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MCL coexpression mm9:703: Difference between revisions

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{{MCL_coexpression_mm9
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part;0.0127685499686556;66929,97165,70454!GO:0005694;chromosome;0.0127685499686556;66929,97165,70454!GO:0044446;intracellular organelle part;0.0139725105329285;108961,21781,66929,97165,70454!GO:0044422;organelle part;0.0139725105329285;108961,21781,66929,97165,70454!GO:0005096;GTPase activator activity;0.0224643601242763;218581,71085!GO:0000785;chromatin;0.0224643601242763;66929,97165!GO:0008047;enzyme activator activity;0.0224643601242763;218581,71085!GO:0006355;regulation of transcription, DNA-dependent;0.0224643601242763;108961,21781,66929,97165!GO:0051320;S phase;0.0224643601242763;21781!GO:0000084;S phase of mitotic cell cycle;0.0224643601242763;21781!GO:0006351;transcription, DNA-dependent;0.0224643601242763;108961,21781,66929,97165!GO:0032774;RNA biosynthetic process;0.0224643601242763;108961,21781,66929,97165!GO:0045449;regulation of transcription;0.0224643601242763;108961,21781,66929,97165!GO:0042393;histone binding;0.0224643601242763;66929!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0224643601242763;108961,21781,66929,97165!GO:0006350;transcription;0.0224643601242763;108961,21781,66929,97165!GO:0010468;regulation of gene expression;0.0239082879941344;108961,21781,66929,97165!GO:0031323;regulation of cellular metabolic process;0.0252058166618859;108961,21781,66929,97165!GO:0006323;DNA packaging;0.0252058166618859;66929,97165!GO:0019222;regulation of metabolic process;0.0258087628220274;108961,21781,66929,97165!GO:0030695;GTPase regulator activity;0.0258087628220274;218581,71085!GO:0016070;RNA metabolic process;0.0258892407357442;108961,21781,66929,97165!GO:0005622;intracellular;0.0258892407357442;108961,21781,66929,97165,218581,70454,71085!GO:0005634;nucleus;0.028991300623026;108961,21781,66929,97165,70454!GO:0051726;regulation of cell cycle;0.0306296449022977;108961,21781!GO:0005667;transcription factor complex;0.0413136355770511;108961,21781!GO:0010467;gene 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|gostat_on_MCL_coexpression=GO:0044427;chromosomal part;0.0127685499686556;66929,97165,70454!GO:0005694;chromosome;0.0127685499686556;66929,97165,70454!GO:0044446;intracellular organelle part;0.0139725105329285;108961,21781,66929,97165,70454!GO:0044422;organelle part;0.0139725105329285;108961,21781,66929,97165,70454!GO:0005096;GTPase activator activity;0.0224643601242763;218581,71085!GO:0000785;chromatin;0.0224643601242763;66929,97165!GO:0008047;enzyme activator activity;0.0224643601242763;218581,71085!GO:0006355;regulation of transcription, DNA-dependent;0.0224643601242763;108961,21781,66929,97165!GO:0051320;S phase;0.0224643601242763;21781!GO:0000084;S phase of mitotic cell cycle;0.0224643601242763;21781!GO:0006351;transcription, DNA-dependent;0.0224643601242763;108961,21781,66929,97165!GO:0032774;RNA biosynthetic process;0.0224643601242763;108961,21781,66929,97165!GO:0045449;regulation of transcription;0.0224643601242763;108961,21781,66929,97165!GO:0042393;histone binding;0.0224643601242763;66929!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0224643601242763;108961,21781,66929,97165!GO:0006350;transcription;0.0224643601242763;108961,21781,66929,97165!GO:0010468;regulation of gene expression;0.0239082879941344;108961,21781,66929,97165!GO:0031323;regulation of cellular metabolic process;0.0252058166618859;108961,21781,66929,97165!GO:0006323;DNA packaging;0.0252058166618859;66929,97165!GO:0019222;regulation of metabolic process;0.0258087628220274;108961,21781,66929,97165!GO:0030695;GTPase regulator activity;0.0258087628220274;218581,71085!GO:0016070;RNA metabolic process;0.0258892407357442;108961,21781,66929,97165!GO:0005622;intracellular;0.0258892407357442;108961,21781,66929,97165,218581,70454,71085!GO:0005634;nucleus;0.028991300623026;108961,21781,66929,97165,70454!GO:0051726;regulation of cell cycle;0.0306296449022977;108961,21781!GO:0005667;transcription factor complex;0.0413136355770511;108961,21781!GO:0010467;gene expression;0.0423535075445992;108961,21781,66929,97165!
}}

