A collaborative network analysis for the interpretation of transcriptomics data in Huntington's disease.

Rare diseases may affect the quality of life of patients and be life-threatening. Therapeutic opportunities are often limited, in part because of the lack of understanding of the molecular mechanisms underlying these diseases. This can be ascribed to the low prevalence of rare diseases and therefore the lower sample sizes available for research.

orsum: a Python package for filtering and comparing enrichment analyses using a simple principle.

Background: Enrichment analyses are widely applied to investigate lists of genes of interest. However, such analyses often result in long lists of annotation terms with high redundancy, making the interpretation and reporting difficult. Long annotation lists and redundancy also complicate the comparison of results obtained from different enrichment analyses.

A multi-objective genetic algorithm to find active modules in multiplex biological networks.

The identification of subnetworks of interest-or active modules-by integrating biological networks with molecular profiles is a key resource to inform on the processes perturbed in different cellular conditions. We here propose MOGAMUN, a Multi-Objective Genetic Algorithm to identify active modules in MUltiplex biological Networks. MOGAMUN optimizes both the density of interactions and the scores of the nodes (e.

A reference genome for pea provides insight into legume genome evolution.

We report the first annotated chromosome-level reference genome assembly for pea, Gregor Mendel's original genetic model. Phylogenetics and paleogenomics show genomic rearrangements across legumes and suggest a major role for repetitive elements in pea genome evolution. Compared to other sequenced Leguminosae genomes, the pea genome shows intense gene dynamics, most likely associated with genome size expansion when the Fabeae diverged from its sister tribes.

Transcriptional Reprogramming of Pea Leaves at Early Reproductive Stages.

Pea ( L.) is an important source of dietary proteins. Nutrient recycling from leaves contributes to the accumulation of seed proteins and is a pivotal determinant of protein yields in this grain legume.

Water stress combined with sulfur deficiency in pea affects yield components but mitigates the effect of deficiency on seed globulin composition.

Water stress and sulfur (S) deficiency are two constraints increasingly faced by crops due to climate change and low-input agricultural practices. To investigate their interaction in the grain legume pea (Pisum sativum), sulfate was depleted at the mid-vegetative stage and a moderate 9-d water stress period was imposed during the early reproductive phase. The combination of the stresses impeded reproductive processes in a synergistic manner, reducing seed weight and seed number, and inducing seed abortion, which highlighted the paramount importance of sulfur for maintaining seed yield components under water stress.

The loss of adipokine genes in the chicken genome and implications for insulin metabolism.

Gene loss is one of the main drivers in the evolution of genomes and species. The demonstration that a gene has been lost by pseudogenization is truly complete when one finds the pseudogene in the orthologous genomic region with respect to active genes in other species. In some cases, the identification of such orthologous loci is not possible because of chromosomal rearrangements or if the gene of interest has not yet been sequenced.