Membrane gene ontology bias in sequencing and microarray obtained by housekeeping-gene analysis

• Housekeeping genes can be used for reliable analysis of difference between microarray and sequencing technologies.
• Microarray tends to enrich gene ontology related to membrane, cell surface, and secreted proteins that are missed by sequencing.
• Sequencing tends to identify gene ontology related to nuclear transcripts that are missed by microarray.
• Both the probe coverage and detection sensitivity have contributed to the missing gene identification by microarray.
• Sequencing technology has greatly improved current microarray probe coverage on the nuclear transcripts

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.