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Informatics For Sciences: A Novel Approach
Published in Alexander V. Vakhrushev, Omari V. Mukbaniani, Heru Susanto, Chemical Technology and Informatics in Chemistry with Applications, 2019
Heru Susanto, Ching Kang Chen, Teuku Beuna Bardant
The growth of metabolic databases through metabolic study pathway will fulfill the need and enhance the development of system biology. One of the popular pathway databases is Kyoto Encyclopedia of Genes and Genomes (KEGG). KEGG databases are the center of information toward system analysis of gene function and connecting genomic information to higher order functional information. KEGG consists of three databases namely pathway, genes, and ligand. Pathway databases are responsible for storing the higher order functional information. These information include the computerized knowledge on molecular interaction networks. These data are often encoded by coupled genes on the chromosome which is crucial for predicting gene functions. The genes databases consist of the collection of genes catalog and sequence of genes and protein produced by the Genome Project. The third databases ligand stored information regarding the chemical compound and chemical reaction which is important to cellular processes.
Biochemistry apps as enabler of compound and DNA computational: next-generation computing technology
Published in A. K. Haghi, Lionello Pogliani, Eduardo A. Castro, Devrim Balköse, Omari V. Mukbaniani, Chin Hua Chia, Applied Chemistry and Chemical Engineering, 2017
The growth of metabolic databases through metabolic study pathway will fulfill the need and enhance the development of system biology. One of the popular pathway databases is KEGG. KEGG refers to the Kyoto Encyclopedia of Genes and Genomes. KEGG database is the center of information for system analysis of gene function and connecting genomic information with higher order functional information. KEGG consists of three databases, namely, PATHWAY, GENES, and LIGAND. PATHWAY database is responsible for storing the higher order functional information. This information includes the computerized knowledge on molecular interaction networks. These data are often encoded by coupled genes on the chromosome which are crucial for predicting gene functions. GENES database consists of the collection of gene catalogs and sequences of genes and proteins produced by the Genome Project. The third database, LIGAND, keeps the information regarding chemical compounds and chemical reactions which are important for cellular processes.
The Development of Improved Therapeutics through a Glycan- “Designer” Approach
Published in Peter Grunwald, Pharmaceutical Biocatalysis, 2019
For a more specific investigation of cancer-associated carbohydrates and their pathways in cancer research, the free database KEGG Cancer can be explored (https://www.genome.jp/kegg/glycan/). KEGG mapping allows one to view the glycan biosynthesis pathway, obtaining additional information of the genetics underlying certain diseases including references. The KEGG glycan structure database relies on the previously mentioned CarBank database. KEGG database is one of the first databases that implement cross-disciplinary data (genes, disease pathways, structures, glycan structures).
Ozone ultrafine bubble water induces the cellular signaling involved in oxidative stress responses in human periodontal ligament fibroblasts
Published in Science and Technology of Advanced Materials, 2019
Anongwee Leewananthawet, Shinichi Arakawa, Tokuju Okano, Ryo Daitoku Kinoshita, Hiroshi Ashida, Yuichi Izumi, Toshihiko Suzuki
Sequencing was carried out using a 2 × 150 bp paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument. In order to remove technical sequences including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, bases lower than 20 bp were processed by Trimmomatic (v0.30) to be high-quality clean data. The clean data were aligned to Hg19 (v_hg19) reference genome via software Hisat2 (v2.0.1). Differential expression analysis was performed with the Bioconductor package edgeR (v3.4.6). DESeq (v1.6.3), a model based on the negative binomial distribution, was used for samples with biological replicates. The gene expression levels were calculated by using fragments per kilobase per million reads (FPKM) based on reading counts from HT-seq (v0.6.1) [13]. After adjusted by Benjamini and Hochberg’s approach for controlling the false discovery rate, the p-value of genes <0.05 and the absolute value of fold change ≥2 were adopted to detect differentially expressed genes. GO-Term Finder was used to identify Gene Ontology (GO) terms that annotate a list of enriched genes with a significant p-value < 0.05. Kyoto Encyclopedia of Genes and Genomes (KEGG) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. We used custom scripts to enrich the significant differential expression gene in KEGG pathways.
Analysis of long non-coding RNA profiled following MC-LR-induced hepatotoxicity using high-throughput sequencing
Published in Journal of Toxicology and Environmental Health, Part A, 2018
Cong Wen, Shu Yang, Shuilin Zheng, Xiangling Feng, Jihua Chen, Fei Yang
Predicting the target gene of lncRNA was performed by correlation analysis between lncRNA and mRNA expression levels with custom scripts. Gene Ontology (GO) enrichment analyses of lncRNA target genes were implemented by the GOseq R package, in which gene length bias was corrected. GO terms with corrected p-value less than 0.05 were considered significantly enriched by differential expressed genes (Young et al. 2010). KEGG is a database resource for determining high-level functions and utilities of the biological system, (http://www.genome.jp/kegg/) (Kanehisa et al. 2008). KOBAS software tested the statistical enrichment of differential expression genes or lncRNA target genes in KEGG pathways (Mao et al. 2005).
Gene expression in human umbilical vein endothelial cells exposed to fine particulate matter: RNA sequencing analysis
Published in International Journal of Environmental Health Research, 2022
Zhixiang Zhou, Mengnan Qin, Sara Khodahemmati, Wenke Li, Bingyu Niu, Jiangshuai Li, Yanghua Liu, Jingfeng Gao
In the organism, different gene products coordinate into pathways to exercise their biological functions. Analysis based on pathways is conducive to further understanding of the biological functions of genes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) is a widely used database of these pathways. Significant enrichment analysis takes the KEGG pathway as the unit and identifies pathways that have a disproportionately high number of DEGs as opposed to other genes. In this study, a KEGG pathway with a Q-value ≤0.10 was defined as significantly enriched in DEGs.