isoformlevel

Isoform level refers to the abundance of distinct isoforms of a gene product, most commonly messenger RNA transcripts or protein variants produced by processes such as alternative splicing, alternative promoter usage, and alternative polyadenylation. It is distinct from gene-level expression, which aggregates all isoforms into a single measure. Isoform-level data capture the diversity of gene products that can have different functions, localizations, or regulatory properties.

Measurement at the transcript level typically relies on RNA sequencing with isoform-aware quantification. Short-read RNA-seq estimates transcript abundance through alignment to reference transcript models, yielding units such as transcripts per million (TPM) or fragments per kilobase of transcript per million mapped reads (FPKM). Long-read sequencing technologies improve isoform resolution by sequencing full-length transcripts directly. Differential isoform usage analyses identify isoforms whose relative abundance changes between conditions, often using metrics like percent spliced in (PSI) for specific exons.

Protein isoforms are quantified by proteomics approaches, principally mass spectrometry. Detection depends on identifying isoform-specific peptides; targeted proteomics methods (MRM/SRM, PRM) enable precise quantification of selected isoforms. Challenges in both domains include isoform ambiguity due to shared sequences, dependence on annotation quality, and low-abundance isoforms that are difficult to detect.

Biological significance of isoform level data includes tissue- and development-specific expression patterns, disease-associated isoform switches, and potential implications for function and therapeutics. Isoform-level analyses complement gene-level studies and are increasingly used in research on development, cancer, neurodegeneration, and biomarker discovery. See also alternative splicing, transcriptomics, and proteomics.