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MCL coexpression mm9:240: Difference between revisions

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{{MCL_coexpression_mm9
{
|coexpression_dpi_cluster_scores_mean=-0

Latest revision as of 14:57, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:126602174..126602281,+p1@B4galnt1
Mm9::chr11:20641583..20641625,-p2@Aftph
Mm9::chr11:55017821..55017888,+p1@Slc36a1
Mm9::chr11:62094959..62094997,+p1@Ttc19
Mm9::chr11:74537807..74537831,-p2@Pafah1b1
Mm9::chr11:75401566..75401653,+p1@Pitpna
Mm9::chr12:101437729..101437748,+p1@Calm1
p1@Calm2
p1@Calm3
Mm9::chr12:4038774..4038855,-p1@Efr3b
Mm9::chr14:105657929..105657975,+p1@Ndfip2
Mm9::chr14:22569764..22569830,+p1@Samd8
Mm9::chr14:32019968..32020001,-p2@Nisch
Mm9::chr14:34260306..34260319,-p2@Mapk8
Mm9::chr17:26551765..26551840,+p1@Neurl1b
Mm9::chr18:20904728..20904740,-p4@B4galt6
Mm9::chr18:20904768..20904834,-p2@B4galt6
Mm9::chr18:20904835..20904895,-p1@B4galt6
Mm9::chr1:192735607..192735681,-p1@Rps6kc1
Mm9::chr1:34906782..34906792,+p2@Plekhb2
Mm9::chr1:87689986..87690092,+p1@Cab39
Mm9::chr4:154975963..154976049,+p1@Slc35e2
Mm9::chr5:124545743..124545754,-p3@Abcb9
Mm9::chr5:124545758..124545829,-p1@Abcb9
Mm9::chr5:139801397..139801442,-p3@Adap1
Mm9::chr5:139801444..139801522,-p1@Adap1
Mm9::chr5:139801711..139801722,-p6@Adap1
Mm9::chr5:144861222..144861252,+p1@Lmtk2
Mm9::chr5:144861256..144861265,+p2@Lmtk2
Mm9::chr7:107756174..107756337,+p1@Rab6a
Mm9::chr7:125849222..125849300,-p1@Gde1
Mm9::chr7:134119793..134119811,+p6@Cdipt
Mm9::chr7:17613202..17613270,-p2@Ppp5c
Mm9::chr7:26022759..26022847,-p1@Gsk3a
Mm9::chr8:88364776..88364856,-p1@Itfg1
Mm9::chr9:44128312..44128373,-p1@C2cd2l
Mm9::chr9:64101375..64101421,-p1@Map2k1


