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MCL coexpression mm9:413: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0016657;oxidoreductase activity, acting on NADH or NADPH, nitrogenous group as acceptor;0.030237461888318;66355!GO:0003920;GMP reductase activity;0.030237461888318;66355!GO:0007216;metabotropic glutamate receptor signaling pathway;0.0403055723210818;26556!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0010314!1.99e-14!92;UBERON:0000468!1.00e-09!333;UBERON:0010371!1.29e-09!73;UBERON:0002346!3.14e-09!64;UBERON:0003075!3.14e-09!64;UBERON:0007284!3.14e-09!64;UBERON:0003056!1.73e-08!49;UBERON:0004111!1.95e-08!122;UBERON:0000073!4.37e-08!54;UBERON:0002021!5.60e-08!10;UBERON:0000411!5.60e-08!10;UBERON:0001950!5.60e-08!10;UBERON:0000025!6.84e-08!114;UBERON:0001049!7.09e-08!52;UBERON:0005068!7.09e-08!52;UBERON:0006241!7.09e-08!52;UBERON:0007135!7.09e-08!52;UBERON:0000955!7.27e-08!47;UBERON:0006238!7.27e-08!47;UBERON:0004121!1.44e-07!95;UBERON:0000924!1.44e-07!95;UBERON:0006601!1.44e-07!95;UBERON:0003528!1.51e-07!29;UBERON:0002791!1.51e-07!29;UBERON:0001893!1.51e-07!29;UBERON:0002020!1.70e-07!34;UBERON:0002616!1.98e-07!46;UBERON:0007100!4.25e-07!18;UBERON:0000948!4.25e-07!18;UBERON:0005498!4.25e-07!18;UBERON:0004140!4.25e-07!18;UBERON:0009881!4.25e-07!18;UBERON:0004141!4.25e-07!18;UBERON:0003084!4.25e-07!18;UBERON:0007005!4.25e-07!18;UBERON:0004139!4.25e-07!18;UBERON:0004291!4.25e-07!18;UBERON:0003080!7.99e-07!40;UBERON:0000479!9.11e-07!349
}}

Latest revision as of 15:15, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:13737752..13737775,+p@chr10:13737752..13737775
+
Mm9::chr11:3995347..3995443,-p1@Mtfp1
Mm9::chr13:45634175..45634208,+p5@Gmpr
Mm9::chr13:46513635..46513685,+p2@Rbm24
Mm9::chr13:46514389..46514406,+p@chr13:46514389..46514406
+
Mm9::chr13:46597418..46597476,+p2@Cap2
Mm9::chr13:46597482..46597509,+p3@Cap2
Mm9::chr13:46597510..46597556,+p1@Cap2
Mm9::chr13:46733595..46733599,+p@chr13:46733595..46733599
+
Mm9::chr13:94074021..94074093,+p1@Homer1
Mm9::chr14:55594201..55594242,-p@chr14:55594201..55594242
-
Mm9::chr17:8476281..8476306,+p2@Brp44l
p2@LOC100503245
Mm9::chr1:136852485..136852532,-p2@Ppp1r12b
Mm9::chr2:120070893..120070982,-p1@Pla2g4e
Mm9::chr7:19918416..19918447,+p@chr7:19918416..19918447
+
Mm9::chrX:80205901..80205930,+p@chrX:80205901..80205930
+
Mm9::chrX:80314745..80314748,+p@chrX:80314745..80314748
+
Mm9::chrX:80333138..80333139,+p@chrX:80333138..80333139
+


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:0016657oxidoreductase activity, acting on NADH or NADPH, nitrogenous group as acceptor0.030237461888318
GO:0003920GMP reductase activity0.030237461888318
GO:0007216metabotropic glutamate receptor signaling pathway0.0403055723210818



