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Data Algorithms by Mahmoud Parsian

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Appendix A. Bioset

Biosets (also called gene signatures1 or assays2) encompass data in the form of experimental sample comparisons (for transcriptomic, epigenetic, and copy-number variation data), as well as genotype signatures (for genome-wide association study [GWAS] and mutational data).

A bioset has an associated data type, which can be gene expression, protein expression, methylation, copy-number variation, miRNA, or somatic mutation. Also, each bioset entry/record has an associated reference type, which can be r1=normal, r2=disease, r3=paired, or r4=unknown. Note that a reference type does not apply to the somatic mutation data type.

The number of entries/records per bioset depends on its data type (see Table A-1).

Table A-1. Number of records per bioset data type
Bioset data type Number of entries/records
Somatic mutation 3,000–20,000
Methylation 30,000
Gene expression 50,000
Copy-number variation 40,000
Germline 4,300,000
Protein expression 30,000
miRNA 30,000

1 A gene signature is a group of genes in a cell whose combined expression pattern is uniquely characteristic of a biological phenotype or medical condition. The phenotypes that may theoretically be defined by a gene expression signature range from those that are used to differentiate between different subtypes of a disease, those that predict the survival or prognosis of an individual with a disease, to those that predict activation of a particular pathway. Ideally, gene signatures can be used ...

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