Membrane Gene Ontology Bias in Sequencing and Microarray Obtained by Housekeeping-Gene Analysis

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 had not to be 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 and cell surface proteins, as well as nuclear proteins regulating transcription prone to differential identification by the two platforms. We hope the discovery can aid the future development of these technologies for comprehensive transcriptomic studies.