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==Data from publications== | ==Data from publications== | ||
- | The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of November | + | The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of November 20, 2016. |
#Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [http://gpmdb.org/data/keyword/12177431 498]. | #Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [http://gpmdb.org/data/keyword/12177431 498]. | ||
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#Plohnke N, Hamann A, Poetsch A, Osiewacz HD, Rögner M, Rexroth S, (2014) "Proteomic analysis of mitochondria from senescent Podospora anserina casts new light on ROS dependent aging mechanisms." <i>Exp Gerontol</i> <b>56</b>:13–25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24556281 24556281]; doi: [https://dx.doi.org/10.1016/j.exger.2014.02.008 10.1016/j.exger.2014.02.008]; GPMDB: [http://gpmdb.org/data/keyword/24556281 36]. | #Plohnke N, Hamann A, Poetsch A, Osiewacz HD, Rögner M, Rexroth S, (2014) "Proteomic analysis of mitochondria from senescent Podospora anserina casts new light on ROS dependent aging mechanisms." <i>Exp Gerontol</i> <b>56</b>:13–25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24556281 24556281]; doi: [https://dx.doi.org/10.1016/j.exger.2014.02.008 10.1016/j.exger.2014.02.008]; GPMDB: [http://gpmdb.org/data/keyword/24556281 36]. | ||
#Kolinko I, Lohße A, Borg S, Raschdorf O, Jogler C, Tu Q, Pósfai M, Tompa E, Plitzko JM, Brachmann A, Wanner G, Müller R, Zhang Y, Schüler D, (2014) "Biosynthesis of magnetic nanostructures in a foreign organism by transfer of bacterial magnetosome gene clusters." <i>Nat Nanotechnol</i> <b>9</b>(3):193–7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24561353 24561353]; doi: [https://dx.doi.org/10.1038/nnano.2014.13 10.1038/nnano.2014.13]; GPMDB: [http://gpmdb.org/data/keyword/24561353 1]. | #Kolinko I, Lohße A, Borg S, Raschdorf O, Jogler C, Tu Q, Pósfai M, Tompa E, Plitzko JM, Brachmann A, Wanner G, Müller R, Zhang Y, Schüler D, (2014) "Biosynthesis of magnetic nanostructures in a foreign organism by transfer of bacterial magnetosome gene clusters." <i>Nat Nanotechnol</i> <b>9</b>(3):193–7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24561353 24561353]; doi: [https://dx.doi.org/10.1038/nnano.2014.13 10.1038/nnano.2014.13]; GPMDB: [http://gpmdb.org/data/keyword/24561353 1]. | ||
+ | #Warinner C, Rodrigues JF, Vyas R, Trachsel C, Shved N, Grossmann J, Radini A, Hancock Y, Tito RY, Fiddyment S, Speller C, Hendy J, Charlton S, Luder HU, Salazar-García DC, Eppler E, Seiler R, Hansen LH, Castruita JA, Barkow-Oesterreicher S, Teoh KY, Kelstrup CD, Olsen JV, Nanni P, Kawai T, Willerslev E, von Mering C, Lewis CM Jr, Collins MJ, Gilbert MT, Rühli F, Cappellini E, (2014) "Pathogens and host immunity in the ancient human oral cavity." <i>Nat Genet</i> <b>46</b>(4):336–44; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24562188 24562188]; doi: [https://dx.doi.org/10.1038/ng.2906 10.1038/ng.2906]; GPMDB: [http://gpmdb.org/data/keyword/24562188 18]. | ||
#Sigdel TK, Nicora CD, Hsieh SC, Dai H, Qian WJ, Camp DG 2nd, Sarwal MM, (2014) "Optimization for peptide sample preparation for urine peptidomics." <i>Clin Proteomics</i> <b>11</b>(1):7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24568099 24568099]; doi: [https://dx.doi.org/10.1186/1559-0275-11-7 10.1186/1559-0275-11-7]; GPMDB: [http://gpmdb.org/data/keyword/24568099 8]. | #Sigdel TK, Nicora CD, Hsieh SC, Dai H, Qian WJ, Camp DG 2nd, Sarwal MM, (2014) "Optimization for peptide sample preparation for urine peptidomics." <i>Clin Proteomics</i> <b>11</b>(1):7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24568099 24568099]; doi: [https://dx.doi.org/10.1186/1559-0275-11-7 10.1186/1559-0275-11-7]; GPMDB: [http://gpmdb.org/data/keyword/24568099 8]. | ||
