{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T04:55:32Z","timestamp":1761540932744},"reference-count":48,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2009,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Understanding how individual genes contribute towards the fitness of an organism is a fundamental problem in biology. Although recent genome-wide screens have generated abundant data on quantitative fitness for single gene knockouts, very few studies have systematically integrated other types of biological information to understand how and why deletion of specific genes give rise to a particular fitness effect. In this study, we combine quantitative fitness data for single gene knock-outs in yeast with large-scale interaction discovery experiments to understand the effect of gene deletion on the modular architecture of protein complexes, under different growth conditions.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Our analysis reveals that genes in complexes show more severe fitness effects upon deletion than other genes but, in contrast to what has been observed in binary protein-protein interaction networks, we find that this is not related to the number of complexes in which they are present. We also find that, in general, the core and attachment components of protein complexes are equally important for the complex machinery to function. However, when quantifying the importance of core and attachments in single complex variations, or <jats:italic>isoforms<\/jats:italic>, we observe that this global trend originates from either the core or the attachment components being more important for strain fitness, both being equally important or both being dispensable. Finally, our study reveals that different isoforms of a complex can exhibit distinct fitness patterns across growth conditions.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>This study presents a powerful approach to unveil the molecular basis for various complex phenotypic profiles observed in gene deletion experiments. It also highlights some interesting cases of potential functional compensation between protein paralogues and suggests a new piece to fit into the histone-code puzzle.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1752-0509-3-74","type":"journal-article","created":{"date-parts":[[2009,7,18]],"date-time":"2009-07-18T06:13:27Z","timestamp":1247897607000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Exploiting gene deletion fitness effects in yeast to understand the modular architecture of protein complexes under different growth conditions"],"prefix":"10.1186","volume":"3","author":[{"given":"Roland A","family":"Pache","sequence":"first","affiliation":[]},{"given":"M Madan","family":"Babu","sequence":"additional","affiliation":[]},{"given":"Patrick","family":"Aloy","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2009,7,18]]},"reference":[{"issue":"5429","key":"342_CR1","doi-asserted-by":"publisher","first-page":"901","DOI":"10.1126\/science.285.5429.901","volume":"285","author":"EA Winzeler","year":"1999","unstructured":"Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, Andre B, Bangham R, Benito R, Boeke JD, Bussey H, Chu AM, Connelly C, Davis K, Dietrich F, Dow SW, El Bakkoury M, Foury F, Friend SH, Gentalen E, Giaever G, Hegemann JH, Jones T, Laub M, Liao H, Liebundguth N, Lockhart DJ, Lucau-Danila A, Lussier M, M'Rabet N, Menard P, Mittmann M, Pai C, Rebischung C, Revuelta JL, Riles L, Roberts CJ, Ross-MacDonald P, Scherens B, Snyder M, Sookhai-Mahadeo S, Storms RK, Veronneau S, Voet M, Volckaert G, Ward TR, Wysocki R, Yen GS, Yu K, Zimmermann K, Philippsen P, Johnston M, Davis RW: Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science. 