{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,6]],"date-time":"2026-02-06T01:10:34Z","timestamp":1770340234890,"version":"3.49.0"},"reference-count":55,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2011,2,3]],"date-time":"2011-02-03T00:00:00Z","timestamp":1296691200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1001074","type":"journal-article","created":{"date-parts":[[2011,2,3]],"date-time":"2011-02-03T21:37:29Z","timestamp":1296769049000},"page":"e1001074","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":34,"title":["Accurate Quantification of Functional Analogy among Close Homologs"],"prefix":"10.1371","volume":"7","author":[{"given":"Maria D.","family":"Chikina","sequence":"first","affiliation":[]},{"given":"Olga G.","family":"Troyanskaya","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2011,2,3]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1101\/gr.4526006","article-title":"Systematic identification of functional orthologs based on protein network comparison.","volume":"16","author":"S Bandyopadhyay","year":"2006","journal-title":"Genome Res"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"D572","DOI":"10.1093\/nar\/gkj118","article-title":"TreeFam: a curated database of phylogenetic trees of animal gene families.","volume":"34","author":"H Li","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"12763","DOI":"10.1073\/pnas.0806627105","article-title":"Global alignment of multiple protein interaction networks with application to functional orthology detection.","volume":"105","author":"R Singh","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"i259","DOI":"10.1093\/bioinformatics\/btp196","article-title":"Global alignment of protein-protein interaction networks by graph matching methods.","volume":"25","author":"M Zaslavskiy","year":"2009","journal-title":"Bioinformatics"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"R114","DOI":"10.1186\/gb-2005-6-13-r114","article-title":"Discovery of biological networks from diverse functional genomic data.","volume":"6","author":"CL Myers","year":"2005","journal-title":"Genome Biol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"e1000322","DOI":"10.1371\/journal.pcbi.1000322","article-title":"Directing experimental biology: a case study in mitochondrial biogenesis.","volume":"5","author":"MA Hibbs","year":"2009","journal-title":"PLoS Comput Biol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"2763","DOI":"10.3390\/ijms10062763","article-title":"Yeast two-hybrid, a powerful tool for systems biology.","volume":"10","author":"A Br\u00fcckner","year":"2009","journal-title":"Int J Mol Sci"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"10967","DOI":"10.1073\/pnas.0602294103","article-title":"Cross-species analysis of biological networks by Bayesian alignment.","volume":"103","author":"J Berg","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"1631","DOI":"10.1093\/bioinformatics\/btm156","article-title":"Alignment of molecular networks by integer quadratic programming.","volume":"23","author":"L Zhenping","year":"2007","journal-title":"Bioinformatics"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1186\/1471-2164-11-35","article-title":"Assessing functional annotation transfers with inter-species conserved coexpression: application to Plasmodium falciparum.","volume":"11","author":"L Brehelin","year":"2010","journal-title":"BMC Genomics"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/gb-2008-9-s1-s2","article-title":"A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.","volume":"9","author":"L Pena-Castillo","year":"2008","journal-title":"Genome Biol"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1504\/IJDMB.2010.034194","article-title":"Genome-wide functional annotation by integrating multiple microarray datasets using meta-analysis.","volume":"4","author":"GP Srivastava","year":"2010","journal-title":"Int J Data Min Bioinform"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"12783","DOI":"10.1073\/pnas.192159399","article-title":"Transitive functional annotation by shortest-path analysis of gene expression data.","volume":"99","author":"X Zhou","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1038\/ng1291","article-title":"Comparing genomic expression patterns across species identifies shared transcriptional profile in aging.","volume":"36","author":"SA McCarroll","year":"2004","journal-title":"Nat Genet"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"3351","DOI":"10.1073\/pnas.0530258100","article-title":"Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms.","volume":"100","author":"O Alter","year":"2003","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"6062","DOI":"10.1073\/pnas.0400782101","article-title":"A gene atlas of the mouse and human protein-encoding transcriptomes.","volume":"101","author":"AI Su","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"2890","DOI":"10.1093\/bioinformatics\/btl492","article-title":"A scalable method for integration and functional analysis of multiple microarray datasets.","volume":"22","author":"C Huttenhower","year":"2006","journal-title":"Bioinformatics"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1186\/1471-2164-7-187","article-title":"Finding function: