Bioinformatic Analysis of Next-Generation Sequencing Data to Identify WT1-Associated Differential Gene and Isoform Expression

Stuart Aitken; Ruthrothaselvi Bharathavikru

doi:10.1007/978-1-4939-4023-3_18

Bioinformatic Analysis of Next-Generation Sequencing Data to Identify WT1-Associated Differential Gene and Isoform Expression

Methods Mol Biol. 2016:1467:211-9. doi: 10.1007/978-1-4939-4023-3_18.

Authors

Stuart Aitken¹, Ruthrothaselvi Bharathavikru²

Affiliations

¹ 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.
² 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. [email protected].

PMID: 27417972
DOI: 10.1007/978-1-4939-4023-3_18

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.

Keywords: Cuffdiff2; DESeq2; Next-generation sequencing (NGS); edgeR.

MeSH terms

Animals
Cells, Cultured
Computational Biology / methods*
Gene Expression Profiling / methods*
Gene Knockout Techniques
High-Throughput Nucleotide Sequencing
Mice
Mouse Embryonic Stem Cells / cytology*
Protein Isoforms / genetics
Repressor Proteins / genetics*
Sequence Analysis, RNA
WT1 Proteins

Substances

Protein Isoforms
Repressor Proteins
WT1 Proteins
WT1 protein, mouse