Obayashi T, Kodate S, Hibara H, Kagaya Y, Kinoshita K.(2023)COXPRESdb v8: an animal gene coexpression database navigating from a global view to detailed investigations.Nucleic Acids Res.in printing
Previous references of COXPRESdb
Obayashi T, Kagaya Y, Aoki Y, Tadaka S, Kinoshita K.(2019)COXPRESdb v7: a gene coexpression database for 11 animal species supported by 23 coexpression platforms for technical evaluation and evolutionary inference.Nucleic Acids Res.47: D55-D62
Okamura Y, Aoki Y, Obayashi T, Tadaka S, Ito S, Narise T, Kinoshita K.(2015)COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems.Nucleic Acids Res.43, D82-6
Obayashi T, Okamura Y, Ito S, Tadaka S, Motoike IN, Kinoshita K.(2013)COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals.Nucleic Acids Res.41, D1014-20
Obayashi T, Kinoshita K.(2011)COXPRESdb: a database to compare gene coexpression in seven model animals.Nucleic Acids Res.39, D1016-22
Obayashi T, Hayashi S, Shibaoka M, Saeki M, Ohta H, Kinoshita K.(2008)COXPRESdb: a database of coexpressed gene networks in mammals.Nucleic Acids Res.36, D77-D82.
Technical papers to construct COXPRESdb;
<MR>Obayashi T, Kinoshita K.(2009)Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression.DNA Res.,16, 249-60.
<Coex stability>Kinoshita K, Obayashi T.(2009)Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis.Bioinformatics.25, 2677-84.
Sallam T et al.(2016)Feedback modulation of cholesterol metabolism by the lipid-responsive non-coding RNA LeXis.Nature
Satoh J et al.(2014)PLD3 is accumulated on neuritic plaques in Alzheimer's disease brains.Alzheimers Res Ther
Bornholdt J et al.(2011)The level of claudin-7 is reduced as an early event in colorectal carcinogenesis.BMC Cancer
Analysis of omics data
Zhu W et al.(2011)Proteins and an inflammatory network expressed in colon tumors.J Proteome Res
Luchtefeld M et al.(2011)Gp130-dependent release of acute phase proteins is linked to the activation of innate immune signaling pathways.PLoS One
Databases/Tools using the coexpression data in COXPRESdb
Ozerov IV et al.(2016)In silico Pathway Activation Network Decomposition Analysis (iPANDA) as a method for biomarker development.Nat Commun
Sakurai N et al.(2011)KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data.Nucleic Acids Res
Patil A et al.(2011)HitPredict: a database of quality assessed protein-protein interactions in nine species.Nucleic Acids Res
Bioinformatic analysis
McShane E et al.(2016)Kinetic Analysis of Protein Stability Reveals Age-Dependent Degradation.Cell
Chen YQ et al.(2010)Sorting out inherent features of head-to-head gene pairs by evolutionary conservation.BMC Bioinformatics.
Other usages
Vos MJ et al.(2009)HSPB7 is a SC35 speckle resident small heat shock protein.Biochim Biophys Acta.
Vicinanza M et al.(2008)Function and dysfunction of the PI system in membrane trafficking.EMBO J.
