Assigning protein functions by comparative genome analysis: protein phylogenetic profiles.

By Matteo Pellegrini, Edward M. Marcotte, Michael J. Thompson, D. Eisenberg, Todd O. Yeates. 1999

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Citations in the corpus

OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more (2020, background): “Thus, such co-evolution patterns can be used to infer functionally related genes––a technique known as ‘phylogenetic profiling’ (28).”
Using phylogenetic profiles to predict functional relationships. (2012, methodology): “The first approach developed to compare profiles used the Hamming distance, or simply the number of positions where two binary profiles have different values (1).”
Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network (2003, background): “Finally, the phylogenetic co-inheritance of proteins in several different proteomes may indicate their functional link [7].”
Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. (2000, background): “, in which process or pathway a particular protein plays a role, or with which other protein it interacts) However, although the correlations between various types of genomic context and functional interactions have been addressed several times (Dandekar et al. 1998; Enright et al. 1999; Marcotte et”
Discovery of Human Signaling Systems: Pairing Peptides to G Protein-Coupled Receptors (2019, background): “Calculation of receptor-ligand fingerprints Wemade use of the large number of available complete DNA genome sequences and employed phylogenetic profiling for all receptor/ligand families by exploring the joint presence or joint absence of two genes (Pellegrini et al., 1999).”
Insights into Ciliary Genes and Evolution from Multi-Level Phylogenetic Profiling (2017, background): “This particular distribution has motivated the application of phylogenetic profile approaches (Pellegrini et al. 1999) to discover ciliary genes present in ciliated species and absent in nonciliated ones.”
Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies (2009, background): “These include taking advantage of co-localization of functionally linked genes [20–23], homology-based annotation transfer using phylogenetic and phylogenomic information [24–26], and experimental proteomics approaches such as mass spectrometry [27].”
OMA standalone: orthology inference among public and custom genomes and transcriptomes (2018, methodology): “Orthology is also used to build phylogenetic profiling—patterns of presence and absence of genes across species (Pellegrini et al. 1999).”
GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function (2008, background): “files [7] or with shared protein domains [8].”
STRING: a database of predicted functional associations between proteins (2003, background): “For example, the need for maintaining functionally associated genes together can become visible as an agreement in occurrence-patterns across several genomes (4,5): the genes tend to be either present together, or absent together—they have the same ‘phylogenetic profile’.”