Expression Patterns of Housekeeping Genes in Cancer

This dissertation, "Expression Patterns of Housekeeping Genes in Cancer" by Wooi-keng, Tan, 陳慧卿, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author. Abstract: Abstract of thesis entitled Expression Patterns of Housekeeping Genes in Cancer Submitted by Tan Wooi Keng for the degree of Master of Philosophy at The University of Hong Kong in August 2004 Housekeeping (HK) genes, also known as maintenance genes, are the genes that are always expressed in a normal cell to maintain basic cellular functions. They are often used as reference nucleic acids or as controls in biological experiments. Some researchers use HK genes to normalize gene expression in a microarray experiment to monitor the relative changes of gene expression between control and test samples. Studies have been performed by others to identify sets of Housekeeping genes in normal human tissues using microarray technology, however no study has been carried out on human cancerous tissues. HK genes identified from normal tissues would be expected to be expressed in most microarray studies, therefore it should be possible to use their expression as a guide to detect defective arrays and to assess the success of microarray experiments on cancerous tissues. Eight sets of published microarray cancer datasets: Prostate cancer, Diffuse B - Cell Lymphoma, Follicular Lymphoma, Embryonal Tumor, Adenocarcinoma, Pulmonary Carcinoma, Small Cell Lung Carcinoma and Squamous Cell Carcinoma were selected from the Whitehead Institute Centre for Genomic Research. The number of genes shown to be "present" across all the arrays in each type of cancer and the number HK genes, as defined by the earlier studies, that are "present" were identified. Affymetrix(R) Microarray Suite (MAS) version 5.1 and DNA Chip-Analyzer (dChip) version 1.3 were used to perform the analysis. It was found that the number of genes, and the number of HK genes called present, varied considerably from microarray to microarray. In some data sets very few HK genes were called present in all the microarrays. Statistical measures were used to detect outliers among the arrays. If microarrays with low numbers of HK genes (low Mi) called present were excluded (outlier arrays), a more consistent level of genes called present in all the data set were obtained. The findings confirm the suggestion of the use of the expression of HK genes as a guide to assess the success of microarray experiments. DOI: 10.5353/th_b2989289 Subjects: Gene expression Cancer - Genetic aspects