1999, 285 (5429): 901-906. 10.1126\/science.285.5429.901","journal-title":"Science"},{"issue":"6896","key":"342_CR2","doi-asserted-by":"publisher","first-page":"387","DOI":"10.1038\/nature00935","volume":"418","author":"G Giaever","year":"2002","unstructured":"Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau-Danila A, Anderson K, Andre B, Arkin AP, Astromoff A, El-Bakkoury M, Bangham R, Benito R, Brachat S, Campanaro S, Curtiss M, Davis K, Deutschbauer A, Entian KD, Flaherty P, Foury F, Garfinkel DJ, Gerstein M, Gotte D, Guldener U, Hegemann JH, Hempel S, Herman Z, Jaramillo DF, Kelly DE, Kelly SL, Kotter P, LaBonte D, Lamb DC, Lan N, Liang H, Liao H, Liu L, Luo C, Lussier M, Mao R, Menard P, Ooi SL, Revuelta JL, Roberts CJ, Rose M, Ross-Macdonald P, Scherens B, Schimmack G, Shafer B, Shoemaker DD, Sookhai-Mahadeo S, Storms RK, Strathern JN, Valle G, Voet M, Volckaert G, Wang CY, Ward TR, Wilhelmy J, Winzeler EA, Yang Y, Yen G, Youngman E, Yu K, Bussey H, Boeke JD, Snyder M, Philippsen P, Davis RW, Johnston M: Functional profiling of the Saccharomyces cerevisiae genome. Nature. 2002, 418 (6896): 387-391. 10.1038\/nature00935","journal-title":"Nature"},{"issue":"4","key":"342_CR3","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1038\/ng929","volume":"31","author":"LM Steinmetz","year":"2002","unstructured":"Steinmetz LM, Scharfe C, Deutschbauer AM, Mokranjac D, Herman ZS, Jones T, Chu AM, Giaever G, Prokisch H, Oefner PJ, Davis RW: Systematic screen for human disease genes in yeast. Nat Genet. 2002, 31 (4): 400-404.","journal-title":"Nat Genet"},{"key":"342_CR4","volume-title":"Mol Syst Biol","author":"AM Dudley","year":"2005","unstructured":"Dudley AM, Janse DM, Tanay A, Shamir R, Church GM: A global view of pleiotropy and phenotypically derived gene function in yeast. Mol Syst Biol. 2005, 1:"},{"issue":"6","key":"342_CR5","doi-asserted-by":"publisher","first-page":"605","DOI":"10.1007\/s00438-006-0112-1","volume":"275","author":"E Ericson","year":"2006","unstructured":"Ericson E, Pylvanainen I, Fernandez-Ricaud L, Nerman O, Warringer J, Blomberg A: Genetic pleiotropy in Saccharomyces cerevisiae quantified by high-resolution phenotypic profiling. Mol Genet Genomics. 2006, 275 (6): 605-614. 10.1007\/s00438-006-0112-1","journal-title":"Mol Genet Genomics"},{"issue":"5874","key":"342_CR6","doi-asserted-by":"publisher","first-page":"362","DOI":"10.1126\/science.1150021","volume":"320","author":"ME Hillenmeyer","year":"2008","unstructured":"Hillenmeyer ME, Fung E, Wildenhain J, Pierce SE, Hoon S, Lee W, Proctor M, St Onge RP, Tyers M, Koller D, Altman RB, Davis RW, Nislow C, Giaever G: The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science. 2008, 320 (5874): 362-365. 10.1126\/science.1150021","journal-title":"Science"},{"issue":"10","key":"342_CR7","doi-asserted-by":"publisher","first-page":"e170","DOI":"10.1371\/journal.pgen.0020170","volume":"2","author":"F Perocchi","year":"2006","unstructured":"Perocchi F, Jensen LJ, Gagneur J, Ahting U, von Mering C, Bork P, Prokisch H, Steinmetz LM: Assessing systems properties of yeast mitochondria through an interaction map of the organelle. PLoS Genet. 2006, 2 (10): e170- 10.1371\/journal.pgen.0020170","journal-title":"PLoS Genet"},{"issue":"6","key":"342_CR8","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1016\/j.tig.2004.04.008","volume":"20","author":"H Yu","year":"2004","unstructured":"Yu H, Greenbaum D, Xin Lu H, Zhu X, Gerstein M: Genomic analysis of essentiality within protein networks. Trends Genet. 