.23839,MA0009.1;0.452863,MA0014.1;1.12934,MA0017.1;0.452527,MA0019.1;0.30302,MA0024.1;1.87787,MA0025.1;0.660968,MA0027.1;2.04174,MA0028.1;3.96383,MA0029.1;0.397373,MA0030.1;0.402861,MA0031.1;0.373333,MA0038.1;0.220281,MA0040.1;0.463641,MA0041.1;0.0860551,MA0042.1;0.0797095,MA0043.1;0.53743,MA0046.1;0.483941,MA0048.1;0.484222,MA0050.1;1.43697,MA0051.1;0.643016,MA0052.1;0.47061,MA0055.1;0.0154442,MA0056.1;0,MA0057.1;0.430886,MA0058.1;0.55981,MA0059.1;0.588924,MA0060.1;0.447532,MA0061.1;0.854791,MA0063.1;0,MA0066.1;0.212546,MA0067.1;0.764133,MA0068.1;0.0205783,MA0069.1;0.470904,MA0070.1;0.462521,MA0071.1;0.149369,MA0072.1;0.455219,MA0073.1;1.49444,MA0074.1;1.05068,MA0076.1;6.71771,MA0077.1;0.436665,MA0078.1;0.250627,MA0081.1;0.312046,MA0083.1;0.536725,MA0084.1;1.07765,MA0087.1;0.4987,MA0088.1;2.47003,MA0089.1;0,MA0090.1;0.107485,MA0091.1;0.418347,MA0092.1;0.107655,MA0093.1;1.16444,MA0095.1;0,MA0098.1;0,MA0100.1;3.05515,MA0101.1;0.610312,MA0103.1;0.218786,MA0105.1;1.29467,MA0106.1;0.256379,MA0107.1;1.22202,MA0108.2;0.85894,MA0109.1;0,MA0111.1;0.744051,MA0113.1;0.664215,MA0114.1;0.287365,MA0115.1;0.539917,MA0116.1;0.174756,MA0117.1;0.511373,MA0119.1;0.0869793,MA0122.1;0.528896,MA0124.1;0.714453,MA0125.1;0.646095,MA0130.1;0,MA0131.1;3.11389,MA0132.1;0,MA0133.1;0,MA0135.1;0.569948,MA0136.1;0.583392,MA0139.1;1.64741,MA0140.1;0.180161,MA0141.1;0.0690765,MA0142.1;0.361451,MA0143.1;0.247626,MA0144.1;0.123063,MA0145.1;0.45978,MA0146.1;2.55888,MA0147.1;2.27347,MA0148.1;0.136186,MA0149.1;0.0894222,MA0062.2;5.43258,MA0035.2;0.18328,MA0039.2;3.29233,MA0138.2;0.796689,MA0002.2;0.91042,MA0137.2;0.514948,MA0104.2;2.26352,MA0047.2;0.219739,MA0112.2;0.295523,MA0065.2;0.0863447,MA0150.1;0.376372,MA0151.1;0,MA0152.1;0.62695,MA0153.1;0.584906,MA0154.1;0.473854,MA0155.1;0.354426,MA0156.1;0.849859,MA0157.1;0.335532,MA0158.1;0,MA0159.1;0.610644,MA0160.1;0.137981,MA0161.1;0,MA0162.1;2.20629,MA0163.1;0.448848,MA0164.1;0.201705,MA0080.2;0.212388,MA0018.2;1.77229,MA0099.2;0.288477,MA0079.2;1.18287,MA0102.2;1.12863,MA0258.1;0.26175,MA0259.1;1.6899,MA0442.1;0}}
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|gostat_on_MCL_coexpression=GO:0005634;nucleus;0.00893147018551157;71041,231452,21815,70428,17975,71991,26939,11834,28036,53319,245000,67628!GO:0044424;intracellular part;0.00893147018551157;71041,12469,231452,21815,70428,17975,13627,24030,67738,71991,26939,11834,28036,53319,245000,67628,72831!GO:0003723;RNA binding;0.00893147018551157;28036,11834,53319,17975,72831!GO:0005622;intracellular;0.00893147018551157;71041,12469,231452,21815,70428,17975,13627,24030,67738,71991,26939,11834,28036,53319,245000,67628,72831!GO:0043231;intracellular membrane-bound organelle;0.00893147018551157;71041,231452,21815,70428,17975,24030,71991,26939,11834,28036,53319,245000,67628,72831!GO:0043227;membrane-bound organelle;0.00893147018551157;71041,231452,21815,70428,17975,24030,71991,26939,11834,28036,53319,245000,67628,72831!GO:0010467;gene expression;0.0124184894000314;71041,21815,70428,13627,24030,71991,11834,28036,26939!GO:0003676;nucleic acid binding;0.0124184894000314;21815,70428,17975,13627,11834,28036,53319,245000,72831!GO:0003899;DNA-directed RNA polymerase activity;0.0124184894000314;26939,70428!GO:0000166;nucleotide binding;0.0250303259944819;13627,12469,28036,53319,57815,17975,72831!GO:0043229;intracellular organelle;0.0250303259944819;71041,231452,21815,70428,17975,24030,71991,26939,11834,28036,53319,245000,67628,72831!GO:0043226;organelle;0.0250303259944819;71041,231452,21815,70428,17975,24030,71991,26939,11834,28036,53319,245000,67628,72831!GO:0032405;MutLalpha complex