Glossary

A quick reference to key terms used across the labs.

Annotation — mapping identifiers (genes, probes, SNPs) to biological information (names, functions, locations, pathways).

BLAST — Basic Local Alignment Search Tool; finds regions of similarity between a query sequence and a database.

Bioconductor — an R project and package repository for the analysis of high-throughput genomic data.

Differential expression — genes whose expression differs systematically between conditions (e.g. disease vs control).

e-value — in a sequence search, the expected number of hits as good as the observed one that would occur by chance; smaller is more significant.

Eigenface / principal component — an orthogonal direction of maximum variance in a dataset; for face images, itself an image.

Enrichment (ORA / GSEA) — testing whether a gene set (e.g. a pathway) is over-represented among hits (over-representation analysis) or shifted in a ranked list (gene-set enrichment analysis).

Expression set (ExpressionSet) — a Bioconductor container bundling an expression matrix with sample (phenotype) and feature (gene) metadata.

FDR (false discovery rate) — the expected proportion of false positives among declared discoveries; controlled with methods such as Benjamini–Hochberg.

Founder — in a pedigree, an individual whose parents are not in the dataset.

Genomic inflation factor (lambda) — the ratio of observed to expected median test statistic in a GWAS; lambda near 1 indicates well-controlled confounding.

GWAS — genome-wide association study; tests each of many SNPs for association with a phenotype.

Homology / orthology / paralogy — shared ancestry between sequences; orthologues diverged by speciation, paralogues by duplication.

HWE (Hardy–Weinberg equilibrium) — the expected relationship between allele and genotype frequencies in an ideal population; departures can flag genotyping error or structure.

IBS / kinship — identity-by-state / relatedness measured from shared alleles across many markers.

Manhattan plot — a GWAS scatter plot of \(-\log_{10}\) p-value against genomic position.

Multidimensional scaling (MDS) — a projection of a distance matrix into few dimensions, used here to reveal population structure.

QQ plot — quantile–quantile plot of observed vs expected p-values; used to judge calibration and inflation.

SNP — single-nucleotide polymorphism; a single-base variant in the genome.