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MCL coexpression mm9:618: Difference between revisions

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{{MCL_coexpression_mm9
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1686116,0.261065738036311,0.158843797677303,0.226790206858766,0.275859125630462,0.201842612947909,0.199037798091534,0.166587725617214,0.235200969299339,0.189990830607665,0.18359421108913,0.18842684556126,0.154734246586651,0.261642642048071,0.249723919395316,0.204343226098226,0.209447282040344,0.141704700595215,0.242897000144792,0.230907198759394,0.185660734839627,0.221874956202416,0.158719081855703,0.0905641158318875|gostat_on_MCL_coexpression=GO:0045941;positive regulation of transcription;0.00456059693951042;13593,13592!GO:0045935;positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.00456059693951042;13593,13592!GO:0031325;positive regulation of cellular metabolic process;0.00456059693951042;13593,13592!GO:0009893;positive regulation of metabolic process;0.00456059693951042;13593,13592!GO:0048522;positive regulation of cellular process;0.0139460471818904;13593,13592!GO:0048518;positive regulation of biological process;0.0154899199155359;13593,13592!GO:0006355;regulation of transcription, DNA-dependent;0.0349260642094763;13593,13592!GO:0006351;transcription, DNA-dependent;0.0349260642094763;13593,13592!GO:0032774;RNA biosynthetic process;0.0349260642094763;13593,13592!GO:0008270;zinc ion binding;0.0349260642094763;13593,13592!GO:0003677;DNA binding;0.0349260642094763;13593,13592!GO:0045449;regulation of transcription;0.0349260642094763;13593,13592!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0349260642094763;13593,13592!GO:0006350;transcription;0.0349260642094763;13593,13592!GO:0010468;regulation of gene expression;0.0349260642094763;13593,13592!GO:0031323;regulation of cellular metabolic process;0.0349260642094763;13593,13592!GO:0007275;multicellular organismal development;0.0349260642094763;13593,13592!GO:0019222;regulation of metabolic process;0.0349260642094763;13593,13592!GO:0016070;RNA metabolic process;0.0349260642094763;13593,13592!GO:0046914;transition metal ion binding;0.0349696642771753;13593,13592!GO:0010467;gene expression;0.0452542399071736;13593,13592!GO:0003676;nucleic acid binding;0.0453069182867025;13593,13592!GO:0032502;developmental process;0.0461573716705461;13593,13592!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic 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|gostat_on_MCL_coexpression=GO:0045941;positive regulation of transcription;0.00456059693951042;13593,13592!GO:0045935;positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.00456059693951042;13593,13592!GO:0031325;positive regulation of cellular metabolic process;0.00456059693951042;13593,13592!GO:0009893;positive regulation of metabolic process;0.00456059693951042;13593,13592!GO:0048522;positive regulation of cellular process;0.0139460471818904;13593,13592!GO:0048518;positive regulation of biological process;0.0154899199155359;13593,13592!GO:0006355;regulation of transcription, DNA-dependent;0.0349260642094763;13593,13592!GO:0006351;transcription, DNA-dependent;0.0349260642094763;13593,13592!GO:0032774;RNA biosynthetic process;0.0349260642094763;13593,13592!GO:0008270;zinc ion binding;0.0349260642094763;13593,13592!GO:0003677;DNA binding;0.0349260642094763;13593,13592!GO:0045449;regulation of transcription;0.0349260642094763;13593,13592!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0349260642094763;13593,13592!GO:0006350;transcription;0.0349260642094763;13593,13592!GO:0010468;regulation of gene expression;0.0349260642094763;13593,13592!GO:0031323;regulation of cellular metabolic process;0.0349260642094763;13593,13592!GO:0007275;multicellular organismal development;0.0349260642094763;13593,13592!GO:0019222;regulation of metabolic process;0.0349260642094763;13593,13592!GO:0016070;RNA metabolic process;0.0349260642094763;13593,13592!GO:0046914;transition metal ion binding;0.0349696642771753;13593,13592!GO:0010467;gene expression;0.0452542399071736;13593,13592!GO:0003676;nucleic acid binding;0.0453069182867025;13593,13592!GO:0032502;developmental process;0.0461573716705461;13593,13592!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0482336750242131;13593,13592!
}}

Latest revision as of 15:36, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr14:67853568..67853573,+p5@Ebf2
Mm9::chr16:7039662..7039675,+p@chr16:7039662..7039675
+
Mm9::chr7:144387481..144387486,-p@chr7:144387481..144387486
-
Mm9::chr7:144388046..144388053,-p@chr7:144388046..144388053
-
Mm9::chr7:144505876..144505884,-p9@Ebf3
Mm9::chr7:144505906..144505913,-p7@Ebf3
Mm9::chr7:144505942..144505949,-p10@Ebf3
Mm9::chr7:144505957..144505972,-p2@Ebf3
Mm9::chr7:144505980..144506010,-p3@Ebf3
Mm9::chr7:144506051..144506062,-p5@Ebf3
Mm9::chr7:144506077..144506128,-p1@Ebf3
Mm9::chr7:144514443..144514468,-p@chr7:144514443..144514468
-