binding;0.0250303259944819;245000!GO:0032407;MutSalpha complex binding;0.0250303259944819;245000!GO:0008432;JUN kinase binding;0.0250303259944819;21815!GO:0032404;mismatch repair complex binding;0.0250303259944819;245000!GO:0042405;nuclear inclusion body;0.0250303259944819;53319!GO:0044428;nuclear part;0.0250303259944819;71991,21815,11834,53319,17975!GO:0000109;nucleotide-excision repair complex;0.034379028864868;71991!GO:0016973;poly(A)+ mRNA export from nucleus;0.0395695407995545;53319!GO:0006283;transcription-coupled nucleotide-excision repair;0.0395695407995545;71991!GO:0016234;inclusion body;0.0395695407995545;53319!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.040060873560071;71041,21815,70428,71991,11834,28036,26939,245000!GO:0016779;nucleotidyltransferase activity;0.0418329151080293;26939,70428!GO:0005528;FK506 binding;0.0418329151080293;67738!GO:0005527;macrolide binding;0.0418329151080293;67738!GO:0043393;regulation of protein binding;0.0464582033755782;245000!GO:0008144;drug binding;0.0464582033755782;67738!GO:0044238;primary metabolic process;0.0464582033755782;71041,12469,21815,70428,13627,24030,67738,71991,11834,28036,26939,245000!GO:0051320;S phase;0.0464582033755782;67628!GO:0000084;S phase of mitotic cell cycle;0.0464582033755782;67628!GO:0044237;cellular metabolic process;0.0464582033755782;71041,12469,21815,70428,13627,24030,67738,71991,11834,28036,26939,245000!GO:0006457;protein folding;0.0464582033755782;12469,67738!GO:0005487;nucleocytoplasmic transporter activity;0.0496520151209464;53319!
|ontology_enrichment_celltype=CL:0000988!1.18e-09!32;CL:0002032!1.18e-09!32;CL:0000037!1.18e-09!32;CL:0000566!1.18e-09!32;CL:0000837!1.18e-09!32;CL:0000542!1.84e-08!13;CL:0000051!1.84e-08!13;CL:0002242!3.12e-08!16;CL:0000838!4.86e-08!12;CL:0000084!2.00e-07!11;CL:0000827!2.00e-07!11;CL:0000791!7.23e-07!9;CL:0000789!7.23e-07!9;CL:0002420!7.23e-07!9;CL:0002419!7.23e-07!9;CL:0000790!7.23e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004177!8.87e-08!29;UBERON:0005057!8.87e-08!29;UBERON:0000153!9.04e-08!43
}}

Latest revision as of 15:06, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:23506949..23506966,-p4@Gm10279
p4@Gm14059
p4@Gm14958
p4@Gm5642
p4@Gm6646
p4@Gm7643
p4@Gm7671
p4@Gm7698
p4@Gm7711
p4@Rps12
Mm9::chr10:84085110..84085155,+p1@Polr3b
Mm9::chr13:108948917..108948948,+p1@Ercc8
Mm9::chr16:87496052..87496065,-p2@Cct8
Mm9::chr16:90810610..90810674,-p1@Urb1
Mm9::chr17:71202822..71202877,-p3@Tgif1
Mm9::chr19:47125313..47125405,-p1@Pcgf6
Mm9::chr19:8831589..8831616,+p2@Nxf1
Mm9::chr1:88256056..88256061,-p2@Ncl
Mm9::chr2:114001010..114001029,-p3@Aqr
Mm9::chr3:127256128..127256143,-p2@Larp7
Mm9::chr3:157694612..157694655,-p5@Srsf11
Mm9::chr3:37319195..37319257,+p1@Spata5
Mm9::chr3:79395359..79395370,+p2@Ppid
Mm9::chr4:135412002..135412039,+p2@Srsf10
Mm9::chr4:46463743..46463759,+p3@Anp32b
Mm9::chr5:121847974..121848013,+p1@Naa25
Mm9::chr5:92738974..92739026,-p1@Sdad1
Mm9::chr7:128061283..128061329,+p1@Polr3e
Mm9::chr7:133645494..133645563,-p@chr7:133645494..133645563
-
Mm9::chr8:126545352..126545415,+p1@Urb2
Mm9::chr9:110003514..110003556,-p2@Dhx30
Mm9::chr9:78329464..78329521,-p1@Eef1a1
Mm9::chr9:95758113..95758129,+p2@Atr


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:0005634nucleus0.00893147018551157
GO:0044424intracellular part0.00893147018551157
GO:0003723RNA binding0.00893147018551157
GO:0005622intracellular0.00893147018551157
GO:0043231intracellular membrane-bound organelle0.00893147018551157
GO:0043227membrane-bound organelle0.00893147018551157
GO:0010467gene expression0.0124184894000314
GO:0003676nucleic acid binding0.0124184894000314
