Regulatory mechanism and functional analysis of S100A9 in acute promyelocytic leukemia cells.

S100A9, a calcium-binding protein, participates in the inflammatory process and development of various tumors, thus attracting much attention in the field of cancer biology. This study aimed to investigate the regulatory mechanism of S100A9 and its function involvement in APL. We used real-time quantitative PCR to determine whether PML/RARα affects the expression of S100A9 in NB4 and PR9 cells upon ATRA treatment.

CNVD: text mining-based copy number variation in disease database.

Copy number variation (CNV) is a kind of chromosomal structural reorganization that has been detected, in this decade, mainly by high-throughput biological technology. Researchers have found that CNVs are ubiquitous in many species and accumulating evidence indicates that CNVs are closely related with complex diseases. The investigation of chromosomal structural alterations has begun to reveal some important clues to the pathologic causes of diseases and to the disease process.

Calculating phenotypic similarity between genes using hierarchical structure data based on semantic similarity.

Phenotypic similarity is correlated with a number of measures of gene function, such as relatedness at the level of direct protein-protein interaction. The phenotypic effect of a deleted or mutated gene, which is one part of gene annotation, has caught broad attention. However, there have been few measures to study phenotypic similarity with the data from Human Phenotype Ontology (HPO) database, therefore more analogous measures should be developed and investigated.

Analysis of functional and pathway association of differential co-expressed genes: a case study in drug addiction.

Drug addiction has been considered as a kind of chronic relapsing brain disease influenced by both genetic and environmental factors. At present, many causative genes and pathways related to diverse kinds of drug addiction have been discovered, while less attention has been paid to common mechanisms shared by different drugs underlying addiction. By applying a co-expression meta-analysis method to mRNA expression profiles of alcohol, cocaine, heroin addicted and normal samples, we identified significant gene co-expression pairs.

The application of gene co-expression network reconstruction based on CNVs and gene expression microarray data in breast cancer.

Copy number variations (CNVs) are one type of the human genetic variations and are pervasive in the human genome. It has been confirmed that they can play a causal role in complex diseases. Previous studies of CNVs focused more on identifying the disease-specific CNV regions or candidate genes on these CNV regions, but less on the synergistic actions between genes on CNV regions and other genes.

Prediction of human protein-protein interaction by a mixed Bayesian model and its application to exploring underlying cancer-related pathway crosstalk.

Protein-protein interaction (PPI) prediction method has provided an opportunity for elucidating potential biological processes and disease mechanisms. We integrated eight features involving proteomic, genomic, phenotype and functional annotation datasets by a mixed model consisting of full connected Bayesian (FCB) model and naive Bayesian model to predict human PPIs, resulting in 40 447 PPIs which contain 2740 common PPIs with the human protein reference database (HPRD) by a likelihood ratio cutoff of 512. Then we applied them to exploring underlying pathway crosstalk where pathways were derived from the pathway interaction database.