2004, 20 (6): 227-231. 10.1016\/j.tig.2004.04.008","journal-title":"Trends Genet"},{"issue":"7084","key":"342_CR9","doi-asserted-by":"publisher","first-page":"631","DOI":"10.1038\/nature04532","volume":"440","author":"AC Gavin","year":"2006","unstructured":"Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dumpelfeld B, Edelmann A, Heurtier MA, Hoffman V, Hoefert C, Klein K, Hudak M, Michon AM, Schelder M, Schirle M, Remor M, Rudi T, Hooper S, Bauer A, Bouwmeester T, Casari G, Drewes G, Neubauer G, Rick JM, Kuster B, Bork P, Russell RB, Superti-Furga G: Proteome survey reveals modularity of the yeast cell machinery. Nature. 2006, 440 (7084): 631-636. 10.1038\/nature04532","journal-title":"Nature"},{"issue":"7084","key":"342_CR10","doi-asserted-by":"publisher","first-page":"637","DOI":"10.1038\/nature04670","volume":"440","author":"NJ Krogan","year":"2006","unstructured":"Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrin-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam MH, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF: Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature. 2006, 440 (7084): 637-643. 10.1038\/nature04670","journal-title":"Nature"},{"issue":"3","key":"342_CR11","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1002\/pmic.200700801","volume":"8","author":"CN Pang","year":"2008","unstructured":"Pang CN, Krycer JR, Lek A, Wilkins MR: Are protein complexes made of cores, modules and attachments?. Proteomics. 2008, 8 (3): 425-434. 10.1002\/pmic.200700801","journal-title":"Proteomics"},{"issue":"5550","key":"342_CR12","doi-asserted-by":"publisher","first-page":"2364","DOI":"10.1126\/science.1065810","volume":"294","author":"AH Tong","year":"2001","unstructured":"Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Page N, Robinson M, Raghibizadeh S, Hogue CW, Bussey H, Andrews B, Tyers M, Boone C: Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science. 2001, 294 (5550): 2364-2368. 10.1126\/science.1065810","journal-title":"Science"},{"issue":"5659","key":"342_CR13","doi-asserted-by":"publisher","first-page":"808","DOI":"10.1126\/science.1091317","volume":"303","author":"AH Tong","year":"2004","unstructured":"Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Menard P, Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, Sdicu AM, Shapiro J, Sheikh B, Suter B, Wong SL, Zhang LV, Zhu H, Burd CG, Munro S, Sander C, Rine J, Greenblatt J, Peter M, Bretscher A, Bell G, Roth FP, Brown GW, Andrews B, Bussey H, Boone C: Global mapping of the yeast genetic interaction network. Science. 2004, 303 (5659): 808-813. 10.1126\/science.1091317","journal-title":"Science"},{"issue":"3","key":"342_CR14","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1016\/j.cell.2005.08.031","volume":"123","author":"M Schuldiner","year":"2005","unstructured":"Schuldiner M, Collins SR, Thompson NJ, Denic V, Bhamidipati A, Punna T, Ihmels J, Andrews B, Boone C, Greenblatt JF, Weissman JS, Krogan NJ: Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell. 2005, 123 (3): 507-519. 10.1016\/j.cell.2005.08.031","journal-title":"Cell"},{"issue":"7137","key":"342_CR15","doi-asserted-by":"publisher","first-page":"806","DOI":"10.1038\/nature05649","volume":"446","author":"SR Collins","year":"2007","unstructured":"Collins SR, Miller KM, Maas NL, Roguev A, Fillingham J, Chu CS, Schuldiner M, Gebbia M, Recht J, Shales M, Ding H, Xu H, Han J, Ingvarsdottir K, Cheng B, Andrews B, Boone C, Berger SL, Hieter P, Zhang Z, Brown GW, Ingles CJ, Emili A, Allis CD, Toczyski DP, Weissman JS, Greenblatt JF, Krogan NJ: Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature. 