Reconstructing gene networks frommicro-array data can provide information on the mechanisms that govern cellular processes. Numerous studies have been devoted to addressing this problem. A popular method is to view the gene network as a Bayesian inference network, and to apply structure learning methods to determine the topology of the gene network. There are, however, several shortcomings with...

The advent of high-throughput measurements of gene expression and bioinformatics analysis methods offers new ways to study gene expression patterns. The primary goal of this study was to determine the time sequence for gene expression in a bone subjected to mechanical loading during key periods of the bone-formation process, including expression of matrix-related genes, the appearance of active...

A transcriptional regulatory network (TRN) constitutes the collection of regulatory rules that link environmental cues to the transcription state of a cell's genome. We recently proposed a matrix formalism that quantitatively represents a system of such rules (a transcriptional regulatory system [TRS]) and allows systemic characterization of TRS properties. The matrix formalism not only allows ...

more than 185 species, strains and unclassified theileria parasites are categorized in the entrez taxonomy. the accurate diagnosis and proper identification of the causative agents are important for understanding the epidemiology, prevention and appropriate treatment. this study aims to discuss the importance of two genes of theileria annulata 18s ribosomal rna (18s rrna) and theileria annulata...

Matrix metalloproteinases (MMPs) are implicated in the degradation of extracellular matrix (ECM). Rheumatoid arthritis (RA) synovial fibroblasts (SFs) produce matrix-degrading enzymes, including MMPs, which facilitate cartilage destruction in the affected joints in RA. Epigenetic mechanisms contribute to change in the chromatin state, resulting in an alteration of gene transcription. Recently, ...

Abstract Background RNA-seq data are increasingly used to derive prognostic signatures for cancer outcome prediction. A limitation of current predictors is their reliance on reference gene annotations, which amounts ignoring large numbers non-canonical RNAs produced in disease tissues. recently introduced kind transcriptome classifier operates entirely a reference-free manner, relying k-mers ex...

Abstract Evidence suggests that shared pathophysiological mechanisms in neuropsychiatric disorders (NPDs) may contribute to risk and resilience. We used single-gene network-level transcriptomic approaches investigate disorder-specific processes underlying posttraumatic stress disorder (PTSD), Parkinson’s disease (PD) schizophrenia a South African sample. RNA-seq was performed on blood obtained ...

Motivation: The investigation of topological modifications of the gene interaction networks in cancer cells is essential for understanding the desease. We study gene interaction networks in various human cancer cells with the random matrix theory. This study is based on the Cancer Network Galaxy (TCNG) database which is the repository of huge gene interactions inferred by Bayesian network algor...

schimke immuno-osseous dysplasia is a rare autosomal recessive multisystem disorder characterized by steroid-resistant nephrotic syndrome, immunodeficiency, and spondyloepiphy-seal dysplasia. mutations in swi/snf2 related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1 (smarcal1) gene are responsible for the disease. the present report describes, for the first tim...