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MCL coexpression mm9:2396: Difference between revisions

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{{MCL_coexpression_mm9
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of transcription, DNA-dependent;0.00264962671142477;59024,18023,13018,20218!GO:0006351;transcription, DNA-dependent;0.00264962671142477;59024,18023,13018,20218!GO:0032774;RNA biosynthetic process;0.00264962671142477;59024,18023,13018,20218!GO:0045449;regulation of transcription;0.00264962671142477;59024,18023,13018,20218!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.00264962671142477;59024,18023,13018,20218!GO:0006350;transcription;0.00264962671142477;59024,18023,13018,20218!GO:0010468;regulation of gene expression;0.00264962671142477;59024,18023,13018,20218!GO:0031323;regulation of cellular metabolic process;0.00264962671142477;59024,18023,13018,20218!GO:0019222;regulation of metabolic process;0.00264962671142477;59024,18023,13018,20218!GO:0016070;RNA metabolic process;0.00264962671142477;59024,18023,13018,20218!GO:0046831;regulation of RNA export from nucleus;0.00264962671142477;20218!GO:0010467;gene expression;0.00493676572862241;59024,18023,13018,20218!GO:0003676;nucleic acid binding;0.00501317796555137;59024,18023,13018,20218!GO:0010216;maintenance of DNA methylation;0.00586084345170822;13018!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.00586084345170822;59024,18023,13018,20218!GO:0050794;regulation of cellular process;0.00726818264355437;59024,18023,13018,20218!GO:0003918;DNA topoisomerase (ATP-hydrolyzing) activity;0.00856950403349945;59024!GO:0050789;regulation of biological process;0.00994081576642363;59024,18023,13018,20218!GO:0006349;genetic imprinting;0.010196033647745;13018!GO:0009048;dosage compensation, by inactivation of X chromosome;0.010196033647745;13018!GO:0003916;DNA topoisomerase activity;0.0109891901210296;59024!GO:0006265;DNA topological change;0.0109891901210296;59024!GO:0007549;dosage compensation;0.0109891901210296;13018!GO:0065007;biological regulation;0.0109891901210296;59024,18023,13018,20218!GO:0005634;nucleus;0.0114538221230214;59024,18023,13018,20218!GO:0043283;biopolymer metabolic process;0.0124452804732688;59024,18023,13018,20218!GO:0046822;regulation of nucleocytoplasmic transport;0.0129420245574463;20218!GO:0005070;SH3/SH2 adaptor activity;0.0140866333941102;20218!GO:0006305;DNA alkylation;0.0140866333941102;13018!GO:0006405;RNA export from nucleus;0.0140866333941102;20218!GO:0006306;DNA methylation;0.0140866333941102;13018!GO:0003677;DNA binding;0.0158713381875643;59024,18023,13018!GO:0006304;DNA modification;0.0158755623720686;13018!GO:0005515;protein binding;0.0174588127541724;59024,18023,13018,20218!GO:0000119;mediator complex;0.0174588127541724;59024!GO:0051168;nuclear export;0.0185873464027477;20218!GO:0030674;protein binding, bridging;0.0196543615796995;20218!GO:0006259;DNA metabolic process;0.0223176074557033;59024,13018!GO:0043170;macromolecule metabolic process;0.0247191938869611;59024,18023,13018,20218!GO:0007049;cell cycle;0.0275956870726719;13018,20218!GO:0043414;biopolymer methylation;0.0297006816389028;13018!GO:0040029;regulation of gene expression, epigenetic;0.0297006816389028;13018!GO:0060090;molecular adaptor activity;0.0297006816389028;20218!GO:0032259;methylation;0.0297006816389028;13018!GO:0050658;RNA transport;0.0301391412602402;20218!GO:0051236;establishment of RNA localization;0.0301391412602402;20218!GO:0016591;DNA-directed RNA polymerase II, holoenzyme;0.0301391412602402;59024!GO:0050657;nucleic acid transport;0.0301391412602402;20218!GO:0006403;RNA localization;0.0301391412602402;20218!GO:0048523;negative regulation of cellular process;0.0301391412602402;13018,20218!GO:0015931;nucleobase, nucleoside, nucleotide and nucleic acid transport;0.0312926256970316;20218!GO:0044238;primary metabolic process;0.0318401864703;59024,18023,13018,20218!GO:0048519;negative regulation of biological 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|gostat_on_MCL_coexpression=GO:0006355;regulation of transcription, DNA-dependent;0.00264962671142477;59024,18023,13018,20218!GO:0006351;transcription, DNA-dependent;0.00264962671142477;59024,18023,13018,20218!GO:0032774;RNA biosynthetic process;0.00264962671142477;59024,18023,13018,20218!GO:0045449;regulation of transcription;0.00264962671142477;59024,18023,13018,20218!