Metagenomics Bioinformatic Pipeline

Garfias-Gallegos, Diego; Zirión-Martínez, Claudia; Bustos-Díaz, Edder D.; Arellano-Fernández, Tania Vanessa; Lovaco-Flores, José Abel; Espinosa-Jaime, Aarón; Avelar-Rivas, J. Abraham; Sélem-Mójica, Nelly

doi:10.1007/978-1-0716-2429-6_10

Cited by 5 publications

(7 citation statements)

References 11 publications

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“…The availability of various tools has led to the development of pipelines for metagenomic analyses [73]. Garfias-Gallegos et al created an effective pipeline as the first step toward quality control in the final visualization of the metagenomic data [74]. Similarly, the Omnibus metagenome-wide association study with robustness (OMARU) pipeline was developed to explore the relationship between microbiomes and disease pathophysiology [75].…”

Section: Fundamentals Of Metagenomicsmentioning

confidence: 99%

Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions

Nam

Khoa

Trinh

et al. 2023

Foods

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Various fields have been identified in the “omics” era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase in discoveries related to the microbial world. Newly discovered microbiomes in different ecologies provide meaningful information on the diversity and functions of microorganisms on the Earth. Therefore, the results of metagenomic studies have enabled new microbe-based applications in human health, agriculture, and the food industry, among others. This review summarizes the fundamental procedures on recent advances in bioinformatic tools. It also explores up-to-date applications of metagenomics in human health, food study, plant research, environmental sciences, and other fields. Finally, metagenomics is a powerful tool for studying the microbial world, and it still has numerous applications that are currently hidden and awaiting discovery. Therefore, this review also discusses the future perspectives of metagenomics.

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Section: Fundamentals Of Metagenomicsmentioning

confidence: 99%

Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions

Nam

Khoa

Trinh

et al. 2023

Foods

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“…Modified from Malla et al (2018), Plyusnin et al (2020), andGarfias-Gallegos et al (2022), the simplified bioinformatics pipeline flowchart in the application of NGS in poultry farms using targeted and crowded primer sets is shown in Fig. 2.…”

Section: Future Directionmentioning

confidence: 99%

Multi-Barcode for Detection of Avian Bacterial and Viral Pathogens: A Review

2023

Int J Vet Sci

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The global poultry industry constantly faces the threat of various bacterial and viral diseases, some of which are underreported, especially in developing countries. Even when official reports are available, the scope of the problem and its impact are unknown. Testing for individual pathogens is costly and tedious and may lead to inappropriate management, especially in the case of immunosuppressive diseases. Next-generation sequencing (NGS) provides an opportunity to discover all the events leading to clinical diseases. NGS for bacteria is well established, but this is not the case for viral agents. Because of their many variants, it is impossible to establish barcodes to detect all viruses. Therefore, we propose to establish a multi-barcode system to detect all bacteria and viruses in clinical avian specimens. The libraries can be generated with a one-step reverse transcription-PCR system for bacteria and RNA and DNA viruses, after priming with a single bacterial primer barcode and primer sets for all viruses or targeted viral genes of interest.

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“…[10] Bioinformatics technology has become a vital tool in contemporary biological and medical research, offering a more in-depth and comprehensive understanding of life's mechanisms and individual variations. [11] Currently, the relationship between CDK1, CCNA2 genes, and OSCC is not well understood. Therefore, this study aims to use bioinformatics technology to explore the core genes between OSCC and normal tissues, conducting enrichment analysis, and pathway analysis.…”

Section: Introductionmentioning

confidence: 99%

“…[10] Bioinformatics technology has become a vital tool in contemporary biological and medical research, offering a more in-depth and comprehensive understanding of life’s mechanisms and individual variations. [11]…”

Section: Introductionmentioning

confidence: 99%

CDK1 and CCNA2 play important roles in oral squamous cell carcinoma

Zhang,

Di,

Zhang

et al. 2024

Medicine

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Oral squamous cell carcinoma (OSCC) is a malignant tumor that occurs in oral cavity and is dominated by squamous cells. The relationship between CDK1, CCNA2, and OSCC is still unclear. The OSCC datasets GSE74530 and GSE85195 configuration files were downloaded from the Gene Expression Omnibus (GEO) database and were derived from platforms GPL570 and GPL6480. Differentially expressed genes (DEGs) were screened. The weighted gene co-expression network analysis, functional enrichment analysis, gene set enrichment analysis, construction and analysis of protein–protein interaction (PPI) network, Comparative Toxicogenomics Database analysis were performed. Gene expression heatmap was drawn. TargetScan was used to screen miRNAs that regulate central DEGs. A total of 1756 DEGs were identified. According to Gene Ontology (GO) analysis, they were predominantly enriched in processes related to organic acid catabolic metabolism, centromeric, and chromosomal region condensation, and oxidoreductase activity. In Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the DEGs were mainly concentrated in metabolic pathways, P53 signaling pathway, and PPAR signaling pathway. Weighted gene co-expression network analysis was performed with a soft-thresholding power set at 9, leading to the identification of 6 core genes (BUB1B, CCNB1, KIF20A, CCNA2, CDCA8, CDK1). The gene expression heatmap revealed that core genes (CDK1, CCNA2) were highly expressed in OSCC samples. Comparative Toxicogenomics Database analysis demonstrated associations between the 6 genes (BUB1B, CCNB1, KIF20A, CCNA2, CDCA8, CDK1) and oral tumors, precancerous lesions, inflammation, immune system disorders, and tongue tumors. The associated miRNAs for CDK1 gene were hsa-miR-203a-3p.2, while for CCNA2 gene, they were hsa-miR-6766-3p, hsa-miR-4782-3p, and hsa-miR-219a-5p. CDK1 and CCNA2 are highly expressed in OSCC. The higher the expression of CDK1 and CCNA2, the worse the prognosis.

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Metagenomics Bioinformatic Pipeline

Cited by 5 publications

References 11 publications

Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions

Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions

Multi-Barcode for Detection of Avian Bacterial and Viral Pathogens: A Review

CDK1 and CCNA2 play important roles in oral squamous cell carcinoma

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