evaluation methods for functional genomic data.","volume":"7","author":"CL Myers","year":"2006","journal-title":"BMC Genomics"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"D211","DOI":"10.1093\/nar\/gkn785","article-title":"InterPro: the integrative protein signature database.","volume":"37","author":"S Hunter","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"D211","DOI":"10.1093\/nar\/gkp985","article-title":"The Pfam protein families database.","volume":"38","author":"RD Finn","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"R23","DOI":"10.1186\/gb-2003-4-3-r23","article-title":"The GRID: the General Repository for Interaction Datasets.","volume":"4","author":"BJ Breitkreutz","year":"2003","journal-title":"Genome Biol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"33023","DOI":"10.1074\/jbc.272.52.33023","article-title":"SNAP-23 is not cleaved by botulinum neurotoxin E and can replace SNAP-25 in the process of insulin secretion.","volume":"272","author":"K Sadoul","year":"1997","journal-title":"J Biol Chem"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"24408","DOI":"10.1016\/S0021-9258(20)80540-7","article-title":"Evolutionary conservation of synaptosome-associated protein 25 kDa (SNAP-25) shown by Drosophila and Torpedo cDNA clones.","volume":"268","author":"C Risinger","year":"1993","journal-title":"J Biol Chem"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"13300","DOI":"10.1074\/jbc.271.23.13300","article-title":"Identification of a novel syntaxin- and synaptobrevin\/VAMP-binding protein, SNAP-23, expressed in non-neuronal tissues.","volume":"271","author":"V Ravichandran","year":"1996","journal-title":"J Biol Chem"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/S0006-8993(99)01371-2","article-title":"Organization of the secretory machinery in the rodent brain: distribution of the t-SNAREs, SNAP-25 and SNAP-23.","volume":"831","author":"D Chen","year":"1999","journal-title":"Brain Res"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1016\/S0092-8674(00)81594-9","article-title":"Relocation of the t-SNARE SNAP-23 from lamellipodia-like cell surface projections regulates compound exocytosis in mast cells.","volume":"94","author":"Z Guo","year":"1998","journal-title":"Cell"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"C1108","DOI":"10.1152\/ajpcell.1999.276.5.C1108","article-title":"SNAP23 promotes insulin-dependent glucose uptake in 3T3-L1 adipocytes: possible interaction with cytoskeleton.","volume":"276","author":"LJ Foster","year":"1999","journal-title":"Am J Physiol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1038\/35077241","article-title":"The microenvironment of the tumour-host interface.","volume":"411","author":"LA Liotta","year":"2001","journal-title":"Nature"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1038\/414799a","article-title":"Insulin signalling and the regulation of glucose and lipid metabolism.","volume":"414","author":"AR Saltiel","year":"2001","journal-title":"Nature"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1038\/nature03353","article-title":"Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans.","volume":"434","author":"B S\u00f6nnichsen","year":"2005","journal-title":"Nature"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1016\/S0092-8674(03)00926-7","article-title":"Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria.","volume":"115","author":"VK Mootha","year":"2003","journal-title":"Cell"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1016\/j.cell.2008.06.016","article-title":"A mitochondrial protein compendium elucidates complex I disease biology.","volume":"134","author":"DJ Pagliarini","year":"2008","journal-title":"Cell"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"13207","DOI":"10.1073\/pnas.2135385100","article-title":"The proteome of Saccharomyces cerevisiae mitochondria.","volume":"100","author":"A Sickmann","year":"2003","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"1543","DOI":"10.1021\/pr050477f","article-title":"Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics.","volume":"5","author":"J Reinders","year":"2006","journal-title":"J Proteome Res"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1038\/nn783","article-title":"Genetic ablation of the t-SNARE SNAP-25 distinguishes mechanisms of neuroexocytosis.","volume":"5","author":"P Washbourne","year":"2002","journal-title":"Nat Neurosci"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1111\/j.1432-1033.1996.00877.x","article-title":"Distinct exocytotic responses of intact and permeabilised chromaffin cells after cleavage of the 25-kDa synaptosomal-associated protein (SNAP-25) or synaptobrevin by botulinum toxin A or B.","volume":"236","author":"GW Lawrence","year":"1996","journal-title":"Eur J Biochem"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"2492","DOI":"10.1074\/jbc.274.4.2492","article-title":"Proteins of the exocytotic core complex mediate platelet alpha-granule secretion. Roles of vesicle-associated membrane protein, SNAP-23, and syntaxin 4.","volume":"274","author":"R Flaumenhaft","year":"1999","journal-title":"J Biol Chem"},{"issue":"Pt 22","key":"ref38","doi-asserted-by":"crossref","first-page":"4055","DOI":"10.1242\/jcs.113.22.4055","article-title":"SNAP-24, a