Categorical data analysis becomes challenging when high-dimensional sparse covariates are involved, which is often the case for omics data. We introduce a statistical procedure based on multinomial logistic regression such scenarios, including variable screening, model selection, order selection response categories, and selection. perform our gene expression with 801 patients, 2426 genes, five ...

Helicobacter pylori establishes a chronic infection in the human stomach, causing gastritis, peptic ulcer, or gastric cancer, and more severe diseases are associated with virulence genes such as the cag pathogenicity island (PAI). The aim of this work was to study gene content differences among H. pylori strains isolated from patients with different gastroduodenal diseases in a Mexican-Mestizo ...

The immune system has evolved specific mechanisms to combat a potentially limitless number of foreign pathogens using a limited arsenal of Ig genes. To diversify the coding potential of the Ig genes, B cells undergo several processes of regulated genetic alterations. Early in their development, B cells in the bone marrow undergo V(D)J recombination to juxtapose variable region V, D, and J segme...

Although the variation of V-1 antigens of Mycoplasma pulmonis has been correlated with variable expression of the cytadherence properties of this organism and has been implicated as a virulence determining factor in M. pulmonis-induced murine respiratory disease, the precise function of these antigens remains unknown. We have cloned and characterized genes encoding V-1 from two M. pulmonis UAB ...

Abstract Pair-wise co-mutation networks of the mitochondrial genome have already provided ample evidences about roles genetic interactions in manifestation phenotype under altered environmental conditions. Here, we present a method to construct and analyze higher-order interactions, namely, three-uniform hypergraphs for different altitude populations decipher role co-mutating variable sites bey...

Phase variation is a common mechanism used by pathogenic bacteria to generate intra-strain diversity that is important in niche adaptation and is strongly associated with virulence determinants. Previous analyses of the complete sequences of the Helicobacter pylori strains 26695 and J99 have identified 36 putative phase-variable genes among the two genomes through their association with homopol...

The 185/333 gene family is highly expressed in two subsets of immune cells in the purple sea urchin in response to immune challenges. The genes encode a surprisingly diverse set of transcripts, which is a function of the variable presence or absence of blocks of shared sequences, known as elements that generate element patterns. Diversity is also the result of a significant level of point mutat...

There is often a need to predict the impact of alterations in one variable on another variable. This is especially the case in cancer research, where much effort has been made to carry out large-scale gene expression screening by microarray techniques. However, the causes of this variability from one cancer to another and from one gene to another often remain unknown. In this study we present a...

The important role of Hox genes in determining the regionalization of the body plan of the vertebrates makes them invaluable candidates for evolutionary analyses regarding functional and morphological innovation. Gene duplication and gene loss led to a variable number of Hox genes in different vertebrate lineages. The evolutionary forces determining the conservation or loss of Hox genes are poo...