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The development of heart failure (HF) is a complex process that can be initiated by multiple etiologies. Identifying common functional modules associated with HF is a challenging task. Here, we developed a systems method to identify these common functional modules by integrating multiple expression profiles, protein interactions from four species, gene function annotations, and text information. We...
Transcription factors (TFs) bind to specific DNA regions, although their binding specificities cannot account for their cell type-specific functions. It has been shown in well-studied systems that TFs combine with co-factors into transcriptional regulatory modules (TRMs), which endow them with cell type-specific functions and additional modes of regulation. Therefore, the prediction of TRMs can provide...
The neutrophil myeloperoxidase (MPO) promotes the oxidative stress by the production of active chlorinated molecules. The aim of this study was to investigate the association between MPO promoter polymorphic variants (rs2243827 and rs2333227) and, its serum level in patients with the stenosis of coronary arteries. Furthermore, a system approach was applied to create the MPO transcription factor network...
Staphylococcus aureus (S. aureus) is an emerging concern in hospital settings as it causes serious human infections. The multidrug resistance (MDR) in S. aureus is a complicated problem that is difficult to overcome due to the presence of numerous antibiotic resistance genes and it exhibit resistance to most of the currently available antibiotics. Presently, the resistance mechanisms of these genes/proteins...
The identification of common gene/protein profiles related to brain alterations, if they exist, may indicate the convergence of the pathogenic mechanisms driving brain disorders. Six genetically engineered mouse lines modelling neurodegenerative diseases and neuropsychiatric disorders were considered. Omics approaches, including transcriptomic and proteomic methods, were used. The gene/protein lists...
The aim of this study was to explore potential crucial genes associated with the steroid-induced necrosis of femoral head (SINFH) and to provide valid biological information for further investigation of SINFH. Gene expression profile of GSE26316, generated from 3 SINFH rat samples and 3 normal rat samples were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes...
The biological roles of small RNAs (sRNAs) in metabolic processes are emerging. However, a systemic study is needed to investigate the wide-spread involvement of the sRNAs in plant metabolism. By using the metabolism-related transcripts retrieved from the public database Plant Metabolic Network, and the publicly available sRNA high-throughput sequencing data, large-scale target identification was...
Liver fibrosis, characterized with the excessive accumulation of extracellular matrix (ECM) proteins, represents the final common pathway of chronic liver inflammation. Ever-increasing evidence indicates microRNAs (miRNAs) dysregulation has important implications in the different stages of liver fibrosis. However, our knowledge of miRNA-gene regulation details pertaining to such disease remains unclear...
Considerable studies demonstrate that plant transcription factors (TFs) play key regulatory roles in abiotic/biotic stress conditions, such as drought and pathogen attack. However, there is no effort dedicated to curate experimentally validated stress-TF regulatory relationships from these individual reports into a central database, which put an obstacle in the exploration of stress-TF regulations...
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