Inferring Nonneutral Evolution from Human-Chimp-Mouse Orthologous Gene Trios

By Andrew G. Clark, S. Glanowski, Rasmus Nielsen, P. Thomas, Anish Kejariwal, M. Todd, D. Tanenbaum, D. Civello, Fu Lu, B. Murphy and 7 more. Science, 2003

648 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/aea6d06903738ab6e3d8322590346b93b7f2d8a6

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Citations in the corpus

PANTHER Pathway: an ontology-based pathway database coupled with data analysis tools (2009, methodology): “The probability that the functional category distribution was drawn randomly from the reference distribution is estimated using the Mann-Whitney Rank-Sum Test (U-Test) (Clark et al. 2003).”
A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective (2008, result): “These results are in accordance with those of Clark et al. (2003) who showed that the genes under selection are overrepresented in this database.”
The PANTHER database of protein families, subfamilies, functions and pathways (2004, methodology): “In addition to the binomial test described previously (9), the Mann–Whitney U-test as described in ( 10 ) can be performed on uploaded data to look for statistically significant differences in distributions of uploaded values (Figure 2). (vii) New: pie and bar charts of functions.”
THE LOCUS OF EVOLUTION: EVO DEVO AND THE GENETICS OF ADAPTATION (2007, background): “For example, hundreds of genes show evidence of positive selection in the hominid lineage (Clark et al. 2003).”
Comparative Genomics (2007, positive): “As was the case for human-mouse comparisons discussed above, the KA/KS ratio was computed in genome-wide comparison of the human and chimpanzee gene sets (Clark et al. 2003; Bustamante et al. 2005; Chimpanzee Sequencing and Analysis Consortium 2005; Nielsen et al. 2005).”
γ-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates (2009, methodology): “To overcome the weakness, there have been methods developed, such as Likelihood Ratio Test (LRT) [53-56] implemented in PAML [57] and Hyphy software [58], to identify positive selection [45,59-61], which tend to be qualitative.”
Large-scale gene function analysis with PANTHER Classification System (2013, methodology): “This tool, based on the work by the PANTHER group 29 and Lander’s group 30 for two different genomic data analyses at about the same time, uses the Mann-Whitney test 31 to determine whether any ontology class or pathway has numeric values that are nonrandomly distributed with respect to the entire…”