2007, 446 (7137): 806-810. 10.1038\/nature05649","journal-title":"Nature"},{"issue":"3","key":"342_CR16","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1016\/S0022-2836(02)01144-0","volume":"324","author":"SA Teichmann","year":"2002","unstructured":"Teichmann SA: The constraints protein-protein interactions place on sequence divergence. J Mol Biol. 2002, 324 (3): 399-407. 10.1016\/S0022-2836(02)01144-0","journal-title":"J Mol Biol"},{"issue":"1467","key":"342_CR17","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1098\/rstb.2005.1807","volume":"361","author":"JB Pereira-Leal","year":"2006","unstructured":"Pereira-Leal JB, Levy ED, Teichmann SA: The origins and evolution of functional modules: lessons from protein complexes. Philos Trans R Soc Lond B Biol Sci. 2006, 361 (1467): 507-517. 10.1098\/rstb.2005.1807","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"issue":"11","key":"342_CR18","doi-asserted-by":"publisher","first-page":"2450","DOI":"10.1101\/gr.1073603","volume":"13","author":"Z Dezso","year":"2003","unstructured":"Dezso Z, Oltvai ZN, Barabasi AL: Bioinformatics analysis of experimentally determined protein complexes in the yeast Saccharomyces cerevisiae. Genome Res. 2003, 13 (11): 2450-2454. 10.1101\/gr.1073603","journal-title":"Genome Res"},{"issue":"1","key":"342_CR19","doi-asserted-by":"publisher","first-page":"236","DOI":"10.1186\/1471-2105-8-236","volume":"8","author":"GT Hart","year":"2007","unstructured":"Hart GT, Lee I, Marcotte EM: A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. BMC Bioinformatics. 2007, 8 (1): 236- 10.1186\/1471-2105-8-236","journal-title":"BMC Bioinformatics"},{"issue":"6","key":"342_CR20","doi-asserted-by":"publisher","first-page":"1361","DOI":"10.1074\/mcp.M800490-MCP200","volume":"8","author":"H Wang","year":"2009","unstructured":"Wang H, Kakaradov B, Collins SR, Karotki L, Fiedler D, Shales M, Shokat KM, Walther T, Krogan NJ, Koller D: A complex-based reconstruction of the S. cerevisiae interactome. Mol Cell Proteomics. 2009, 8 (6): 1361-1381. 10.1074\/mcp.M800490-MCP200","journal-title":"Mol Cell Proteomics"},{"issue":"6868","key":"342_CR21","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1038\/415141a","volume":"415","author":"AC Gavin","year":"2002","unstructured":"Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, Remor M, Hofert C, Schelder M, Brajenovic M, Ruffner H, Merino A, Klein K, Hudak M, Dickson D, Rudi T, Gnau V, Bauch A, Bastuck S, Huhse B, Leutwein C, Heurtier MA, Copley RR, Edelmann A, Querfurth E, Rybin V, Drewes G, Raida M, Bouwmeester T, Bork P, Seraphin B, Kuster B, Neubauer G, Superti-Furga G: Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 2002, 415 (6868): 141-147. 10.1038\/415141a","journal-title":"Nature"},{"issue":"6833","key":"342_CR22","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1038\/35075138","volume":"411","author":"H Jeong","year":"2001","unstructured":"Jeong H, Mason SP, Barabasi AL, Oltvai ZN: Lethality and centrality in protein networks. Nature. 2001, 411 (6833): 41-42. 10.1038\/35075138","journal-title":"Nature"},{"issue":"6","key":"342_CR23","doi-asserted-by":"publisher","first-page":"e88","DOI":"10.1371\/journal.pgen.0020088","volume":"2","author":"X He","year":"2006","unstructured":"He X, Zhang J: Why do hubs tend to be essential in protein networks?. PLoS Genet. 