Statistical Analysis of Mapped Reads from mRNA-Seq Data

• Published in: Advances in Statistical Bioinformatics pp. 77 - 104
• Main Authors: Turro, Ernest, Lewin, Alex
• Format: Book Chapter
• Language: English
• Published: Cambridge University Press 10.06.2013
• ISBN: 1107027527; 9781107027527
• DOI: 10.1017/CBO9781139226448.005

BackgroundRNA BiologyA common and important aim in the field of genomics is the characterization of populations of RNA molecules. Investigators within the field typically wish to uncover the sequence and concentration of each RNA in a set of samples, either as an objective in its own right or as an early step in a larger analysis pipeline. Later steps might include the identification of differentially expressed genes between treatment and control groups, the clustering of genes into sets sharing putative, common regulatory pathways, or the association of genomic polymorphisms with patterns of expression.Roughly 4% of the RNAs in a typical unprocessed RNA sample consists of messenger RNAs (mRNAs), which code for proteins. Non-coding RNAs largely comprise ribosomal and transfer RNAs, which are involved in protein synthesis but do not code for proteins themselves. The remainder of the non-coding RNAs include a set of less abundant types of molecules with diverse functions. As a result of their direct role in protein synthesis, mRNAs have been in the limelight of genomic research. Protein-coding genes are transcribed by RNA polymerase from their 5′ (upstream) end to their 3′ (downstream) end to produce pre-mRNA. As this process takes place, certain regions may be spliced out from the pre-mRNA and discarded, leaving behind only an mRNA sequence of connected exons, known as an isoform. Multiple combinations of exons may be produced, which is known as alternative splicing, and different isoforms may have different 5′ and 3′ transcript start and end sites. This allows a single gene to produce multiple distinct transcripts and contributes to the phenotypic complexity of eukaryotes. The collection of possible transcripts produced by a single gene is known as the gene model.