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.00264962671142477;59024,18023,13018,20218!GO:0006350;transcription;0.00264962671142477;59024,18023,13018,20218!GO:0010468;regulation of gene expression;0.00264962671142477;59024,18023,13018,20218!GO:0031323;regulation of cellular metabolic process;0.00264962671142477;59024,18023,13018,20218!GO:0019222;regulation of metabolic process;0.00264962671142477;59024,18023,13018,20218!GO:0016070;RNA metabolic process;0.00264962671142477;59024,18023,13018,20218!GO:0046831;regulation of RNA export from nucleus;0.00264962671142477;20218!GO:0010467;gene expression;0.00493676572862241;59024,18023,13018,20218!GO:0003676;nucleic acid binding;0.00501317796555137;59024,18023,13018,20218!GO:0010216;maintenance of DNA methylation;0.00586084345170822;13018!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.00586084345170822;59024,18023,13018,20218!GO:0050794;regulation of cellular process;0.00726818264355437;59024,18023,13018,20218!GO:0003918;DNA topoisomerase (ATP-hydrolyzing) activity;0.00856950403349945;59024!GO:0050789;regulation of biological process;0.00994081576642363;59024,18023,13018,20218!GO:0006349;genetic imprinting;0.010196033647745;13018!GO:0009048;dosage compensation, by inactivation of X chromosome;0.010196033647745;13018!GO:0003916;DNA topoisomerase activity;0.0109891901210296;59024!GO:0006265;DNA topological change;0.0109891901210296;59024!GO:0007549;dosage compensation;0.0109891901210296;13018!GO:0065007;biological regulation;0.0109891901210296;59024,18023,13018,20218!GO:0005634;nucleus;0.0114538221230214;59024,18023,13018,20218!GO:0043283;biopolymer metabolic process;0.0124452804732688;59024,18023,13018,20218!GO:0046822;regulation of nucleocytoplasmic transport;0.0129420245574463;20218!GO:0005070;SH3/SH2 adaptor activity;0.0140866333941102;20218!GO:0006305;DNA alkylation;0.0140866333941102;13018!GO:0006405;RNA export from nucleus;0.0140866333941102;20218!GO:0006306;DNA methylation;0.0140866333941102;13018!GO:0003677;DNA binding;0.0158713381875643;59024,18023,13018!GO:0006304;DNA modification;0.0158755623720686;13018!GO:0005515;protein binding;0.0174588127541724;59024,18023,13018,20218!GO:0000119;mediator complex;0.0174588127541724;59024!GO:0051168;nuclear export;0.0185873464027477;20218!GO:0030674;protein binding, bridging;0.0196543615796995;20218!GO:0006259;DNA metabolic process;0.0223176074557033;59024,13018!GO:0043170;macromolecule metabolic process;0.0247191938869611;59024,18023,13018,20218!GO:0007049;cell cycle;0.0275956870726719;13018,20218!GO:0043414;biopolymer methylation;0.0297006816389028;13018!GO:0040029;regulation of gene expression, epigenetic;0.0297006816389028;13018!GO:0060090;molecular adaptor activity;0.0297006816389028;20218!GO:0032259;methylation;0.0297006816389028;13018!GO:0050658;RNA transport;0.0301391412602402;20218!GO:0051236;establishment of RNA localization;0.0301391412602402;20218!GO:0016591;DNA-directed RNA polymerase II, holoenzyme;0.0301391412602402;59024!GO:0050657;nucleic acid transport;0.0301391412602402;20218!GO:0006403;RNA localization;0.0301391412602402;20218!GO:0048523;negative regulation of cellular process;0.0301391412602402;13018,20218!GO:0015931;nucleobase, nucleoside, nucleotide and nucleic acid transport;0.0312926256970316;20218!GO:0044238;primary metabolic process;0.0318401864703;59024,18023,13018,20218!GO:0048519;negative regulation of biological process;0.0318401864703;13018,20218!GO:0044237;cellular metabolic process;0.0318401864703;59024,18023,13018,20218!GO:0043231;intracellular membrane-bound organelle;0.0318401864703;59024,18023,13018,20218!GO:0043227;membrane-bound organelle;0.0318401864703;59024,18023,13018,20218!GO:0003713;transcription coactivator activity;0.0345795460137525;59024!GO:0006730;one-carbon compound metabolic process;0.0384526715069959;13018!GO:0051049;regulation of transport;0.0412136454567188;20218!GO:0006913;nucleocytoplasmic transport;0.0441006895042575;20218!GO:0051169;nuclear transport;0.0441006895042575;20218!GO:0043229;intracellular organelle;0.0464795240315621;59024,18023,13018,20218!GO:0043226;organelle;0.0464795240315621;59024,18023,13018,20218!
}}

