title: Bioinformatic Analysis of Next-Generation Sequencing Data to Identify WT1-Associated Differential Gene and Isoform Expression.
abstract: Differential gene expression analysis has been conventionally performed by microarray techniques; however with the recent advent of next-generation sequencing (NGS) approaches, it has become easier to analyze the coding as well as the noncoding components. Additionally, NGS data analysis also provides information regarding the expression changes of specific isoforms. There are several bioinformatics tools available to analyze NGS data but with different parameters. This chapter provides a comparative insight into these tools by utilizing NGS datasets available from Wt1 knockout and embryonic stem cell line model.
authors.affiliation: Medical Research Council-Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, Scotland, UK.
authors.forename: Stuart
authors.initials: S
authors.lastname: Aitken
authors.affiliation: Medical Research Council-Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, Scotland, UK. ruthrothaselvi.bharathavikru@igmm.ed.ac.uk.
authors.forename: Ruthrothaselvi
authors.initials: R
authors.lastname: Bharathavikru
mesh_terms: D000818:Animals; D002478:Cells, Cultured; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D055786:Gene Knockout Techniques; D059014:High-Throughput Nucleotide Sequencing; D051379:Mice; D000066450:Mouse Embryonic Stem Cells / Q000166:cytology*; D020033:Protein Isoforms / Q000235:genetics; D012097:Repressor Proteins / Q000235:genetics*; D017423:Sequence Analysis, RNA; D025721:WT1 Proteins
chemical_list: D020033:Protein Isoforms; D012097:Repressor Proteins; D025721:WT1 Proteins; C000602896:WT1 protein, mouse
keywords: Cuffdiff2; DESeq2; Next-generation sequencing (NGS); edgeR