Drosophila SNAP-25 homologue on granule membranes, is a putative mediator of secretion and granule-granule fusion in salivary glands.","volume":"113","author":"BA Niemeyer","year":"2000","journal-title":"J Cell Sci"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1016\/j.jmb.2003.08.055","article-title":"Neuron cell type-specific SNAP-25 expression driven by multiple regulatory elements in the nematode Caenorhabditis elegans.","volume":"333","author":"SB Hwang","year":"2003","journal-title":"J Mol Biol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"16350","DOI":"10.1073\/pnas.0803617105","article-title":"Intestinal signaling to GABAergic neurons regulates a rhythmic behavior in Caenorhabditis elegans.","volume":"105","author":"TR Mahoney","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"1918","DOI":"10.1091\/mbc.E03-09-0684","article-title":"SNAP-23 functions in docking\/fusion of granules at low Ca2+.","volume":"15","author":"E Chieregatti","year":"2004","journal-title":"Mol Biol Cell"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0074-7696(03)01001-5","article-title":"The nuclear lamina and its functions in the nucleus.","volume":"226","author":"Y Gruenbaum","year":"2003","journal-title":"Int Rev Cytol"},{"issue":"Pt 10","key":"ref43","doi-asserted-by":"crossref","first-page":"3189","DOI":"10.1242\/jcs.108.10.3189","article-title":"Expression of Drosophila lamin C is developmentally regulated: analogies with vertebrate A-type lamins.","volume":"108","author":"D Riemer","year":"1995","journal-title":"J Cell Sci"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1534\/genetics.105.043208","article-title":"Molecular genetic analysis of the nested Drosophila melanogaster lamin C gene.","volume":"171","author":"SR Schulze","year":"2005","journal-title":"Genetics"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"e532","DOI":"10.1371\/journal.pone.0000532","article-title":"Characterization of lamin mutation phenotypes in Drosophila and comparison to human laminopathies.","volume":"2","author":"A Mu\u00f1oz-Alarc\u00f3n","year":"2007","journal-title":"PLoS One"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"e7564","DOI":"10.1371\/journal.pone.0007564","article-title":"A comparative study of Drosophila and human A-type lamins.","volume":"4","author":"SR Schulze","year":"2009","journal-title":"PLoS One"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"3937","DOI":"10.1091\/mbc.11.11.3937","article-title":"Essential roles for Caenorhabditis elegans lamin gene in nuclear organization, cell cycle progression, and spatial organization of nuclear pore complexes.","volume":"11","author":"J Liu","year":"2000","journal-title":"Mol Biol Cell"},{"key":"ref48","article-title":"Disparate Effects of the Five C. elegans Superoxide Dismutases on Dauer Formation, Stress Resistance and Aging.","author":"R Doonan","year":"2008"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"1621","DOI":"10.1242\/dev.00363","article-title":"Global analysis of dauer gene expression in Caenorhabditis elegans.","volume":"130","author":"J Wang","year":"2003","journal-title":"Development"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"e1000417","DOI":"10.1371\/journal.pcbi.1000417","article-title":"Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans.","volume":"5","author":"MD Chikina","year":"2009","journal-title":"PLoS Comput Biol"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"D562","DOI":"10.1093\/nar\/gki022","article-title":"NCBI GEO: mining millions of expression profiles\u2014database and tools.","volume":"33","author":"T Barrett","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: open software development for computational biology and bioinformatics.","volume":"5","author":"RC Gentleman","year":"2004","journal-title":"Genome Biol"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"2547","DOI":"10.1093\/bioinformatics\/btl412","article-title":"Variance stabilization and normalization for one-color microarray data using a data-driven multiscale approach.","volume":"22","author":"ES Motakis","year":"2006","journal-title":"Bioinformatics"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"1093","DOI":"10.1101\/gr.082214.108","article-title":"Exploring the human genome with functional maps.","volume":"19","author":"C Huttenhower","year":"2009","journal-title":"Genome Res"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"1559","DOI":"10.1093\/bioinformatics\/btn237","article-title":"The Sleipnir library for computational functional genomics.","volume":"24","author":"C Huttenhower","year":"2008","journal-title":"Bioinformatics"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1001074","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,11,18]],"date-time":"2021-11-18T13:42:42Z","timestamp":1637242962000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1001074"}},"subtitle":[],"editor":[{"given":"Richard","family":"Bonneau","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2011,2,3]]},"references-count":55,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2011,2,3]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1001074","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,2,3]]}}}