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MCL coexpression mm9:3070: Difference between revisions

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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_mean=-0

Latest revision as of 19:31, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr16:91931888..91931899,-p2@Atp5o
Mm9::chr9:50412012..50412057,+p1@Timm8b
Mm9::chr9:79607562..79607579,-p2@Cox7a2


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:0022891substrate-specific transmembrane transporter activity0.00250991568074336
GO:0015078hydrogen ion transmembrane transporter activity0.00250991568074336
GO:0015077monovalent inorganic cation transmembrane transporter activity0.00250991568074336
GO:0022857transmembrane transporter activity0.00250991568074336
GO:0022892substrate-specific transporter activity0.00250991568074336
GO:0005739mitochondrion0.00250991568074336
GO:0015399primary active transmembrane transporter activity0.00250991568074336
GO:0015405P-P-bond-hydrolysis-driven transmembrane transporter activity0.00250991568074336
GO:0022890inorganic cation transmembrane transporter activity0.00250991568074336
GO:0005743mitochondrial inner membrane0.0057225342407789
GO:0019866organelle inner membrane0.0057225342407789
GO:0031966mitochondrial membrane0.0057225342407789
GO:0005740mitochondrial envelope0.0057225342407789
GO:0042719mitochondrial intermembrane space protein transporter complex0.0057225342407789
GO:0007007inner mitochondrial membrane organization and biogenesis0.0057225342407789
GO:0045039protein import into mitochondrial inner membrane0.0057225342407789
GO:0043681protein import into mitochondrion0.0057225342407789
GO:0022804active transmembrane transporter activity0.00690195750783833
GO:0044429mitochondrial part0.00690195750783833
GO:0045261proton-transporting ATP synthase complex, catalytic core F(1)0.00729543162843668
GO:0006626protein targeting to mitochondrion0.00768195958890141
GO:0033178proton-transporting two-sector ATPase complex, catalytic domain0.00768195958890141
GO:0031975envelope0.00768195958890141
GO:0031967organelle envelope0.00768195958890141
GO:0006091generation of precursor metabolites and energy0.00876348180750257
GO:0005758mitochondrial intermembrane space0.0100713616879707
GO:0008324cation transmembrane transporter activity0.0100713616879707
GO:0022884macromolecule transmembrane transporter activity0.0105338042889815
GO:0015450P-P-bond-hydrolysis-driven protein transmembrane transporter activity0.0105338042889815
GO:0007006mitochondrial membrane organization and biogenesis0.0105338042889815
GO:0031090organelle membrane0.011469811440207
GO:0045259proton-transporting ATP synthase complex0.013083604919028
GO:0008320protein transmembrane transporter activity0.013083604919028
GO:0015075ion transmembrane transporter activity0.013083604919028
GO:0004129cytochrome-c oxidase activity0.013083604919028
GO:0031970organelle envelope lumen0.013083604919028
GO:0016676oxidoreductase activity, acting on heme group of donors, oxygen as acceptor0.013083604919028
GO:0015002heme-copper terminal oxidase activity0.013083604919028
GO:0016675oxidoreductase activity, acting on heme group of donors0.013083604919028
GO:0006839mitochondrial transport0.0133632354221828
GO:0008553hydrogen-exporting ATPase activity, phosphorylative mechanism0.014220953171138
GO:0005746mitochondrial respiratory chain0.016171419771992
GO:0044444cytoplasmic part0.016171419771992
GO:0015985energy coupled proton transport, down electrochemical gradient0.016729534515831
GO:0015986ATP synthesis coupled proton transport0.016729534515831
GO:0006754ATP biosynthetic process0.0179648478012853
GO:0006753nucleoside phosphate metabolic process0.0179648478012853
GO:0046933hydrogen ion transporting ATP synthase activity, rotational mechanism0.0179648478012853
GO:0016469proton-transporting two-sector ATPase complex0.0179648478012853
GO:0046961hydrogen ion transporting ATPase activity, rotational mechanism0.0179648478012853
GO:0046034ATP metabolic process0.0190375126296127
GO:0044455mitochondrial membrane part0.0198541431756748
GO:0009145purine nucleoside triphosphate biosynthetic process0.0198541431756748
GO:0009206purine ribonucleoside triphosphate biosynthetic process0.0198541431756748
GO:0009201ribonucleoside triphosphate biosynthetic process0.0198541431756748
GO:0019829cation-transporting ATPase activity0.0202814394360515
GO:0009142nucleoside triphosphate biosynthetic process0.0202814394360515
GO:0009205purine ribonucleoside triphosphate metabolic process0.0202814394360515
GO:0009199ribonucleoside triphosphate metabolic process0.0202814394360515
GO:0006119oxidative phosphorylation0.0202814394360515
GO:0009144purine nucleoside triphosphate metabolic process0.0202814394360515
GO:0015992proton transport0.0204644825670295
GO:0065002intracellular protein transport across a membrane0.0204644825670295
GO:0006752group transfer coenzyme metabolic process0.0204644825670295
GO:0009141nucleoside triphosphate metabolic process0.0208936356106975
GO:0009152purine ribonucleotide biosynthetic process0.020943364298783
GO:0006818hydrogen transport0.020991568887858
GO:0015662ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism0.0213937248210542
GO:0009260ribonucleotide biosynthetic process0.0214338896913356
GO:0009150purine ribonucleotide metabolic process0.0218509542515154
GO:0017038protein import0.0218509542515154
GO:0006164purine nucleotide biosynthetic process0.0218829475959845
GO:0007005mitochondrion organization and biogenesis0.022244838478027
GO:0009259ribonucleotide metabolic process0.0229230373481143
GO:0006163purine nucleotide metabolic process0.0239045732786988
GO:0042625ATPase activity, coupled to transmembrane movement of ions0.0258116144597875
GO:0009108coenzyme biosynthetic process0.0261025808848761
GO:0051188cofactor biosynthetic process0.0297826186884842
GO:0043492ATPase activity, coupled to movement of substances0.0346164408385876
GO:0042626ATPase activity, coupled to transmembrane movement of substances0.0346164408385876
GO:0016820hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances0.0346164408385876
GO:0009165nucleotide biosynthetic process0.0359511133638621
GO:0043234protein complex0.0367369378447161
GO:0009055electron carrier activity0.0390923774018828
GO:0008565protein transporter activity0.040605287285226
GO:0005737cytoplasm0.0424474218572633
GO:0006732coenzyme metabolic process0.044071881129752
GO:0009117nucleotide metabolic process0.0495398307059036



