Data Algorithms

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 ...