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Full-Text Articles in Medicine and Health Sciences
Primate Phylogenomics: Developing Numerous Nuclear Non-Coding, Non-Repetitive Markers For Ecological And Phylogenetic Applications And Analysis Of Evolutionary Rate Variation, Zuogang Peng, Navin Elango, Derek E. Wildman, Soojin V. Yi
Primate Phylogenomics: Developing Numerous Nuclear Non-Coding, Non-Repetitive Markers For Ecological And Phylogenetic Applications And Analysis Of Evolutionary Rate Variation, Zuogang Peng, Navin Elango, Derek E. Wildman, Soojin V. Yi
Wayne State University Associated BioMed Central Scholarship
Abstract
Background
Genetic analyses are often limited by the availability of appropriate molecular markers. Markers from neutrally evolving genomic regions may be particularly useful for inferring evolutionary histories because they escape the constraints of natural selection. For the majority of taxa however, obtaining such markers is challenging. Advances in genomics have the potential to alleviate the shortage of neutral markers. Here we present a method to develop numerous markers from putatively neutral regions of primate genomes.
Results
We began with the available whole genome sequences of human, chimpanzee and macaque. Using computational methods, we identified a total of 280 potential …
Development And Evaluation Of New Mask Protocols For Gene Expression Profiling In Humans And Chimpanzees, Donna M. Toleno, Gabriel Renaud, Tyra G. Wolfsberg, Munirul Islam, Derek E. Wildman, Kimberly D. Siegmund, Joseph G. Hacia
Development And Evaluation Of New Mask Protocols For Gene Expression Profiling In Humans And Chimpanzees, Donna M. Toleno, Gabriel Renaud, Tyra G. Wolfsberg, Munirul Islam, Derek E. Wildman, Kimberly D. Siegmund, Joseph G. Hacia
Wayne State University Associated BioMed Central Scholarship
Abstract
Background
Cross-species gene expression analyses using oligonucleotide microarrays designed to evaluate a single species can provide spurious results due to mismatches between the interrogated transcriptome and arrayed probes. Based on the most recent human and chimpanzee genome assemblies, we developed updated and accessible probe masking methods that allow human Affymetrix oligonucleotide microarrays to be used for robust genome-wide expression analyses in both species. In this process, only data from oligonucleotide probes predicted to have robust hybridization sensitivity and specificity for both transcriptomes are retained for analysis.
Results
To characterize the utility of this resource, we applied our mask protocols …