fusca. Gene family-based pangenome of North American Malus identified 60,211 orthogroups containing 340,087 genes. Genes involved in basic cellular and metabolic processes, growth, and development were core to the existence of these species, whereas genes involved in secondary metabolism, stress ...
The microbial pan-genome. Curr. Opin. Genet. Dev. 15, 589–594 (2005). CAS PubMed Google Scholar Blankenship, R. E. & Hartman, H. The origin and evolution of oxygenic photosynthesis. Trends Biochem. Sci. 23, 94–97 (1998). CAS PubMed Google Scholar Ondov, B. D., Bergman, N...
Microbial strains of variable functional capacities coexist in microbiomes. Current bioinformatics methods of strain analysis cannot provide the direct linkage between strain composition and their gene contents from metagenomic data. Here we present Strain-level Pangenome Decomposition Analysis (StrainPanDA),...
Neuroticism is a personality trait, which is an important risk factor for psychiatric disorders. Recent genome-wide studies reported about 600 genes potentially influencing neuroticism. Little is known about the mechanisms of their action. Here, we aimed
From the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, we gathered BLCA patient data, which was classified into distinct subgroups using non-negative matrix factorization (NMF). Survival and pathway analyses were conducted between these clusters. The PMRGs model, created ...
Furthermore, core gene sets based on pan-genome have been defined for phylogenetic analysis within different taxo- nomic ranks, particularly from species to family [8]. However, the considerable bioinformatics skills needed in analyzing a large volume of genomic data and the complex formats of ...
Xiao P, Chen Y, Jiang H, Liu YZ, Pan F, Yang TL, Tang ZH, Larsen JA, Lappe JM, Recker RR, Deng HW (2008) In vivo genome-wide expression study on human circulating B cells suggests a novel ESR1 and MAPK3 network for postmenopausal osteoporosis. J Bone Miner Res 23(5):644–654...
Recurrently mutated genes derived from pan-cancer The Cancer Genome Atlas datasets were recognized as well-known tumor suppressors genes (TSGs) or oncogenes. Total 49 orthologs of human TSGs were found in mouse genome, and the mouse TSG library containing 280 sgRNAs targeting 56 different genes ...
Draft genome sequence of 14Acanthamoebaspecies The draft genome sequences of 14Acanthamoebaspecies publicly available on the NCBI website (http://www.ncbi.nlm.nih.gov/bioproject/; accession: PRJEB7687; Supplementary TableS1) were downloaded. They were part of the project «Phylogenomics ofAcanthamo...
The Cancer Genome Atlas GEO: Gene Expression Omnibus WGCNA: Weighted correlation network analysis RF: Random Forest PPI: Protein–protein interaction ROC: Receiver operating characteristic curve DCA: Decision curve analysis DGE: Differential gene expression ...