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)4.60e-1023
neuroblast (sensu Vertebrata)4.60e-1023
ectodermal cell4.67e-0844
neurectodermal cell4.67e-0844
neural cell5.72e-0843
non-terminally differentiated cell7.93e-0749

Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.29e-1554
structure with developmental contribution from neural crest2.96e-1592
central nervous system8.73e-1573
nervous system9.80e-1575
neural tube3.95e-1452
neural rod3.95e-1452
future spinal cord3.95e-1452
neural keel3.95e-1452
gray matter8.08e-1434
brain3.34e-1147
future brain3.34e-1147
brain grey matter3.65e-1129
regional part of telencephalon3.65e-1129
telencephalon3.65e-1129
regional part of brain5.14e-1146
neurectoderm1.82e-0964
neural plate1.82e-0964
presumptive neural plate1.82e-0964
anterior neural tube5.14e-0940
compound organ9.58e-0943
regional part of forebrain1.35e-0839
forebrain1.35e-0839
future forebrain1.35e-0839
cerebral cortex1.64e-0821
cerebral hemisphere1.64e-0821
pallium1.64e-0821
ectoderm-derived structure2.25e-0895
ectoderm2.25e-0895
presumptive ectoderm2.25e-0895
regional part of cerebral cortex1.29e-0717
primary circulatory organ1.41e-0718
heart1.41e-0718
primitive heart tube1.41e-0718
primary heart field1.41e-0718
anterior lateral plate mesoderm1.41e-0718
heart tube1.41e-0718
heart primordium1.41e-0718
cardiac mesoderm1.41e-0718
cardiogenic plate1.41e-0718
heart rudiment1.41e-0718
tube2.67e-07114
anatomical conduit6.85e-07122
occipital lobe8.90e-0710
visual cortex8.90e-0710
neocortex8.90e-0710
ecto-epithelium9.73e-0773


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)
MA0003.10.0699972
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.10.416365
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.11.49373
MA0029.11.20789
MA0030.11.21482
MA0031.11.17722
MA0038.10.963265
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.10.353763
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.190475
MA0056.10
MA0057.10.337566
MA0058.10.690848
MA0059.10.705317
MA0060.10.502699
MA0061.10.5406
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.343188
MA0069.12.89084
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.00834468
MA0074.10.911576
MA0076.12.67392
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.11.40099
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.10.62555
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.10.71579
MA0103.10.647985
MA0105.10.405648
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.10.537669
MA0115.11.38041
MA0116.10.602598
MA0117.11.34691
MA0119.10.716476
MA0122.11.36752
MA0124.11.57762
MA0125.11.5017
MA0130.10
MA0131.11.07881
MA0132.10
MA0133.10
MA0135.11.4152
MA0136.10.933582
MA0139.10.462282
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.11.33779
MA0145.10.292366
MA0146.10.151124
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.21.06145
MA0035.20.903829
MA0039.20.181475
MA0138.21.07027
MA0002.20.466067
MA0137.21.60348
MA0104.20.48458
MA0047.20.962424
MA0112.20.29236
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.10.312898
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.10.166722
MA0163.10.157796
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.20.00937321
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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