Zheng, Linli Chen, Weishen Xian, Guoyan Pan, Baiqi Ye, Yongyu Gu, Minghui Ma, Yinyue Zhang, Ziji Sheng, Puyi
Published in
Clinical rheumatology
To investigate abnormally methylated-differentially expressed genes (DEGs) and their related pathways in osteoarthritis (OA) by comprehensive bioinformatic analysis. Gene expression profiles of GSE51588 and GSE114007, and a gene methylation microarray data GSE63695 were downloaded from the Gene Expression Omnibus (GEO) repository. Abnormally methyl...
Liu, Mengyuan Zhi, Xiaona Wang, Yi Wang, Yang
Published in
BMC Plant Biology
BackgroundTomato (Solanum lycopersicum) is one of the most important horticultural crops, with a marked preference for nitrate as an inorganic nitrogen source. The molecular mechanisms of nitrate uptake and assimilation are poorly understood in tomato. NIN-like proteins (NLPs) are conserved, plant-specific transcription factors that play crucial ro...
Becker, Ton E Jakobsson, Eric
Published in
Journal of Biomedical Semantics
BackgroundThe revolution in molecular biology has shown how protein function and structure are based on specific sequences of amino acids. Thus, an important feature in many papers is the mention of the significance of individual amino acids in the context of the entire sequence of the protein. MutationFinder is a widely used program for finding me...
Chen, Weijian Lin, Tianye He, Qi Yang, Peng Zhang, Gangyu Huang, Fayi Wang, Zihao Peng, Hao Li, Baolin Liang, Du
...
Published in
Journal of Orthopaedic Surgery and Research
BackgroundKnee osteoarthritis is a common joint degenerative disease. Xiao Huoluo Pills (XHLP) has been used to treat degenerative diseases such as osteoarthritis and hyperosteogeny. However, XHLP’s specific effective ingredients and mechanism of action against osteoarthritis have not been explored. Therefore, bioinformatics technology and molecula...
Sefer, Emre
Published in
Applied Network Science
Chromosome conformation capture experiments such as Hi–C map the three-dimensional spatial organization of genomes in a genome-wide scale. Even though Hi–C interactions are not biased towards any of the histone modifications, previous analysis has revealed denser interactions around many histone modifications. Nevertheless, simultaneous effects of ...
Wu, Rui Long, Li Zhou, Qiao Su, Jiang Su, Wei Zhu, Jing
Published in
Journal of Orthopaedic Surgery and Research
BackgroundRheumatoid arthritis (RA) is a common chronic autoimmune disease characterized by inflammation of the synovial membrane. However, the etiology and underlying molecular events of RA are unclear. Here, we applied bioinformatics analysis to identify the key genes involved in RA.MethodsGSE77298 was downloaded from the Gene Expression Omnibus ...
Plaisier, Heleen Meagher, Thomas R. Barker, Daniel
Published in
BMC Research Notes
ObjectiveVisualisation methods, primarily color-coded representation of sequence data, have been a predominant means of representation of DNA data. Algorithmic conversion of DNA sequence data to sound—sonification—represents an alternative means of representation that uses a different range of human sensory perception. We propose that sonification ...
Gao, Shiyong Gang, Jian Yu, Miao Xin, Guosong Tan, Huixin
Published in
BMC Cancer
BackgroundLiver cancer is the sixth most commonly diagnosed cancer and the fourth most common cause of cancer death. The purpose of this work is to find new diagnostic biomarkers or prognostic biomarkers and explore the biological functions related to the prognosis of liver cancer.MethodsGSE25097 datasets were firstly obtained and compared with TCG...
Lu, Xiaoyuan Li, Guilin Liu, Sicong Wang, Haihong Chen, Buze
Published in
Journal of Ovarian Research
BackgroundAberrant expression of microRNAs (miRNAs) contributes to the development of high grade serous ovarian cancer (HGSOC). However, the molecular mechanism by which miRNA-585-3p mediates high-grade serous ovarian carcinogenesis is unclear. This study aims to investigate the specific mechanism of action of miR-585-3p in HGSOC.MethodsExpression ...
Koonchanok, Ratanond Daulatabad, Swapna Vidhur Mir, Quoseena Reda, Khairi Janga, Sarath Chandra
Published in
BMC Genomics
BackgroundDirect-sequencing technologies, such as Oxford Nanopore’s, are delivering long RNA reads with great efficacy and convenience. These technologies afford an ability to detect post-transcriptional modifications at a single-molecule resolution, promising new insights into the functional roles of RNA. However, realizing this potential requires...