#Husi H, Van Agtmael T, Mullen W, Bahlmann FH, Schanstra JP, Vlahou A, Delles C, Perco P, Mischak H, (2014) "Proteome-based systems biology analysis of the diabetic mouse aorta reveals major changes in fatty acid biosynthesis as potential hallmark in diabetes mellitus-associated vascular disease." <i>Circ Cardiovasc Genet</i> <b>7</b>(2):161–70; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24573165 24573165]; doi: [https://dx.doi.org/10.1161/CIRCGENETICS.113.000196 10.1161/CIRCGENETICS.113.000196]; GPMDB: [http://gpmdb.org/data/keyword/24573165 14]. | #Husi H, Van Agtmael T, Mullen W, Bahlmann FH, Schanstra JP, Vlahou A, Delles C, Perco P, Mischak H, (2014) "Proteome-based systems biology analysis of the diabetic mouse aorta reveals major changes in fatty acid biosynthesis as potential hallmark in diabetes mellitus-associated vascular disease." <i>Circ Cardiovasc Genet</i> <b>7</b>(2):161–70; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24573165 24573165]; doi: [https://dx.doi.org/10.1161/CIRCGENETICS.113.000196 10.1161/CIRCGENETICS.113.000196]; GPMDB: [http://gpmdb.org/data/keyword/24573165 14]. | ||
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#Peebo K, Valgepea K, Nahku R, Riis G, Oun M, Adamberg K, Vilu R, (2014) "Coordinated activation of PTA-ACS and TCA cycles strongly reduces overflow metabolism of acetate in Escherichia coli." <i>Appl Microbiol Biotechnol</i> <b>98</b>(11):5131–43; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24633370 24633370]; doi: [https://dx.doi.org/10.1007/s00253-014-5613-y 10.1007/s00253-014-5613-y]; GPMDB: [http://gpmdb.org/data/keyword/24633370 10]. | #Peebo K, Valgepea K, Nahku R, Riis G, Oun M, Adamberg K, Vilu R, (2014) "Coordinated activation of PTA-ACS and TCA cycles strongly reduces overflow metabolism of acetate in Escherichia coli." <i>Appl Microbiol Biotechnol</i> <b>98</b>(11):5131–43; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24633370 24633370]; doi: [https://dx.doi.org/10.1007/s00253-014-5613-y 10.1007/s00253-014-5613-y]; GPMDB: [http://gpmdb.org/data/keyword/24633370 10]. | ||
#Clark CG, Chong PM, McCorrister SJ, Simon P, Walker M, Lee DM, Nguy K, Cheng K, Gilmour MW, Westmacott GR, (2014) "The CJIE1 prophage of Campylobacter jejuni affects protein expression in growth media with and without bile salts." <i>BMC Microbiol</i> <b>14</b>:70; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24641125 24641125]; doi: [https://dx.doi.org/10.1186/1471-2180-14-70 10.1186/1471-2180-14-70]; GPMDB: [http://gpmdb.org/data/keyword/24641125 163]. | #Clark CG, Chong PM, McCorrister SJ, Simon P, Walker M, Lee DM, Nguy K, Cheng K, Gilmour MW, Westmacott GR, (2014) "The CJIE1 prophage of Campylobacter jejuni affects protein expression in growth media with and without bile salts." <i>BMC Microbiol</i> <b>14</b>:70; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24641125 24641125]; doi: [https://dx.doi.org/10.1186/1471-2180-14-70 10.1186/1471-2180-14-70]; GPMDB: [http://gpmdb.org/data/keyword/24641125 163]. | ||
+ | #Zhang Q, Matzke M, Schepmoes AA, Moore RJ, Webb-Robertson BJ, Hu Z, Monroe ME, Qian WJ, Smith RD, Morgan WF, (2014) "High and low doses of ionizing radiation induce different secretome profiles in a human skin model." <i>PLoS One</i> <b>9</b>(3):e92332; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24642900 24642900]; doi: [https://dx.doi.org/10.1371/journal.pone.0092332 10.1371/journal.pone.0092332]; GPMDB: [http://gpmdb.org/data/keyword/24642900 85]. | ||