2006, 2 (6): e88- 10.1371\/journal.pgen.0020088","journal-title":"PLoS Genet"},{"issue":"4","key":"342_CR24","doi-asserted-by":"publisher","first-page":"e59","DOI":"10.1371\/journal.pcbi.0030059","volume":"3","author":"H Yu","year":"2007","unstructured":"Yu H, Kim PM, Sprecher E, Trifonov V, Gerstein M: The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol. 2007, 3 (4): e59- 10.1371\/journal.pcbi.0030059","journal-title":"PLoS Comput Biol"},{"issue":"8","key":"342_CR25","doi-asserted-by":"publisher","first-page":"e1000140","DOI":"10.1371\/journal.pcbi.1000140","volume":"4","author":"E Zotenko","year":"2008","unstructured":"Zotenko E, Mestre J, O'Leary DP, Przytycka TM: Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality. PLoS Comput Biol. 2008, 4 (8): e1000140- 10.1371\/journal.pcbi.1000140","journal-title":"PLoS Comput Biol"},{"issue":"1573","key":"342_CR26","doi-asserted-by":"publisher","first-page":"1721","DOI":"10.1098\/rspb.2005.3128","volume":"272","author":"S Coulomb","year":"2005","unstructured":"Coulomb S, Bauer M, Bernard D, Marsolier-Kergoat MC: Gene essentiality and the topology of protein interaction networks. Proc Biol Sci. 2005, 272 (1573): 1721-1725. 10.1098\/rspb.2005.3128","journal-title":"Proc Biol Sci"},{"issue":"3","key":"342_CR27","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1038\/ng1747","volume":"38","author":"TK Gandhi","year":"2006","unstructured":"Gandhi TK, Zhong J, Mathivanan S, Karthick L, Chandrika KN, Mohan SS, Sharma S, Pinkert S, Nagaraju S, Periaswamy B, Mishra G, Nandakumar K, Shen B, Deshpande N, Nayak R, Sarker M, Boeke JD, Parmigiani G, Schultz J, Bader JS, Pandey A: Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet. 2006, 38 (3): 285-293. 10.1038\/ng1747","journal-title":"Nat Genet"},{"issue":"5898","key":"342_CR28","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1126\/science.1158684","volume":"322","author":"H Yu","year":"2008","unstructured":"Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, Sahalie J, Hirozane-Kishikawa T, Gebreab F, Li N, Simonis N, Hao T, Rual JF, Dricot A, Vazquez A, Murray RR, Simon C, Tardivo L, Tam S, Svrzikapa N, Fan C, de Smet AS, Motyl A, Hudson ME, Park J, Xin X, Cusick ME, Moore T, Boone C, Snyder M, Roth FP, Barabasi AL, Tavernier J, Hill DE, Vidal M: High-quality binary protein interaction map of the yeast interactome network. Science. 2008, 322 (5898): 104-110. 10.1126\/science.1158684","journal-title":"Science"},{"key":"342_CR29","doi-asserted-by":"crossref","unstructured":"Guldener U, Munsterkotter M, Oesterheld M, Pagel P, Ruepp A, Mewes HW, Stumpflen V: MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res. 2006, D436-441. 34 Database","DOI":"10.1093\/nar\/gkj003"},{"issue":"6959","key":"342_CR30","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1038\/nature02046","volume":"425","author":"S Ghaemmaghami","year":"2003","unstructured":"Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, Dephoure N, O'Shea EK, Weissman JS: Global analysis of protein expression in yeast. Nature. 2003, 425 (6959): 737-741. 10.1038\/nature02046","journal-title":"Nature"},{"issue":"5568","key":"342_CR31","doi-asserted-by":"publisher","first-page":"750","DOI":"10.1126\/science.1068696","volume":"296","author":"HB Fraser","year":"2002","unstructured":"Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW: Evolutionary rate in the protein interaction network. Science. 2002, 296 (5568): 750-752. 10.1126\/science.1068696","journal-title":"Science"},{"issue":"32","key":"342_CR32","doi-asserted-by":"publisher","first-page":"28368","DOI":"10.1074\/jbc.C200348200","volume":"277","author":"J Dover","year":"2002","unstructured":"Dover J, Schneider J, Tawiah-Boateng MA, Wood A, Dean K, Johnston M, Shilatifard A: Methylation of histone H3 by COMPASS requires ubiquitination of histone H2B by Rad6. J Biol Chem. 2002, 277 (32): 28368-28371. 