title: Membrane gene ontology bias in sequencing and microarray obtained by housekeeping-gene analysis.
abstract: Microarray (MA) and high-throughput sequencing are two commonly used detection systems for global gene expression profiling. Although these two systems are frequently used in parallel, the differences in their final results have not been examined thoroughly. Transcriptomic analysis of housekeeping (HK) genes provides a unique opportunity to reliably examine the technical difference between these two systems. We investigated here the structure, genome location, expression quantity, microarray probe coverage, as well as biological functions of differentially identified human HK genes by 9 MA and 6 sequencing studies. These in-depth analyses allowed us to discover, for the first time, a subset of transcripts encoding membrane, cell surface and nuclear proteins that were prone to differential identification by the two platforms. We hope that the discovery can aid the future development of these technologies for comprehensive transcriptomic studies.
authors.affiliation: Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
authors.forename: Yijuan
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
authors.forename: Oluwafemi S
authors.initials: OS
authors.lastname: Akintola
authors.affiliation: Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
authors.forename: Ken J A
authors.initials: KJA
authors.lastname: Liu
authors.affiliation: Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada. Electronic address: bingyun_sun@sfu.ca.
authors.forename: Bingyun
authors.initials: B
authors.lastname: Sun
mesh_terms: D002874:Chromosome Mapping; D020869:Gene Expression Profiling / Q000379:methods; D063990:Gene Ontology; D020043:Genes, Essential; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008565:Membrane Proteins / Q000235:genetics*; D009687:Nuclear Proteins / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results
chemical_list: D008565:Membrane Proteins; D009687:Nuclear Proteins
keywords: Gene expression; Gene ontology; Gene structure; Housekeeping genes; Microarray; Next-generation sequencing; Probe coverage; RNA-seq; Sequencing; Transcriptome