GO:0003899DNA-directed RNA polymerase activity0.0124184894000314
GO:0000166nucleotide binding0.0250303259944819
GO:0043229intracellular organelle0.0250303259944819
GO:0043226organelle0.0250303259944819
GO:0032405MutLalpha complex binding0.0250303259944819
GO:0032407MutSalpha complex binding0.0250303259944819
GO:0008432JUN kinase binding0.0250303259944819
GO:0032404mismatch repair complex binding0.0250303259944819
GO:0042405nuclear inclusion body0.0250303259944819
GO:0044428nuclear part0.0250303259944819
GO:0000109nucleotide-excision repair complex0.034379028864868
GO:0016973poly(A)+ mRNA export from nucleus0.0395695407995545
GO:0006283transcription-coupled nucleotide-excision repair0.0395695407995545
GO:0016234inclusion body0.0395695407995545
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.040060873560071
GO:0016779nucleotidyltransferase activity0.0418329151080293
GO:0005528FK506 binding0.0418329151080293
GO:0005527macrolide binding0.0418329151080293
GO:0043393regulation of protein binding0.0464582033755782
GO:0008144drug binding0.0464582033755782
GO:0044238primary metabolic process0.0464582033755782
GO:0051320S phase0.0464582033755782
GO:0000084S phase of mitotic cell cycle0.0464582033755782
GO:0044237cellular metabolic process0.0464582033755782
GO:0006457protein folding0.0464582033755782
GO:0005487nucleocytoplasmic transporter activity0.0496520151209464



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
hemopoietic organ8.87e-0829
immune organ8.87e-0829
anterior region of body9.04e-0843


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)
MA0003.11.87655
MA0004.10.794862
MA0006.10.394627
MA0007.11.23839
MA0009.10.452863
MA0014.11.12934
MA0017.10.452527
MA0019.10.30302
MA0024.11.87787
MA0025.10.660968
MA0027.12.04174
MA0028.13.96383
MA0029.10.397373
MA0030.10.402861
MA0031.10.373333
MA0038.10.220281
MA0040.10.463641
MA0041.10.0860551
MA0042.10.0797095
MA0043.10.53743
MA0046.10.483941
MA0048.10.484222
MA0050.11.43697
MA0051.10.643016
MA0052.10.47061
MA0055.10.0154442
MA0056.10
MA0057.10.430886
MA0058.10.55981
MA0059.10.588924
MA0060.10.447532
MA0061.10.854791
MA0063.10
MA0066.10.212546
MA0067.10.764133
MA0068.10.0205783
MA0069.10.470904
MA0070.10.462521
MA0071.10.149369
MA0072.10.455219
MA0073.11.49444
MA0074.11.05068
MA0076.16.71771
MA0077.10.436665
MA0078.10.250627
MA0081.10.312046
MA0083.10.536725
MA0084.11.07765
MA0087.10.4987
MA0088.12.47003
MA0089.10
MA0090.10.107485
MA0091.10.418347
MA0092.10.107655
MA0093.11.16444
MA0095.10
MA0098.10
MA0100.13.05515
MA0101.10.610312
MA0103.10.218786
MA0105.11.29467
MA0106.10.256379
MA0107.11.22202
MA0108.20.85894
MA0109.10
MA0111.10.744051
MA0113.10.664215
MA0114.10.287365
MA0115.10.539917
MA0116.10.174756
MA0117.10.511373
MA0119.10.0869793
MA0122.10.528896
MA0124.10.714453
MA0125.10.646095
MA0130.10
MA0131.13.11389
MA0132.10
MA0133.10
MA0135.10.569948
MA0136.10.583392
MA0139.11.64741
MA0140.10.180161
MA0141.10.0690765
MA0142.10.361451
MA0143.10.247626
MA0144.10.123063
MA0145.10.45978
MA0146.12.55888
MA0147.12.27347
MA0148.10.136186
MA0149.10.0894222
MA0062.25.43258
MA0035.20.18328
MA0039.23.29233
MA0138.20.796689
MA0002.20.91042
MA0137.20.514948
MA0104.22.26352
MA0047.20.219739
MA0112.20.295523
MA0065.20.0863447
MA0150.10.376372
MA0151.10
MA0152.10.62695
MA0153.10.584906
MA0154.10.473854
MA0155.10.354426
MA0156.10.849859
MA0157.10.335532
MA0158.10
MA0159.10.610644
MA0160.10.137981
MA0161.10
MA0162.12.20629
MA0163.10.448848
MA0164.10.201705
MA0080.20.212388
MA0018.21.77229
MA0099.20.288477
MA0079.21.18287
MA0102.21.12863
MA0258.10.26175
MA0259.11.6899
MA0442.10
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