#de Groot RE, Ganji RS, Bernatik O, Lloyd-Lewis B, Seipel K, Šedová K, Zdráhal Z, Dhople VM, Dale TC, Korswagen HC, Bryja V, (2014) "Huwe1-mediated ubiquitylation of dishevelled defines a negative feedback loop in the Wnt signaling pathway." <i>Sci Signal</i> <b>7</b>(317):ra26; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24643799 24643799]; doi: [https://dx.doi.org/10.1126/scisignal.2004985 10.1126/scisignal.2004985]; GPMDB: [http://gpmdb.org/data/keyword/24643799 10]. | #de Groot RE, Ganji RS, Bernatik O, Lloyd-Lewis B, Seipel K, Šedová K, Zdráhal Z, Dhople VM, Dale TC, Korswagen HC, Bryja V, (2014) "Huwe1-mediated ubiquitylation of dishevelled defines a negative feedback loop in the Wnt signaling pathway." <i>Sci Signal</i> <b>7</b>(317):ra26; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24643799 24643799]; doi: [https://dx.doi.org/10.1126/scisignal.2004985 10.1126/scisignal.2004985]; GPMDB: [http://gpmdb.org/data/keyword/24643799 10]. | ||
#Sahasrabuddhe NA, Barbhuiya MA, Bhunia S, Subbannayya T, Gowda H, Advani J, Shrivastav BR, Navani S, Leal P, Roa JC, Chaerkady R, Gupta S, Chatterjee A, Pandey A, Tiwari PK, (2014) "Identification of prosaposin and transgelin as potential biomarkers for gallbladder cancer using quantitative proteomics." <i>Biochem Biophys Res Commun</i> <b>446</b>(4):863–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24657443 24657443]; doi: [https://dx.doi.org/10.1016/j.bbrc.2014.03.017 10.1016/j.bbrc.2014.03.017]; GPMDB: [http://gpmdb.org/data/keyword/24657443 29]. | #Sahasrabuddhe NA, Barbhuiya MA, Bhunia S, Subbannayya T, Gowda H, Advani J, Shrivastav BR, Navani S, Leal P, Roa JC, Chaerkady R, Gupta S, Chatterjee A, Pandey A, Tiwari PK, (2014) "Identification of prosaposin and transgelin as potential biomarkers for gallbladder cancer using quantitative proteomics." <i>Biochem Biophys Res Commun</i> <b>446</b>(4):863–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24657443 24657443]; doi: [https://dx.doi.org/10.1016/j.bbrc.2014.03.017 10.1016/j.bbrc.2014.03.017]; GPMDB: [http://gpmdb.org/data/keyword/24657443 29]. | ||
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#Toriyama M, Lee C, Taylor SP, Duran I, Cohn DH, Bruel AL, Tabler JM, Drew K, Kelly MR, Kim S, Park TJ, Braun DA, Pierquin G, Biver A, Wagner K, Malfroot A, Panigrahi I, Franco B, Al-Lami HA, Yeung Y, Choi YJ, University of Washington Center for Mendelian Genomics., Duffourd Y, Faivre L, Rivière JB, Chen J, Liu KJ, Marcotte EM, Hildebrandt F, Thauvin-Robinet C, Krakow D, Jackson PK, Wallingford JB, (2016) "The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery." <i>Nat Genet</i> <b>48</b>(6):648–56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27158779 27158779]; doi: [https://dx.doi.org/10.1038/ng.3558 10.1038/ng.3558]; GPMDB: [http://gpmdb.org/data/keyword/27158779 44]. | #Toriyama M, Lee C, Taylor SP, Duran I, Cohn DH, Bruel AL, Tabler JM, Drew K, Kelly MR, Kim S, Park TJ, Braun DA, Pierquin G, Biver A, Wagner K, Malfroot A, Panigrahi I, Franco B, Al-Lami HA, Yeung Y, Choi YJ, University of Washington Center for Mendelian Genomics., Duffourd Y, Faivre L, Rivière JB, Chen J, Liu KJ, Marcotte EM, Hildebrandt F, Thauvin-Robinet C, Krakow D, Jackson PK, Wallingford JB, (2016) "The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery." <i>Nat Genet</i> <b>48</b>(6):648–56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27158779 27158779]; doi: [https://dx.doi.org/10.1038/ng.3558 10.1038/ng.3558]; GPMDB: [http://gpmdb.org/data/keyword/27158779 44]. | ||