Latest revision as of 15:45, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:117864832..117864836,+p@chr11:117864832..117864836
+
Mm9::chr13:109106534..109106552,+p2@Depdc1b
Mm9::chr13:109106560..109106581,+p1@Depdc1b
Mm9::chr19:41876518..41876550,-p1@Arhgap19
Mm9::chr1:163001055..163001137,+p1@Cenpl
Mm9::chr5:100929640..100929676,-p1@Lin54
Mm9::chr7:56136974..56136989,-p4@E2f8
Mm9::chr8:13338760..13338817,+p1@Tfdp1
Mm9::chr8:59990690..59990727,+p2@Hmgb2
Mm9::chr8:86479602..86479620,+p1@Asf1b


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:0044427chromosomal part0.0127685499686556
GO:0005694chromosome0.0127685499686556
GO:0044446intracellular organelle part0.0139725105329285
GO:0044422organelle part0.0139725105329285
GO:0005096GTPase activator activity0.0224643601242763
GO:0000785chromatin0.0224643601242763
GO:0008047enzyme activator activity0.0224643601242763
GO:0006355regulation of transcription, DNA-dependent0.0224643601242763
GO:0051320S phase0.0224643601242763
GO:0000084S phase of mitotic cell cycle0.0224643601242763
GO:0006351transcription, DNA-dependent0.0224643601242763
GO:0032774RNA biosynthetic process0.0224643601242763
GO:0045449regulation of transcription0.0224643601242763
GO:0042393histone binding0.0224643601242763
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0224643601242763
GO:0006350transcription0.0224643601242763
GO:0010468regulation of gene expression0.0239082879941344
GO:0031323regulation of cellular metabolic process0.0252058166618859
GO:0006323DNA packaging0.0252058166618859
GO:0019222regulation of metabolic process0.0258087628220274
GO:0030695GTPase regulator activity0.0258087628220274
GO:0016070RNA metabolic process0.0258892407357442
GO:0005622intracellular0.0258892407357442
GO:0005634nucleus0.028991300623026
GO:0051726regulation of cell cycle0.0306296449022977
GO:0005667transcription factor complex0.0413136355770511
GO:0010467gene expression0.0423535075445992



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)
MA0003.13.4793
MA0004.11.68813
MA0006.10.210471
MA0007.10.916416
MA0009.10.780842
MA0014.11.80909
MA0017.10.233089
MA0019.10.603066
MA0024.11.74864
MA0025.11.01089
MA0027.12.42079
MA0028.10.219287
MA0029.10.716673
MA0030.10.723093
MA0031.10.688336
MA0038.12.14884
MA0040.10.79313
MA0041.10.291712
MA0042.10.76637
MA0043.10.875991
MA0046.10.816137
MA0048.10.509074
MA0050.10.396459
MA0051.10.504875
MA0052.10.801048
MA0055.10.17385
MA0056.10
MA0057.10.216209
MA0058.12.11833
MA0059.10.777514
MA0060.17.98829
MA0061.11.54987
MA0063.10
MA0066.10.485868
MA0067.11.12095
MA0068.10.484739
MA0069.10.801381
MA0070.10.791856
MA0071.10.395679
MA0072.10.783532
MA0073.10.0413021
MA0074.10.451832
MA0076.10.249619
MA0077.10.762273
MA0078.10.536502
MA0081.10.305576
MA0083.10.875209
MA0084.11.44691
MA0087.10.832758
MA0088.10.623059
MA0089.10
MA0090.10.877277
MA0091.10.372635
MA0092.10.877917
MA0093.12.62807
MA0095.10
MA0098.10
MA0100.10.440912
MA0101.10.292867
MA0103.10.242398
MA0105.11.56265
MA0106.11.34295
MA0107.10.66744
MA0108.20.625209
MA0109.10
MA0111.10.90605
MA0113.10.516916
MA0114.10.167085
MA0115.10.878749
MA0116.10.210297
MA0117.10.846964
MA0119.10.293392
MA0122.10.866511
MA0124.11.06819
MA0125.10.994853
MA0130.10
MA0131.11.45836
MA0132.10
MA0133.10
MA0135.10.911905
MA0136.10.470672
MA0139.10.385513
MA0140.10.440804
MA0141.10.259554
MA0142.10.674191
MA0143.10.53259
MA0144.10.169559
MA0145.11.03071
MA0146.10.642452
MA0147.10.530496
MA0148.10.375491
MA0149.10.2978
MA0062.20.0948004
MA0035.20.44524
MA0039.21.66029
MA0138.20.590987
MA0002.20.123715
MA0137.20.257017
MA0104.21.34242
MA0047.20.495607
MA0112.20.371983
MA0065.20.163769
MA0150.10.346631
MA0151.10
MA0152.10.495709
MA0153.10.92832
MA0154.10.501928
MA0155.10.416651
MA0156.10.248865
MA0157.10.642984
MA0158.10
MA0159.10.187774
MA0160.10.378276
MA0161.10
MA0162.12.70539
MA0163.10.679942
MA0164.10.471016
MA0080.20.237846
MA0018.20.480226
MA0099.20.584892
MA0079.21.27236
MA0102.21.49914
MA0258.10.156336
MA0259.10.981631
MA0442.10
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