- Introduction to Cancer Systems Biology 3
2.2. Transcriptome
The central dogma is an explanation of the flow of genetic information from
DNA to RNA to protein in a biological system. A transcriptome is a set of
mRNAs or total set of transcripts in a cell or organism. We also call the
transcriptome the gene expression profile because it examines the expression
level of mRNAs. The study of transcriptomes is termed transcriptomics. The
high-throughput techniques on transcriptome include DNA microarray and
next-generation sequencing (RNA-sequencing).
TCGA dataset includes not only genomics data but also transcriptomics
and proteomics data. The Gene Expression Omnibus (GEO) is a public
functional genomics data repository which accepts array- and sequence-
based data (https://www.ncbi.nlm.nih.gov/geo/). ArrayExpress is the other
functional genomics data archive supported by the European Bioinformat-
ics Institute (EMBL-EBI, https://www.ebi.ac.uk/arrayexpress/). TCGA,
GEO, and ArrayExpress provide their data for reuse to the research
community.
2.3. Proteome
The definition of proteome is the protein set in a cell, a tissue and
an organism at a certain time. The study of proteomes is known as
proteomics. The term “proteome” was coined by Marc Wilkins in 1994.
The most popular and high-throughput technique in proteomics is liquid
chromatography–mass spectrometry (LC–MS). Proteomics can measure
protein expression level and discover post-translational modifications such
as phosphorylation, ubiquitination and acetylation. Post-translational mod-
ifications affect the activities of proteins to regulate cellular progression and
development.
The ProteomeXchange (PX) Consortium (http://www.proteomex
change.org) was founded in 2011 to provide proteomics resources and
standardize data submission and dissemination of mass spectrometry (MS)-
based proteomics data.^3 PX contains 4,534 datasets. The top five species
are:Homo sapiens, Mus musculus, Saccharomyces cerevisiae, Arabidopsis
thaliana and Rattus norvegicus. Since 2015, the journal Molecular and
Cellular Proteomics, one of the most prominent scientific proteomics
journals, has mandated the deposition of raw data with every submitted
paper.