Latest revision as of 18:28, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr4:129419477..129419512,-p2@Khdrbs1
Mm9::chr6:29998062..29998078,+p2@Nrf1
Mm9::chr8:108160490..108160512,+p2@Ctcf
Mm9::chrX:98469402..98469427,+p3@Med12


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:0006355regulation of transcription, DNA-dependent0.00264962671142477
GO:0006351transcription, DNA-dependent0.00264962671142477
GO:0032774RNA biosynthetic process0.00264962671142477
GO:0045449regulation of transcription0.00264962671142477
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00264962671142477
GO:0006350transcription0.00264962671142477
GO:0010468regulation of gene expression0.00264962671142477
GO:0031323regulation of cellular metabolic process0.00264962671142477
GO:0019222regulation of metabolic process0.00264962671142477
GO:0016070RNA metabolic process0.00264962671142477
GO:0046831regulation of RNA export from nucleus0.00264962671142477
GO:0010467gene expression0.00493676572862241
GO:0003676nucleic acid binding0.00501317796555137
GO:0010216maintenance of DNA methylation0.00586084345170822
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00586084345170822
GO:0050794regulation of cellular process0.00726818264355437
GO:0003918DNA topoisomerase (ATP-hydrolyzing) activity0.00856950403349945
GO:0050789regulation of biological process0.00994081576642363
GO:0006349genetic imprinting0.010196033647745
GO:0009048dosage compensation, by inactivation of X chromosome0.010196033647745
GO:0003916DNA topoisomerase activity0.0109891901210296
GO:0006265DNA topological change0.0109891901210296
GO:0007549dosage compensation0.0109891901210296
GO:0065007biological regulation0.0109891901210296
GO:0005634nucleus0.0114538221230214
GO:0043283biopolymer metabolic process0.0124452804732688
GO:0046822regulation of nucleocytoplasmic transport0.0129420245574463
GO:0005070SH3/SH2 adaptor activity0.0140866333941102
GO:0006305DNA alkylation0.0140866333941102
GO:0006405RNA export from nucleus0.0140866333941102
GO:0006306DNA methylation0.0140866333941102
GO:0003677DNA binding0.0158713381875643
GO:0006304DNA modification0.0158755623720686
GO:0005515protein binding0.0174588127541724
GO:0000119mediator complex0.0174588127541724
GO:0051168nuclear export0.0185873464027477
GO:0030674protein binding, bridging0.0196543615796995
GO:0006259DNA metabolic process0.0223176074557033
GO:0043170macromolecule metabolic process0.0247191938869611
GO:0007049cell cycle0.0275956870726719
GO:0043414biopolymer methylation0.0297006816389028
GO:0040029regulation of gene expression, epigenetic0.0297006816389028
GO:0060090molecular adaptor activity0.0297006816389028
GO:0032259methylation0.0297006816389028
GO:0050658RNA transport0.0301391412602402
GO:0051236establishment of RNA localization0.0301391412602402
GO:0016591DNA-directed RNA polymerase II, holoenzyme0.0301391412602402
GO:0050657nucleic acid transport0.0301391412602402
GO:0006403RNA localization0.0301391412602402
GO:0048523negative regulation of cellular process0.0301391412602402
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0312926256970316
GO:0044238primary metabolic process0.0318401864703
GO:0048519negative regulation of biological process0.0318401864703
GO:0044237cellular metabolic process0.0318401864703
GO:0043231intracellular membrane-bound organelle0.0318401864703
GO:0043227membrane-bound organelle0.0318401864703
GO:0003713transcription coactivator activity0.0345795460137525
GO:0006730one-carbon compound metabolic process0.0384526715069959
GO:0051049regulation of transport0.0412136454567188
GO:0006913nucleocytoplasmic transport0.0441006895042575
GO:0051169nuclear transport0.0441006895042575
GO:0043229intracellular organelle0.0464795240315621
GO:0043226organelle0.0464795240315621



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
lymphocyte7.80e-0713
common lymphoid progenitor7.80e-0713


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)
MA0003.11.34944
MA0004.11.64673
MA0006.11.24418
MA0007.10.672186
MA0009.11.15569
MA0014.12.62764
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.11.26991
MA0029.11.08753
MA0030.11.09438
MA0031.11.05719
MA0038.10.846479
MA0040.11.16866
MA0041.10.604221
MA0042.10.589368
MA0043.11.25564
MA0046.11.1929
MA0048.11.35097
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.11.28762
MA0056.10
MA0057.11.29714
MA0058.11.4226
MA0059.10.59559
MA0060.10.403071
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.256913
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.216408
MA0074.10.795862
MA0076.11.35592
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.11.1032
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.10.651119
MA0093.11.29026
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.10.605676
MA0103.10.540576
MA0105.10.841866
MA0106.10.899777
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.10.43587
MA0115.11.25852
MA0116.10.497293
MA0117.11.22527
MA0119.10.606338
MA0122.11.24573
MA0124.11.45461
MA0125.11.37907
MA0130.10
MA0131.10.960068
MA0132.10
MA0133.10
MA0135.11.29308
MA0136.10.817395
MA0139.10.957842
MA0140.10.78318
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.10.439506
MA0145.11.14526
MA0146.10.647546
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.856416
MA0035.20.788288
MA0039.21.47117
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.21.0034
MA0047.20.845655
MA0112.20.211985
MA0065.20.212467
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.263609
MA0155.10.230016
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.12.31798
MA0163.11.64105
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.24.73893
MA0102.21.8929
MA0258.10.419871
MA0259.11.12353
MA0442.10
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