Current Bioinformatics - Volume 16, Issue 1, 2021

Objective: As a result of the development of microarray technologies, gene expression levels of thousands of genes involved in a given biological process can be measured simultaneously, and it is important to study their temporal behavior to understand their mechanisms. Since the dependence between gene expression levels over time for a given gene is often too complicated to model parametrically, sparse functi Read More

Background: Persistent high-risk genital human papillomavirus (HPV) infection is a major cause of cervical cancer in women. The products of the viral transforming genes E6 and E7 in the high-risk HPVs are known to be similar in their amino acid composition and structure. We performed a comparative analysis of codon usage patterns in the E6 and E7 genes of HPVs. Methods: The E6 and E7 gene sequences of eight HPV su Read More

Background: Synechococcus sp. WH8102 is one of the most abundant photosynthetic organisms in many ocean regions. Objective: The aim of this study is to identify genomic islands (GIs) in Synechococcus sp. WH8102 with integrated methods. Methods: We have applied a genomic barcode to identify the GIs in Synechococcus sp. WH8102, which could make genomic regions of different origins visually apparent. The gene expre Read More

Background: Liver hepatocellular carcinoma (LIHC) and cholangiocarcinoma (CHOL) are two main histological subtypes of primary liver cancer with a unified molecular landscape, and feed-forward loops (FFLs) have been shown to be relevant in these complex diseases. Objective: To date, there has been no comparative analysis of the pathogenesis of LIHC and CHOL based on regulatory relationships. Therefore, we investigated t Read More

Background: Knowledge of protein functions is very crucial for the understanding of biological processes. Experimental methods for protein function prediction are of no use to treat the growing amount of protein sequence and structure data. Objective: To develop some computational techniques for the protein function prediction. Methods: Based on the residue interaction network features and the motion mode inform Read More

Background: Microsatellite instability (MSI) is a prognostic biomarker used to guide medication selection in multiple cancers, such as colorectal cancer. Traditional PCR with capillary electrophoresis and next-generation sequencing using paired tumor tissue and leukocyte samples are the main approaches for MSI detection due to their high sensitivity and specificity. Currently, patient tissue samples are obtained through pu Read More

Background: Microarray data is widely utilized for disease analysis and diagnosis. However, it is hard to process them directly and achieve high classification accuracy due to the intrinsic characteristics of high dimensionality and small size samples. As an important data preprocessing technique, feature selection is usually used to reduce the dimensionality of some datasets. Methods: Given the limitations of employing f Read More

Aims: The discontinuous pattern of genome size variation in angiosperms is an unsolved problem related to genome evolution. In this study, we introduced a genome evolution operator and solved the related eigenvalue equation to deduce the discontinuous pattern. Background: Genome is a well-defined system for studying the evolution of species. One of the basic problems is the genome size evolution. The DNA amounts f Read More

Background: Osteoporosis is the most common bone metabolic disease. Abnormal osteoclast formation and resorption play a fundamental role in osteoporosis pathogenesis. Recent researches have greatly broadened our understanding of molecular mechanisms of osteoporosis. However, the molecular mechanisms leading to osteoporosis are still not entirely clear. Objective: The purpose of this work is to study the critical regul Read More

Background: Gastric cancer (GC) is one of the most common malignancies worldwide. However, the biomarkers for the prognosis and diagnosis of Gastric cancer are still need. Objective: The present study aimed to evaluate whether CPZ could be a potential biomarker for GC. Methods: Kaplan-Meier plotter (http://kmplot.com/analysis/) was used to determine the correlation between CPZ expression and overall survival (OS) and Read More

Background: Non-small cell lung carcinoma (NSCLC) accounts for 80% of all lung cancer cases, which have been a leading cause of morbidity and mortality worldwide. Previous studies demonstrated that centromere proteins were dysregulated and involved in regulating the tumorigenesis and development of human cancers. However, the roles of centromere protein family members in NSCLC remained to be further elucidated Read More

Background: Malignant gliomas are the most prevalent malignancy of the brain. However, there was still lack of sensitive and accurate biomarkers for gliomas. Objective: To explore the mechanisms underlying glioma progression and identify novel diagnostic and prognostic markers for glioma. Methods: By analyzing TCGA dataset, whole-genome genes expression levels were evaluated in 19 different types of human cancers. A Read More

Background: Non-small cell lung cancer (NSCLC) is one of the most leading cause of tumor related mortality worldwide. However, the prognosis of NSCLC remained to be poor and the mechanisms remained to be further investigated. Objective: This study aimed to evaluate whether GPRIN1 could be a potential biomarker for NSCLC. Methods: The Cancer Genome Atlas (TCGA, https://cancergenome.nih.gov/) and GEO databas Read More

Background: Radioresistance remains a significant obstacle in the treatment of prostate cancer (PCa). The mechanisms underlying the radioresistance in PCa remained to be further investigated. Methods: GSE53902 dataset was used in this study to identify radioresistance-related mRNAs. Protein-protein interaction (PPI) network was constructed based on STRING analysis. DAVID system was used to predict the pote Read More

Background: In the past decades, the incidence of thyroid cancer (TC) has been gradually increasing, owing to the widespread use of ultrasound scanning devices. However, the key mRNAs, miRNAs, and mRNA-miRNA network in papillary thyroid carcinoma (PTC) has not been fully understood. Methods: In this study, multiple bioinformatics methods were employed, including differential expression analysis, gene set enrichment a Read More

Background: Osteosarcoma (OS) is one of the most common primary malignant bone tumors in teenagers. Emerging studies demonstrated TWEAK and Fn14 were involved in regulating cancer cell differentiation, proliferation, apoptosis, migration and invasion. Objective: The present study identified differently expressed mRNAs and lncRNAs after anti- TWEAK treatment in OS cells using GSE41828. Methods: We identified 92 Read More

Aim: To facilitate researchers and practitioners for unveiling the mysterious functional aspects of the human cellular system through performing exploratory searching on semantically integrated heterogeneous and geographically dispersed omics annotations. Background: Improving health standards of life is one of the motives, which continuously instigates researchers and practitioners to strive for uncovering the mysteriou Read More