#Hsu CH, Hsu CW, Hsueh C, Wang CL, Wu YC, Wu CC, Liu CC, Yu JS, Chang YS, Yu CJ, (2016) "Identification and Characterization of Potential Biomarkers by Quantitative Tissue Proteomics of Primary Lung Adenocarcinoma." <i>Mol Cell Proteomics</i> <b>15</b>(7):2396–410; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27161446 27161446]; doi: [https://dx.doi.org/10.1074/mcp.M115.057026 10.1074/mcp.M115.057026]; GPMDB: [http://gpmdb.org/data/keyword/27161446 60]. | #Hsu CH, Hsu CW, Hsueh C, Wang CL, Wu YC, Wu CC, Liu CC, Yu JS, Chang YS, Yu CJ, (2016) "Identification and Characterization of Potential Biomarkers by Quantitative Tissue Proteomics of Primary Lung Adenocarcinoma." <i>Mol Cell Proteomics</i> <b>15</b>(7):2396–410; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27161446 27161446]; doi: [https://dx.doi.org/10.1074/mcp.M115.057026 10.1074/mcp.M115.057026]; GPMDB: [http://gpmdb.org/data/keyword/27161446 60]. | ||
+ | #Sigdel TK, Gao Y, He J, Wang A, Nicora CD, Fillmore TL, Shi T, Webb-Robertson BJ, Smith RD, Qian WJ, Salvatierra O, Camp DG 2nd, Sarwal MM, (2016) "Mining the human urine proteome for monitoring renal transplant injury." <i>Kidney Int</i> <b>89</b>(6):1244–52; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27165815 27165815]; doi: [https://dx.doi.org/10.1016/j.kint.2015.12.049 10.1016/j.kint.2015.12.049]; GPMDB: [http://gpmdb.org/data/keyword/27165815 227]. | ||
#Taha MK, Claus H, Lappann M, Veyrier FJ, Otto A, Becher D, Deghmane AE, Frosch M, Hellenbrand W, Hong E, Parent du Châtelet I, Prior K, Harmsen D, Vogel U, (2016) "Evolutionary Events Associated with an Outbreak of Meningococcal Disease in Men Who Have Sex with Men." <i>PLoS One</i> <b>11</b>(5):e0154047; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27167067 27167067]; doi: [https://dx.doi.org/10.1371/journal.pone.0154047 10.1371/journal.pone.0154047]; GPMDB: [http://gpmdb.org/data/keyword/27167067 12]. | #Taha MK, Claus H, Lappann M, Veyrier FJ, Otto A, Becher D, Deghmane AE, Frosch M, Hellenbrand W, Hong E, Parent du Châtelet I, Prior K, Harmsen D, Vogel U, (2016) "Evolutionary Events Associated with an Outbreak of Meningococcal Disease in Men Who Have Sex with Men." <i>PLoS One</i> <b>11</b>(5):e0154047; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27167067 27167067]; doi: [https://dx.doi.org/10.1371/journal.pone.0154047 10.1371/journal.pone.0154047]; GPMDB: [http://gpmdb.org/data/keyword/27167067 12]. | ||
#Tuveng TR, Arntzen MØ, Bengtsson O, Gardner JG, Vaaje-Kolstad G, Eijsink VG, (2016) "Proteomic investigation of the secretome of Cellvibrio japonicus during growth on chitin." <i>Proteomics</i> <b>16</b>(13):1904–14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27169553 27169553]; doi: [https://dx.doi.org/10.1002/pmic.201500419 10.1002/pmic.201500419]; GPMDB: [http://gpmdb.org/data/keyword/27169553 18]. | #Tuveng TR, Arntzen MØ, Bengtsson O, Gardner JG, Vaaje-Kolstad G, Eijsink VG, (2016) "Proteomic investigation of the secretome of Cellvibrio japonicus during growth on chitin." <i>Proteomics</i> <b>16</b>(13):1904–14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27169553 27169553]; doi: [https://dx.doi.org/10.1002/pmic.201500419 10.1002/pmic.201500419]; GPMDB: [http://gpmdb.org/data/keyword/27169553 18]. | ||
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#Jean Beltran PM, Mathias RA, Cristea IM, (2016) "A Portrait of the Human Organelle Proteome In Space and Time during Cytomegalovirus Infection." <i>Cell Syst</i> <b>3</b>(4):361–373.e6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27641956 27641956]; doi: [https://dx.doi.org/10.1016/j.cels.2016.08.012 10.1016/j.cels.2016.08.012]; GPMDB: [http://gpmdb.org/data/keyword/27641956 45]. | #Jean Beltran PM, Mathias RA, Cristea IM, (2016) "A Portrait of the Human Organelle Proteome In Space and Time during Cytomegalovirus Infection." <i>Cell Syst</i> <b>3</b>(4):361–373.e6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27641956 27641956]; doi: [https://dx.doi.org/10.1016/j.cels.2016.08.012 10.1016/j.cels.2016.08.012]; GPMDB: [http://gpmdb.org/data/keyword/27641956 45]. | ||