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:0030148sphingolipid biosynthetic process0.000275570624844799
GO:0046467membrane lipid biosynthetic process0.000325801728708788
GO:0006665sphingolipid metabolic process0.00226674747335891
GO:0006643membrane lipid metabolic process0.00308518386545464
GO:0005737cytoplasm0.00368528854038752
GO:0004674protein serine/threonine kinase activity0.0081145539147967
GO:0008610lipid biosynthetic process0.00994169698327652
GO:0006793phosphorus metabolic process0.0127269923622035
GO:0006796phosphate metabolic process0.0127269923622035
GO:0030145manganese ion binding0.0188146851278551
GO:0004672protein kinase activity0.0188146851278551
GO:0006629lipid metabolic process0.019674405790246
GO:0006468protein amino acid phosphorylation0.019674405790246
GO:0016740transferase activity0.0208809496858233
GO:0016772transferase activity, transferring phosphorus-containing groups0.0220511696707391
GO:0016773phosphotransferase activity, alcohol group as acceptor0.0220511696707391
GO:0016310phosphorylation0.0220511696707391
GO:0003881CDP-diacylglycerol-inositol 3-phosphatidyltransferase activity0.0220511696707391
GO:0003947(N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase activity0.0220511696707391
GO:0047395glycerophosphoinositol glycerophosphodiesterase activity0.0220511696707391
GO:0043412biopolymer modification0.0293661340611442
GO:0008654phospholipid biosynthetic process0.0293661340611442
GO:0015824proline transport0.0293661340611442
GO:0015808L-alanine transport0.0293661340611442
GO:0015180L-alanine transmembrane transporter activity0.0293661340611442
GO:0007258JUN phosphorylation0.0293661340611442
GO:0022858alanine transmembrane transporter activity0.0293661340611442
GO:0050321tau-protein kinase activity0.0293661340611442
GO:0043489RNA stabilization0.0293661340611442
GO:0048255mRNA stabilization0.0293661340611442
GO:0044255cellular lipid metabolic process0.0293661340611442
GO:0005524ATP binding0.0293661340611442
GO:0016301kinase activity0.0293661340611442
GO:0043687post-translational protein modification0.0293661340611442
GO:0032559adenyl ribonucleotide binding0.0293661340611442
GO:0032328alanine transport0.0293661340611442
GO:0001574ganglioside biosynthetic process0.0293661340611442
GO:0015193L-proline transmembrane transporter activity0.0293661340611442
GO:0015187glycine transmembrane transporter activity0.0293661340611442
GO:0005280hydrogen:amino acid symporter activity0.0293661340611442
GO:0015816glycine transport0.0293661340611442
GO:0004705JUN kinase activity0.0293661340611442
GO:0001675acrosome formation0.0293661340611442
GO:0006686sphingomyelin biosynthetic process0.0293661340611442
GO:0008090retrograde axon cargo transport0.0293661340611442
GO:0005794Golgi apparatus0.0342754849664895
GO:0016477cell migration0.0342754849664895
GO:0030554adenyl nucleotide binding0.0342754849664895
GO:0015295solute:hydrogen symporter activity0.0352181300262588
GO:0030259lipid glycosylation0.0352181300262588
GO:0047496vesicle transport along microtubule0.0407371706749331
GO:0016909SAP kinase activity0.0407371706749331
GO:0043388positive regulation of DNA binding0.0407371706749331
GO:0006688glycosphingolipid biosynthetic process0.0407371706749331
GO:0048699generation of neurons0.042577059280297
GO:0006464protein modification process0.042577059280297
GO:0004708MAP kinase kinase activity0.042577059280297
GO:0015804neutral amino acid transport0.042577059280297
GO:0017169CDP-alcohol phosphatidyltransferase activity0.042577059280297
GO:0048011nerve growth factor receptor signaling pathway0.042577059280297
GO:0006928cell motility0.042577059280297
GO:0051674localization of cell0.042577059280297
GO:0022008neurogenesis0.044945394224751
GO:0051099positive regulation of binding0.044945394224751
GO:0018210peptidyl-threonine modification0.044945394224751
GO:0018107peptidyl-threonine phosphorylation0.044945394224751
GO:0006684sphingomyelin metabolic process0.044945394224751
GO:0015198oligopeptide transporter activity0.044945394224751
GO:0044444cytoplasmic part0.044945394224751
GO:0006644phospholipid metabolic process0.0462281175578805
GO:0001573ganglioside metabolic process0.0462281175578805
GO:0015197peptide transporter activity0.0462281175578805
GO:0006857oligopeptide transport0.0462281175578805
GO:0009247glycolipid biosynthetic process0.0462281175578805
GO:0004712protein serine/threonine/tyrosine kinase activity0.0462281175578805
GO:0008889glycerophosphodiester phosphodiesterase activity0.0462281175578805
GO:0032553ribonucleotide binding0.0482456793523307
GO:0032555purine ribonucleotide binding0.0482456793523307
GO:0005416cation:amino acid symporter activity0.0493765590700311
GO:0015175neutral amino acid transmembrane transporter activity0.0493765590700311



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)1.41e-0923
neuroblast (sensu Vertebrata)1.41e-0923

