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We used the GENCONV method to characterize the gene conversions that occurred amongst the 1434 protein coding human gene families with three or more genes. Conversions occur at a frequency of 0.88% (483 conversion events/55,050 gene pairs compared) and have an average length of 371±752 bp (±standard deviation). Both the size and the frequency of conversions are positively correlated with the similarity...
Demonstrating an association between a polymorphism and a disease phenotype through case-control studies requires reliable large-scale genotyping, but accurate measurement of copy number variation has proven to be technically challenging. Here we build on our previous experience with Paralogue Ratio Tests (PRT) to develop PRT copy number determination at the CCL3L1/CCL4L1 copy number variant. A multiplex...
MSRAs (methionine sulfoxide reductases A) are enzymes that reverse the effects of oxidative damage by reducing methionine sulfoxide back to methionine and recovering protein function. In this study we demonstrate that the transcriptional regulation of the human MSRA gene is complex and driven by two distinct promoters. Both promoters demonstrate high expression in human brain and kidney tissues. The...
The availability of the human genome sequence and progress in sequencing and bioinformatic technologies have enabled genome-wide investigation of somatic mutations in human cancers. This article briefly reviews challenges arising in the statistical analysis of mutational data of this kind. A first challenge is that of designing studies that efficiently allocate sequencing resources. We show that this...
Data for genome-wide association studies are being collected for a myriad of phenotypes. Many of these studies do not include control samples selected to reflect ancestry similar to the case samples. At the same time “control databases” are becoming available to be utilized as a common resource. These data are often genotyped using a large-scale SNP array. Human populations exhibit complex structure...
Pathogen–host interaction plays an essential role in pathogenicity. In this study, we investigated transcriptomes of one Streptococcus pneumoniae TIGR4-derived unencapsulated strain upon exposure to THP-1 human macrophage-like cells for 0.5 h, 1 h and 3 h, respectively. Expression of most genes was up-regulated and the changes of selected genes were validated by qRT-PCR. To characterize the functions...
Gastric cancer is one of the most common cancers worldwide, and there are clinical caveats in predicting tumor response to chemotherapy. This study describes the construction of an in vitro pharmacogenomic database, and the selection of genes associated with chemosensitivity in gastric cancer cell lines. Gene expression and chemosensitivity databases were integrated using the Pearson correlation coefficient...
The chorioallantoic placenta is a shared derived feature of “placental” mammals essential for the success of eutherian reproduction. Identifying the genes involved in the emergence of the placenta may provide clues for understanding the biology of this organ. Here we identify among 4960 single copy genes in mammals, 222 that show high expression levels in human placentas at term. Further, we present...
The identification of cellular responses to damage can promote mechanistic insight into stress signalling. We have screened a library of 3968 Escherichia coli gene-deletion mutants to identify 99 gene products that modulate the toxicity of the alkylating agent methyl methanesulfonate (MMS). We have developed an ontology mapping approach to identify functional categories over-represented with MMS-toxicity...
Structural genetic variation, including copy-number variation (CNV), constitutes a substantial fraction of total genetic variability and the importance of structural genetic variants in modulating human disease is increasingly being recognized. Early successes in identifying disease-associated CNVs via a candidate gene approach mandate that future disease association studies need to include structural...
Retrogenes are processed copies of genes that are inserted into new genomic regions and that acquire new regulatory elements from the sequences in their surroundings. Here we use a comparative approach of phylogenetic footprinting and a non-comparative approach of measuring motif over-representation in retrogenes in order to describe putative elements present in cis-regulatory regions of 94 retrogenes...
Mutations, which can alter amino acid constitution, contribute greatly to protein evolution. However, little is reported of their pattern during protein structural evolution. We investigated the distribution of non-synonymous single nucleotide polymorphisms (nsSNPs) and insertions/deletions (indels) along mammal and fruit fly proteins. We found the nsSNPs (and d N ) and indels increased in...
Gene–environment interactions are of interest in genetic association studies for several reasons. First, the power to detect genetic effects may be substantially decreased if those effects differ according to environmental exposure and if no account is taken of this interaction with environmental exposure in the analysis. Second, such interactions may indicate a phenomenon of genuine biological interest...
Most diseases are complex in that they are caused by the joint action of multiple factors, both genetic and environmental. Over the past few decades, the mathematical convenience of logistic regression has served to enshrine the multiplicative model, to the point where many epidemiologists believe that departure from additivity on a log scale implies that two factors interact in causing disease. Other...
With the development of new technologies for assaying biological activity on a global basis in experimental samples, various new “-omics” signatures have been developed to predict disease progression. Such signatures hold the potential to alter the nature of clinical management of human disease. In this article, we describe some necessary statistical considerations needed to take these signatures...
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