10.1074\/jbc.C200348200","journal-title":"J Biol Chem"},{"issue":"3","key":"342_CR33","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1016\/S1097-2765(04)00026-7","volume":"13","author":"E Ezhkova","year":"2004","unstructured":"Ezhkova E, Tansey WP: Proteasomal ATPases link ubiquitylation of histone H2B to methylation of histone H3. Mol Cell. 2004, 13 (3): 435-442. 10.1016\/S1097-2765(04)00026-7","journal-title":"Mol Cell"},{"issue":"13","key":"342_CR34","doi-asserted-by":"publisher","first-page":"10753","DOI":"10.1074\/jbc.C200023200","volume":"277","author":"NJ Krogan","year":"2002","unstructured":"Krogan NJ, Dover J, Khorrami S, Greenblatt JF, Schneider J, Johnston M, Shilatifard A: COMPASS, a histone H3 (Lysine 4) methyltransferase required for telomeric silencing of gene expression. J Biol Chem. 2002, 277 (13): 10753-10755. 10.1074\/jbc.C200023200","journal-title":"J Biol Chem"},{"issue":"6893","key":"342_CR35","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1038\/nature00883","volume":"418","author":"ZW Sun","year":"2002","unstructured":"Sun ZW, Allis CD: Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast. Nature. 2002, 418 (6893): 104-108. 10.1038\/nature00883","journal-title":"Nature"},{"issue":"7143","key":"342_CR36","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1038\/nature05915","volume":"447","author":"SL Berger","year":"2007","unstructured":"Berger SL: The complex language of chromatin regulation during transcription. Nature. 2007, 447 (7143): 407-412. 10.1038\/nature05915","journal-title":"Nature"},{"issue":"7","key":"342_CR37","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1101\/gad.1541507","volume":"21","author":"RN Laribee","year":"2007","unstructured":"Laribee RN, Fuchs SM, Strahl BD: H2B ubiquitylation in transcriptional control: a FACT-finding mission. Genes Dev. 2007, 21 (7): 737-743. 10.1101\/gad.1541507","journal-title":"Genes Dev"},{"key":"342_CR38","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1146\/annurev.biochem.75.103004.142422","volume":"75","author":"A Shilatifard","year":"2006","unstructured":"Shilatifard A: Chromatin modifications by methylation and ubiquitination: implications in the regulation of gene expression. Annu Rev Biochem. 2006, 75: 243-269. 10.1146\/annurev.biochem.75.103004.142422","journal-title":"Annu Rev Biochem"},{"issue":"6905","key":"342_CR39","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1038\/nature01080","volume":"419","author":"H Santos-Rosa","year":"2002","unstructured":"Santos-Rosa H, Schneider R, Bannister AJ, Sherriff J, Bernstein BE, Emre NC, Schreiber SL, Mellor J, Kouzarides T: Active genes are tri-methylated at K4 of histone H3. Nature. 2002, 419 (6905): 407-411. 10.1038\/nature01080","journal-title":"Nature"},{"issue":"6","key":"342_CR40","doi-asserted-by":"publisher","first-page":"849","DOI":"10.1016\/j.molcel.2005.07.024","volume":"19","author":"J Schneider","year":"2005","unstructured":"Schneider J, Wood A, Lee JS, Schuster R, Dueker J, Maguire C, Swanson SK, Florens L, Washburn MP, Shilatifard A: Molecular regulation of histone H3 trimethylation by COMPASS and the regulation of gene expression. Mol Cell. 2005, 19 (6): 849-856. 10.1016\/j.molcel.2005.07.024","journal-title":"Mol Cell"},{"issue":"6","key":"342_CR41","doi-asserted-by":"publisher","first-page":"1084","DOI":"10.1016\/j.cell.2007.09.046","volume":"131","author":"JS Lee","year":"2007","unstructured":"Lee JS, Shukla A, Schneider J, Swanson SK, Washburn MP, Florens L, Bhaumik SR, Shilatifard A: Histone crosstalk between H2B monoubiquitination and H3 methylation mediated by COMPASS. Cell. 2007, 131 (6): 1084-1096. 