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:0045941positive regulation of transcription0.00456059693951042
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00456059693951042
GO:0031325positive regulation of cellular metabolic process0.00456059693951042
GO:0009893positive regulation of metabolic process0.00456059693951042
GO:0048522positive regulation of cellular process0.0139460471818904
GO:0048518positive regulation of biological process0.0154899199155359
GO:0006355regulation of transcription, DNA-dependent0.0349260642094763
GO:0006351transcription, DNA-dependent0.0349260642094763
GO:0032774RNA biosynthetic process0.0349260642094763
GO:0008270zinc ion binding0.0349260642094763
GO:0003677DNA binding0.0349260642094763
GO:0045449regulation of transcription0.0349260642094763
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0349260642094763
GO:0006350transcription0.0349260642094763
GO:0010468regulation of gene expression0.0349260642094763
GO:0031323regulation of cellular metabolic process0.0349260642094763
GO:0007275multicellular organismal development0.0349260642094763
GO:0019222regulation of metabolic process0.0349260642094763
GO:0016070RNA metabolic process0.0349260642094763
GO:0046914transition metal ion binding0.0349696642771753
GO:0010467gene expression0.0452542399071736
GO:0003676nucleic acid binding0.0453069182867025
GO:0032502developmental process0.0461573716705461
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0482336750242131



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
CNS neuron (sensu Vertebrata)1.31e-0823
neuroblast (sensu Vertebrata)1.31e-0823

Uber Anatomy
Ontology termp-valuen
spinal cord5.24e-076
dorsal region element5.24e-076
dorsum5.24e-076


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)
MA0003.12.63894
MA0004.10.303605
MA0006.10.496735
MA0007.10.290695
MA0009.10.709264
MA0014.110.6649
MA0017.10.186015
MA0019.10.535691
MA0024.10.667197
MA0025.10.936082
MA0027.12.34178
MA0028.10.173587
MA0029.10.64639
MA0030.10.65267
MA0031.10.618697
MA0038.10.432665
MA0040.10.721328
MA0041.10.239557
MA0042.10.228771
MA0043.10.802848
MA0046.10.743934
MA0048.10.168666
MA0050.10.337476
MA0051.10.440863
MA0052.10.729105
MA0055.10.00695701
MA0056.10
MA0057.10.630087
MA0058.10.223242
MA0059.10.233271
MA0060.10.108526
MA0061.10.40468
MA0063.10
MA0066.10.422624
MA0067.11.04514
MA0068.10.157638
MA0069.10.729433
MA0070.10.720077
MA0071.10.336739
MA0072.10.711905
MA0073.10.0375233
MA0074.10.390075
MA0076.10.200996
MA0077.10.691048
MA0078.10.471303
MA0081.10.252371
MA0083.116.0882
MA0084.11.3693
MA0087.10.760279
MA0088.10.0983922
MA0089.10
MA0090.12.95061
MA0091.10.315003
MA0092.10.274547
MA0093.10.179936
MA0095.10
MA0098.10
MA0100.10.379666
MA0101.10.240622
MA0103.10.19444
MA0105.11.28106
MA0106.10.478503
MA0107.10.189625
MA0108.23.44681
MA0109.10
MA0111.10.286331
MA0113.10.452439
MA0114.10.127366
MA0115.10.805567
MA0116.10.165534
MA0117.10.774259
MA0119.10.241106
MA0122.10.793507
MA0124.10.992825
MA0125.10.920215
MA0130.10
MA0131.12.26454
MA0132.10
MA0133.10
MA0135.10.838263
MA0136.10.408073
MA0139.10.61859
MA0140.10.379562
MA0141.10.210047
MA0142.10.604892
MA0143.10.467531
MA0144.10.807435
MA0145.10.0257706
MA0146.13.24101
MA0147.10.428193
MA0148.10.317692
MA0149.10.245177
MA0062.20.0662974
MA0035.20.383789
MA0039.21.12665
MA0138.20.523978
MA0002.20.0901987
MA0137.24.169
MA0104.20.326825
MA0047.20.431964
MA0112.20.109037
MA0065.22.04796
MA0150.10.290598
MA0151.10
MA0152.10.432062
MA0153.10.854464
MA0154.10.670722
MA0155.12.21027
MA0156.10.200311
MA0157.10.574484
MA0158.10
MA0159.10.145521
MA0160.10.320315
MA0161.10
MA0162.12.12712
MA0163.11.27382
MA0164.10.408402
MA0080.20.190316
MA0018.21.88337
MA0099.20.518072
MA0079.23.07806
MA0102.21.42135
MA0258.10.118033
MA0259.10.408856
MA0442.10
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