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A major challenge in microarray data analysis is the functional interpretation of gene lists. A common approach to address this is over-representation analysis (ORA), which uses the hypergeometric test (or its variants) to evaluate whether a particular functionally defined group of genes is represented more than expected by chance within a gene list. Existing applications of ORA have been largely limited to pre-defined terminologies such as GO and KEGG. We report our explorations of whether ORA can be applied to a wider mining of free-text. We found that a hitherto underappreciated feature of experimentally derived gene lists is that the constituents have substantially more annotation associated with them, as they have been researched upon for a longer period of time. This bias, a result of patterns of research activity within the biomedical community, is a major problem for classical hypergeometric test-based ORA approaches, which cannot account for such bias. We have therefore developed three approaches to overcome this bias, and demonstrate their usability in a wide range of published datasets covering different species. A comparison with existing tools that use GO terms suggests that mining PubMed abstracts can reveal additional biological insight that may not be possible by mining pre-defined ontologies alone.

Motivation: Experimental limitations have resulted in the popularity of parametric statistical tests as a method for identifying differentially regulated genes in microarray data sets. However, these tests assume that the data follow a normal distribution. To date, the assumption that replicate expression values for any gene are normally distributed, has not been critically addressed for Affymetrix GeneChip data., Results: The normality of the expression values calculated using four different commercial and academic software packages was investigated using a data set consisting of the same target RNA applied to 59 human Affymetrix U95A GeneChips using a combination of statistical tests and visualization techniques. For the majority of probe sets obtained from each analysis suite, the expression data showed a good correlation with normality. The exception was a large number of low-expressed genes in the data set produced using Affymetrix Microarray Suite 5.0, which showed a striking non-normal distribution. In summary, our data provide strong support for the application of parametric tests to GeneChip data sets without the need for data transformation.

Background: The melanoma susceptibility locus cyclin-dependent kinase inhibitor 2A encodes two unrelated cell growth inhibitors, p16 and alternative reading frame (ARF). In fibroblasts, both proteins are implicated in cellular senescence, a key barrier to tumor development. The p16 coding sequence is more often mutated in melanoma families than is the ARF sequence. To investigate the role of p16 in melanocytes, we assessed aspects of growth, apoptosis, and immortalization in melanocytes cultured from two melanoma patients, both of whom had two inactive p16 alleles but functional ARF., Methods: Growth and senescence were evaluated by cumulative population-doubling curves, and apoptosis by terminal deoxytransferase labeling. Expression of p53 and p21, which are associated with fibroblast senescence, was assessed by immunoblotting. Amphotropic retroviruses were used to transfer exogenous gene sequences into the melanocytes., Results: Both melanocyte cultures showed high rates of apoptosis, which were reduced when the cells were grown in the presence of keratinocyte feeder cells or human stem cell factor plus endothelin 1. With these growth factors, both cultures proliferated for 45-55 net population doublings, markedly longer than the maximum of 10 net population doublings of normal adult human melanocytes in similar media, indicating impaired senescence. One of the cultures developed chromosomal aberrations, with numerous dicentric chromosomes at senescence, consistent with telomere dysfunction. p53 and p21 levels were not elevated in senescent normal melanocytes but were elevated in senescent p16-deficient melanocytes. Interference with p53 function by transfer of human papillomavirus 16-E6 further extended the lifespan of p16-deficient melanocytes. Human telomerase reverse transcriptase was sufficient to immortalize both these cell strains but not normal melanocytes., Conclusion: Normal senescence in human melanocytes requires p16 activity. p53 contributes to a delayed form of senescence that requires telomere shortening, in p16-deficient melanocytes. These findings provide some basis for the role of p16 in melanoma susceptibility.

In an attempt to identify trans-acting factors involved in replication origin function, we have characterized the RAR3 and RAR5 genes, identified by mutations which increase the mitotic stability of artificial chromosomes whose replication is dependent on the activity of weak ARS elements. Sequence analysis has shown that the RAR3 gene is identical to GAL11/SPT13, which encodes a putative transcription factor involved in the expression of a wide range of genes. Change-of-function mutations that truncate the RAR3 protein appear to be required to enhance chromosome stability. In contrast, loss of the RAR5 protein results in enhanced chromosome stability, as if the protein is an inhibitor of ARS function. The RAR5 gene encodes the 175 kDa DNA strand transfer protein beta, an activity that can promote the transfer of a strand from a double-stranded DNA molecule to a complementary single strand. This observation implies that a presumed recombination activity can affect eukaryotic chromosomal replication.