10.1016\/j.cell.2007.09.046","journal-title":"Cell"},{"issue":"3","key":"342_CR42","doi-asserted-by":"publisher","first-page":"1867","DOI":"10.1074\/jbc.C300494200","volume":"279","author":"JA Daniel","year":"2004","unstructured":"Daniel JA, Torok MS, Sun ZW, Schieltz D, Allis CD, Yates JR, Grant PA: Deubiquitination of histone H2B by a yeast acetyltransferase complex regulates transcription. J Biol Chem. 2004, 279 (3): 1867-1871. 10.1074\/jbc.C300494200","journal-title":"J Biol Chem"},{"issue":"21","key":"342_CR43","doi-asserted-by":"publisher","first-page":"2648","DOI":"10.1101\/gad.1144003","volume":"17","author":"KW Henry","year":"2003","unstructured":"Henry KW, Wyce A, Lo WS, Duggan LJ, Emre NC, Kao CF, Pillus L, Shilatifard A, Osley MA, Berger SL: Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8. Genes Dev. 2003, 17 (21): 2648-2663. 10.1101\/gad.1144003","journal-title":"Genes Dev"},{"issue":"3","key":"342_CR44","doi-asserted-by":"publisher","first-page":"1162","DOI":"10.1128\/MCB.25.3.1162-1172.2005","volume":"25","author":"K Ingvarsdottir","year":"2005","unstructured":"Ingvarsdottir K, Krogan NJ, Emre NC, Wyce A, Thompson NJ, Emili A, Hughes TR, Greenblatt JF, Berger SL: H2B ubiquitin protease Ubp8 and Sgf11 constitute a discrete functional module within the Saccharomyces cerevisiae SAGA complex. Mol Cell Biol. 2005, 25 (3): 1162-1172. 10.1128\/MCB.25.3.1162-1172.2005","journal-title":"Mol Cell Biol"},{"issue":"3","key":"342_CR45","doi-asserted-by":"publisher","first-page":"1173","DOI":"10.1128\/MCB.25.3.1173-1182.2005","volume":"25","author":"KK Lee","year":"2005","unstructured":"Lee KK, Florens L, Swanson SK, Washburn MP, Workman JL: The deubiquitylation activity of Ubp8 is dependent upon Sgf11 and its association with the SAGA complex. Mol Cell Biol. 2005, 25 (3): 1173-1182. 10.1128\/MCB.25.3.1173-1182.2005","journal-title":"Mol Cell Biol"},{"issue":"6992","key":"342_CR46","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1038\/nature02636","volume":"429","author":"B Papp","year":"2004","unstructured":"Papp B, Pal C, Hurst LD: Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature. 2004, 429 (6992): 661-664. 10.1038\/nature02636","journal-title":"Nature"},{"issue":"6918","key":"342_CR47","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1038\/nature01198","volume":"421","author":"Z Gu","year":"2003","unstructured":"Gu Z, Steinmetz LM, Gu X, Scharfe C, Davis RW, Li WH: Role of duplicate genes in genetic robustness against null mutations. Nature. 2003, 421 (6918): 63-66. 10.1038\/nature01198","journal-title":"Nature"},{"issue":"17","key":"342_CR48","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"SF Altschul","year":"1997","unstructured":"Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25 (17): 3389-3402. 10.1093\/nar\/25.17.3389","journal-title":"Nucleic Acids Res"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-3-74.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T11:01:45Z","timestamp":1630494105000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/1752-0509-3-74"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,7,18]]},"references-count":48,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2009,12]]}},"alternative-id":["342"],"URL":"https:\/\/doi.org\/10.1186\/1752-0509-3-74","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,7,18]]},"assertion":[{"value":"15 December 2008","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 July 2009","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 July 2009","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"74"}}