#Athanason MG, Stevens SM Jr, Burkhardt BR, (2016) "Hepatic SILAC proteomic data from PANDER transgenic model." <i>Data Brief</i> <b>9</b>:159–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27642623 27642623]; doi: [https://dx.doi.org/10.1016/j.dib.2016.08.017 10.1016/j.dib.2016.08.017]; GPMDB: [http://gpmdb.org/data/keyword/27642623 18]. | #Athanason MG, Stevens SM Jr, Burkhardt BR, (2016) "Hepatic SILAC proteomic data from PANDER transgenic model." <i>Data Brief</i> <b>9</b>:159–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27642623 27642623]; doi: [https://dx.doi.org/10.1016/j.dib.2016.08.017 10.1016/j.dib.2016.08.017]; GPMDB: [http://gpmdb.org/data/keyword/27642623 18]. | ||
- | #Vu LD, Stes E, Van Bel M, Nelissen H, Maddelein D, Inzé D, Coppens F, Martens L, Gevaert K, De Smet I, (2016) "Up-to-Date Workflow for Plant (Phospho)proteomics Identifies Differential Drought-Responsive Phosphorylation Events in Maize Leaves." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27643528 27643528]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00348 10.1021/acs.jproteome.6b00348]; GPMDB: [http://gpmdb.org/data/keyword/27643528 | + | #Vu LD, Stes E, Van Bel M, Nelissen H, Maddelein D, Inzé D, Coppens F, Martens L, Gevaert K, De Smet I, (2016) "Up-to-Date Workflow for Plant (Phospho)proteomics Identifies Differential Drought-Responsive Phosphorylation Events in Maize Leaves." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27643528 27643528]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00348 10.1021/acs.jproteome.6b00348]; GPMDB: [http://gpmdb.org/data/keyword/27643528 28]. |
#Kubicek-Sutherland JZ, Lofton H, Vestergaard M, Hjort K, Ingmer H, Andersson DI, (2016) "Antimicrobial peptide exposure selects for Staphylococcus aureus resistance to human defence peptides." <i>J Antimicrob Chemother</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27650186 27650186]; doi: [https://dx.doi.org/10.1093/jac/dkw381 10.1093/jac/dkw381]; GPMDB: [http://gpmdb.org/data/keyword/27650186 42]. | #Kubicek-Sutherland JZ, Lofton H, Vestergaard M, Hjort K, Ingmer H, Andersson DI, (2016) "Antimicrobial peptide exposure selects for Staphylococcus aureus resistance to human defence peptides." <i>J Antimicrob Chemother</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27650186 27650186]; doi: [https://dx.doi.org/10.1093/jac/dkw381 10.1093/jac/dkw381]; GPMDB: [http://gpmdb.org/data/keyword/27650186 42]. | ||
#Goldman AR, Bitler BG, Schug Z, Conejo-Garcia JR, Zhang R, Speicher DW, (2016) "The Primary Effect on the Proteome of ARID1A-mutated Ovarian Clear Cell Carcinoma is Downregulation of the Mevalonate Pathway at the Post-transcriptional Level." <i>Mol Cell Proteomics</i> <b>15</b>(11):3348–3360; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27654507 27654507]; doi: [https://dx.doi.org/10.1074/mcp.M116.062539 10.1074/mcp.M116.062539]; GPMDB: [http://gpmdb.org/data/keyword/27654507 12]. | #Goldman AR, Bitler BG, Schug Z, Conejo-Garcia JR, Zhang R, Speicher DW, (2016) "The Primary Effect on the Proteome of ARID1A-mutated Ovarian Clear Cell Carcinoma is Downregulation of the Mevalonate Pathway at the Post-transcriptional Level." <i>Mol Cell Proteomics</i> <b>15</b>(11):3348–3360; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27654507 27654507]; doi: [https://dx.doi.org/10.1074/mcp.M116.062539 10.1074/mcp.M116.062539]; GPMDB: [http://gpmdb.org/data/keyword/27654507 12]. | ||
