Similar to the bone marrow, the mammary gland contains a distinct population of Hoechst-effluxing side population cells, mammary gland side population cells (MG-SPs). To better characterize MG-SPs, their microarray gene profiles were compared to the remaining cells, which retain Hoechst dye (mammary gland non-side population cells [MG-NSPs]). For analysis, Gene Ontology (GO) that describes gene...

The present study aimed to investigate the genes and signaling pathways associated with squamous cell carcinoma (SCC) by bioinformatics analysis. For this purpose, the GSE2503 was downloaded from the Gene Expression Omnibus database, and the differentially expressed genes (DEGs) between 6 normal skin and 5 SCC samples were analyzed using the Linear Models for Microarray Data package. Gene Ontol...

BACKGROUND Literature mining of gene-gene interactions has been enhanced by ontology-based name classifications. However, in biomedical literature mining, interaction keywords have not been carefully studied and used beyond a collection of keywords. METHODS In this study, we report the development of a new Interaction Network Ontology (INO) that classifies >800 interaction keywords and incorp...

Objective Duchenne muscular dystrophy (DMD) is one of the mortal diseases, subjected to study in terms of molecular investigation. In this study, the protein interaction map of this muscle-wasting condition was generated to gain a better knowledge of interactome profile of DMD. Materials & Methods Applying Cytoscape and String Database, the protein-protein interaction network was constructed ...

Identifying genetic variants that affect drug response or play a role in disease is an important task for clinicians and researchers. Before individual variants can be explored efficiently for effect on drug response or disease relationships, specific candidate genes must be identified. While many methods rank candidate genes through the use of sequence features and network topology, only a few...

The molecular physiology underlying human milk production is largely unknown because of limitations in obtaining tissue samples. Determining gene expression in normal lactating women would be a potential step toward understanding why some women struggle with or fail at breastfeeding their infants. Recently, we demonstrated the utility of RNA obtained from breast milk fat globule (MFG) to detect...

In this paper, we used experimental ecology methods and third-generation transcriptome sequencing to see the differences in growth, development, reproduction of three strains Daphniopsis tibetana Sars, 1903 from different locations Tibet (Lake Namukacuo, NMKC; Lake Pengcuo, PC; Zigetangcuo, ZGTC). We also wanted determine if genes had changed after seawater-domesticated D. was reared a laborato...

Analyzing the function of gene sets is a critical step in interpreting the results of high-throughput experiments in systems biology. A variety of enrichment analysis tools have been developed in recent years, but most output a long list of significantly enriched terms that are often redundant, making it difficult to extract the most meaningful functions. In this paper, we present GOMA, a novel...

Sheath blight disease (ShB) is considered to be the second most important affecting rice, and genetic mechanism of ShB resistance in rice great complicated. Uncovering strong resistant varieties are premise for improvement. A genome-wide association study (GWAS) was performed using approximately five million SNPs within Ting’s core collection. “Early pradifice”, one typical japonica, determined...