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>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
structure with developmental contribution from neural crest1.99e-1492
multi-cellular organism1.00e-09333
ecto-epithelium1.29e-0973
neurectoderm3.14e-0964
neural plate3.14e-0964
presumptive neural plate3.14e-0964
pre-chordal neural plate1.73e-0849
anatomical conduit1.95e-08122
regional part of nervous system4.37e-0854
occipital lobe5.60e-0810
visual cortex5.60e-0810
neocortex5.60e-0810
tube6.84e-08114
neural tube7.09e-0852
neural rod7.09e-0852
future spinal cord7.09e-0852
neural keel7.09e-0852
brain7.27e-0847
future brain7.27e-0847
ectoderm-derived structure1.44e-0795
ectoderm1.44e-0795
presumptive ectoderm1.44e-0795
brain grey matter1.51e-0729
regional part of telencephalon1.51e-0729
telencephalon1.51e-0729
gray matter1.70e-0734
regional part of brain1.98e-0746
primary circulatory organ4.25e-0718
heart4.25e-0718
primitive heart tube4.25e-0718
primary heart field4.25e-0718
anterior lateral plate mesoderm4.25e-0718
heart tube4.25e-0718
heart primordium4.25e-0718
cardiac mesoderm4.25e-0718
cardiogenic plate4.25e-0718
heart rudiment4.25e-0718
anterior neural tube7.99e-0740
tissue9.11e-07349


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)
MA0003.12.45436
MA0004.10.191582
MA0006.10.289293
MA0007.10.181021
MA0009.10.5557
MA0014.11.20392
MA0017.10.0999826
MA0019.10.394308
MA0024.10.516087
MA0025.11.82115
MA0027.12.16618
MA0028.11.05513
MA0029.11.24219
MA0030.10.502474
MA0031.10.470779
MA0038.10.301835
MA0040.10.567108
MA0041.10.433432
MA0042.10.412259
MA0043.10.644695
MA0046.10.58854
MA0048.10.842786
MA0050.10.219748
MA0051.10.309072
MA0052.12.40508
MA0055.10.12934
MA0056.10
MA0057.12.31972
MA0058.10.127732
MA0059.10.13543
MA0060.10.0476793
MA0061.10.218812
MA0063.10
MA0066.10.293002
MA0067.10.879099
MA0068.10.153549
MA0069.10.574784
MA0070.10.565924
MA0071.10.219128
MA0072.10.558195
MA0073.11.05676
MA0074.10.264633
MA0076.11.19166
MA0077.10.538513
MA0078.10.336143
MA0081.10.150322
MA0083.11.55326
MA0084.11.1979
MA0087.10.604077
MA0088.10.336188
MA0089.10
MA0090.10.167748
MA0091.11.10231
MA0092.10.502322
MA0093.10.316906
MA0095.10
MA0098.10
MA0100.10.255651
MA0101.10.141127
MA0103.10.345124
MA0105.10.0968542
MA0106.10.342589
MA0107.10.102611
MA0108.20.413973
MA0109.10
MA0111.10.177475
MA0113.10.319332
MA0114.10.815722
MA0115.10.647296
MA0116.10.08535
MA0117.10.617392
MA0119.10.141504
MA0122.10.635764
MA0124.10.828115
MA0125.10.757653
MA0130.10
MA0131.10.390422
MA0132.10
MA0133.10
MA0135.10.67864
MA0136.10.280269
MA0139.10.94327
MA0140.11.31082
MA0141.10.11774
MA0142.10.457961
MA0143.10.332773
MA0144.10.478562
MA0145.12.79398
MA0146.10.343991
MA0147.10.236435
MA0148.10.203219
MA0149.10.144679
MA0062.20.471565
MA0035.21.32437
MA0039.20.689349
MA0138.20.383644
MA0002.20.0367869
MA0137.20.371067
MA0104.20.371038
MA0047.20.301217
MA0112.20.84781
MA0065.21.90626
MA0150.10.180943
MA0151.10
MA0152.10.301303
MA0153.10.694211
MA0154.10.548533
MA0155.10.246884
MA0156.10.722377
MA0157.10.429861
MA0158.10
MA0159.10.0715631
MA0160.10.205397
MA0161.10
MA0162.12.31997
MA0163.10.96608
MA0164.10.280556
MA0080.20.103116
MA0018.20.288261
MA0099.20.37828
MA0079.25.60982
MA0102.21.24942
MA0258.11.64291
MA0259.10.482458
MA0442.10
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