When assessing differential gene expression from RNA sequencing data, commonly used statistical tests tend to have greater power to detect differential expression of genes encoding longer transcripts. This phenomenon, called "length bias", will influence subsequent analyses such as Gene Ontology enrichment analysis. In the presence of length bias, Gene Ontology categories that include longer ge...

The present study aimed to identify molecular targets that have important roles in the progression of Parkinson's disease. The gene expression profile dataset GSE7621 and the microRNA (miRNA) expression profile dataset GSE16658 were downloaded from the Gene Expression Omnibus database. R programing software was used to identify differentially expressed genes and miRNAs. Subsequently, enriched G...

Rhododendron liliiflorum H. Lév., with white outer edges and yellow inner of petals, is an ornamental flower that originated in China. In this study, we analysed the (W) (Y) parts R. flowers by RNA sequencing. Then, unigene assembly, annotation, classification Eukaryotic Orthologous Groups (KOGs) were performed. Gene ontology (GO) pathway enrichment analysis for unigenes also conducted. A total...

Enterococcus faecalis is an etiological agent of endodontic infections. The present study was performed to investigate the gene profiles E. induced by type I collagen stimulation. ATCC 19433 cultivated with [collagen (+)] or without (−)], and transcriptome analysis using high-throughput sequencing technology. A total 3.6 gb information obtained sequence 77 differentially expressed genes (DEGs) ...

CDCA7 is a copy number amplification gene that promotes tumorigenesis. However, the clinical relevance and potential mechanisms of in glioma are unclear. expression level data were obtained from Chinese Glioma Genome Atlas (CGGA) The Cancer (TCGA) databases, enriched genes related signaling pathways explored. Data on CDCA7-related nine marker ferroptosis retrieved protein–protein interaction (P...

A new functional gene database, FOAM (Functional Ontology Assignments for Metagenomes), was developed to screen environmental metagenomic sequence datasets. FOAM provides a new functional ontology dedicated to classify gene functions relevant to environmental microorganisms based on Hidden Markov Models (HMMs). Sets of aligned protein sequences (i.e. 'profiles') were tailored to a large group o...

We sought to find significant gene x gene interaction in a genome-wide association analysis of rheumatoid arthritis (RA) by performing pair-wise tests of interaction among collections of single-nucleotide polymorphisms (SNPs) obtained by one of two methods. The first method involved screening the results of the genome-wide association analysis for main effects p-values < 1 x 10-4. The second me...

Gene ontology analysis has become a popular and important tool in bioinformatics study, and current ontology analyses are mainly conducted in individual gene or a gene list. However, recent molecular network analysis reveals that the same list of genes with different interactions may perform different functions. Therefore, it is necessary to consider molecular interactions to correctly and spec...

This paper presents a novel method integrating gene-gene interaction information and Gene Ontology for the construction of new gene sets that are potentially enriched. Enrichment of a gene set is determined by Gene Set Enrichment Analysis, which is a microarray data analysis method that uses ranks of the genes, according to their differentially expression values, to identify significant biologi...

ABSTRACT Genome characterization of California poppy (Eschscholzia californica cv. “Hitoezaki”), which produces pharmaceutically important benzylisoquinoline alkaloids (BIAs), was carried out using the draft genome sequence. The numbers tRNA and rRNA genes were close to those other plant species tested, whereas frequency repetitive sequences distinct from species. Comparison predicted with Ambo...