Uber Anatomy
Ontology termp-valuen
regional part of nervous system5.77e-1754
neural tube9.63e-1652
neural rod9.63e-1652
future spinal cord9.63e-1652
neural keel9.63e-1652
nervous system1.19e-1575
gray matter1.55e-1534
central nervous system2.93e-1573
ectoderm-derived structure1.12e-1495
ectoderm1.12e-1495
presumptive ectoderm1.12e-1495
brain1.42e-1347
future brain1.42e-1347
brain grey matter2.35e-1329
regional part of telencephalon2.35e-1329
telencephalon2.35e-1329
regional part of brain4.68e-1346
neurectoderm8.32e-1364
neural plate8.32e-1364
presumptive neural plate8.32e-1364
ecto-epithelium2.93e-1273
anterior neural tube1.52e-1140
regional part of forebrain4.98e-1139
forebrain4.98e-1139
future forebrain4.98e-1139
cerebral cortex8.98e-1021
cerebral hemisphere8.98e-1021
pallium8.98e-1021
pre-chordal neural plate1.42e-0949
adult organism5.62e-0951
regional part of cerebral cortex9.83e-0917
occipital lobe8.60e-0810
visual cortex8.60e-0810
neocortex8.60e-0810
intestine8.66e-0831
structure with developmental contribution from neural crest3.65e-0792


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)
MA0003.18.87099
MA0004.10.842581
MA0006.10.909674
MA0007.10.208642
MA0009.10.328429
MA0014.17.69112
MA0017.10.226589
MA0019.10.198145
MA0024.10.295217
MA0025.10.520387
MA0027.11.87879
MA0028.11.74676
MA0029.10.27914
MA0030.10.283968
MA0031.10.258132
MA0038.10.131209
MA0040.10.338117
MA0041.10.0370907
MA0042.10.0333732
MA0043.10.405289
MA0046.10.356455
MA0048.11.33931
MA0050.10.270889
MA0051.10.13618
MA0052.10.344399
MA0055.10.179681
MA0056.10
MA0057.10.724994
MA0058.10.557854
MA0059.10.139654
MA0060.11.82621
MA0061.11.69289
MA0063.10
MA0066.10.125212
MA0067.10.61835
MA0068.10.756783
MA0069.10.344664
MA0070.10.337108
MA0071.10.269872
MA0072.10.330543
MA0073.10.0979954
MA0074.10.704165
MA0076.12.00831
MA0077.10.313935
MA0078.10.470801
MA0081.10.368949
MA0083.11.0438
MA0084.10.922325
MA0087.10.369857
MA0088.11.78346
MA0089.10
MA0090.10.419299
MA0091.10.0680529
MA0092.10.188341
MA0093.10.675465
MA0095.10
MA0098.10
MA0100.10.330817
MA0101.10.147962
MA0103.10.243664
MA0105.10.634302
MA0106.11.49634
MA0107.10.233864
MA0108.20.213222
MA0109.10
MA0111.10.203092
MA0113.10.143312
MA0114.10.247529
MA0115.10.407576
MA0116.12.61112
MA0117.11.76066
MA0119.10.969343
MA0122.10.397452
MA0124.10.571
MA0125.10.506387
MA0130.10
MA0131.11.69924
MA0132.10
MA0133.10
MA0135.10.435302
MA0136.10.116708
MA0139.11.90122
MA0140.10.100709
MA0141.10.276137
MA0142.10.247834
MA0143.10.152801
MA0144.10.0433959
MA0145.11.09324
MA0146.19.64835
MA0147.10.480974
MA0148.10.0693066
MA0149.10.0391014
MA0062.21.50171
MA0035.20.103023
MA0039.29.03566
MA0138.20.19008
MA0002.20.143884
MA0137.20.0266693
MA0104.21.33101
MA0047.20.130787
MA0112.21.93547
MA0065.20.0780766
MA0150.10.208519
MA0151.10
MA0152.10.130846
MA0153.10.449181
MA0154.12.30282
MA0155.12.55044
MA0156.10.255756
MA0157.10.225588
MA0158.10
MA0159.11.88787
MA0160.10.247499
MA0161.10
MA0162.15.80592
MA0163.12.63771
MA0164.10.116897
MA0080.20.0946724
MA0018.20.77438
MA0099.20.186055
MA0079.24.53005
MA0102.20.972341
MA0258.10.611276
MA0259.11.3264
MA0442.10
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