Figure 1: A historical timeline of transcriptomics.

Illustrated is the lockstep development of experimental and computational aspects of transcriptomics. Advances in the experimental protocols for the high-throughput profiling of RNA necessitate the development of databases to catalogue the results and trigger curation efforts to define reference transcriptomes. However, these endeavours depend on the development of accurate and scalable computational methods to search, quantify and assemble RNA molecules. Within each field, the most influential, seminal or unique references were selected. AceView, a gene annotation resource²⁶⁷; ArrayDB, a database of microarray gene expression data²⁶⁸; ArrayExpress, a public repository for microarray gene expression data⁷⁸; BLAST, Basic Local Alignment Search Tool⁷³; CAGE, cap analysis of gene expression²⁶⁹; CEL-seq, cell expression by linear amplification and sequencing⁴⁹; CGAP, Cancer Genome Anatomy Project²⁷⁰; CIBERSORT, a tool for estimating the abundances of cell types in a mixed cell population²⁶⁰; dbEST, a database for expressed sequence tags⁶⁸; EdgeR, a package for differential expression analysis¹⁷⁰; EMBL, European Molecular Biology Laboratory; Ensembl, a genome browser for vertebrate genomes⁷⁴; ESTs, expressed sequence tags²⁸; FANTOM5, Functional Annotation of the Mammalian Genome 5 (Ref. 271); FASTA, a text format for representing nucleotide or peptide sequences⁷²; GenBank, the US National Institutes of Health (NIH) genetic sequence database; GENCODE, the genome annotation project of the Encyclopedia of DNA Elements (ENCODE)²⁷²; GenomeSpace, a cloud-based resource for integrative genomics analyses⁸³; GEO, Gene Expression Omnibus⁷⁷; GSEA, gene set enrichment analysis²⁷³; InsilicoDB, a database of microarray and RNA-seq data⁸²; Known Genes, a resource of RNA and protein data²⁷⁴; Limma, Linear Models for Microarray Data¹⁶⁷; MiTranscriptome, a human RNA-seq database⁷⁶; Mitelman, Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer²⁷⁵; MPSS, massively parallel signature sequencing⁴²; Oncomine, a cancer microarray database and integrated data mining platform¹⁸⁰; qPCR, quantitative PCR²⁹; RACE, rapid amplification of cDNA ends²⁷⁶; Refseq, NCBI Reference Sequence Database⁷⁵; RNAscope, an in situ hybridization assay for RNA detection²⁷⁷; RNA-seq, RNA sequencing; RNA-seq 454, RNA sequencing using the 454 (Roche) pyrosequencing platform⁴⁴; RNA-seq SBS, RNA sequencing using sequencing-by-synthesis platforms²⁷⁸; RT-qPCR, reverse transcription quantitative PCR^30,31,32; SAGE, serial analysis of gene expression³⁶; SAGEmap, SAGE tag to gene mapping²⁷⁹; Sailfish, a transcript isoform quantification tool²⁸⁰; SAM, Significance Analysis of Microarrays²⁸¹; Smith–Waterman, a local sequence alignment algorithm⁷⁰; STAR, Spliced Transcripts Alignment to a Reference²⁸²; Symatlas, gene expression and annotation resource, now superseded by BioGPS²⁸³; TACO, Transcriptome Assemblies Combined into One (a consensus transcriptome tool)²⁸⁴; TopHat and Cufflinks, software tools for RNA-seq alignment and transcriptome assembly⁵; Trans-ABySS, Transcript Assembly By Short Sequences²⁸⁵; Trinity, a tool for de novo assembly of RNA-seq data²⁸⁶; UMI, unique molecular identifier⁴⁸; Xena, a genomic data mining and analysis portal²⁸⁷.

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