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#Wang Q, Drouin EE, Yao C, Zhang J, Huang Y, Leon DR, Steere AC, Costello CE, (2016) "Immunogenic HLA-DR-Presented Self-Peptides Identified Directly from Clinical Samples of Synovial Tissue, Synovial Fluid, or Peripheral Blood in Patients with Rheumatoid Arthritis or Lyme Arthritis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27726376 27726376]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00386 10.1021/acs.jproteome.6b00386]; GPMDB: [http://gpmdb.org/data/keyword/27726376 61]. | #Wang Q, Drouin EE, Yao C, Zhang J, Huang Y, Leon DR, Steere AC, Costello CE, (2016) "Immunogenic HLA-DR-Presented Self-Peptides Identified Directly from Clinical Samples of Synovial Tissue, Synovial Fluid, or Peripheral Blood in Patients with Rheumatoid Arthritis or Lyme Arthritis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27726376 27726376]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00386 10.1021/acs.jproteome.6b00386]; GPMDB: [http://gpmdb.org/data/keyword/27726376 61]. | ||
#Al-Daghri NM, Alokail MS, Manousopoulou A, Heinson A, Al-Attas O, Al-Saleh Y, Sabico S, Yakout S, Woelk CH, Chrousos GP, Garbis SD, (2016) "Sex-specific vitamin D effects on blood coagulation among overweight adults." <i>Eur J Clin Invest</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27727459 27727459]; doi: [https://dx.doi.org/10.1111/eci.12688 10.1111/eci.12688]; GPMDB: [http://gpmdb.org/data/keyword/27727459 50]. | #Al-Daghri NM, Alokail MS, Manousopoulou A, Heinson A, Al-Attas O, Al-Saleh Y, Sabico S, Yakout S, Woelk CH, Chrousos GP, Garbis SD, (2016) "Sex-specific vitamin D effects on blood coagulation among overweight adults." <i>Eur J Clin Invest</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27727459 27727459]; doi: [https://dx.doi.org/10.1111/eci.12688 10.1111/eci.12688]; GPMDB: [http://gpmdb.org/data/keyword/27727459 50]. | ||
+ | #Duncan O, Trösch J, Fenske R, Taylor NL, Millar AH, (2016) "Mapping the Triticum aestivum proteome." <i>Plant J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27775198 27775198]; doi: [https://dx.doi.org/10.1111/tpj.13402 10.1111/tpj.13402]; GPMDB: [http://gpmdb.org/data/keyword/27775198 28]. | ||
#Mardakheh FK, Self A, Marshall CJ, (2016) "RHO binding to FAM65A regulates Golgi reorientation during cell migration." <i>J Cell Sci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27807006 27807006]; doi: [https://dx.doi.org/10.1242/jcs.198614 10.1242/jcs.198614]; GPMDB: [http://gpmdb.org/data/keyword/27807006 18]. | #Mardakheh FK, Self A, Marshall CJ, (2016) "RHO binding to FAM65A regulates Golgi reorientation during cell migration." <i>J Cell Sci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27807006 27807006]; doi: [https://dx.doi.org/10.1242/jcs.198614 10.1242/jcs.198614]; GPMDB: [http://gpmdb.org/data/keyword/27807006 18]. |
GPMDB was originally constructed to serve as a reference work for all publicly available proteomics generated using tandem mass spectrometry. Public data is downloaded and reanalyzed using the current version of X! Tandem. The result files generated by the reanalysis and the relevant metadata are imported into the database and made available through the associated web site, ftp site and REST interfaces.
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The following public data repositories are checked daily for new suitable raw data for reanalysis:
Data made available from specific large projects, such as CPTAC or the Human Proteome Atlas, are also included when they are made available. Every effort is made so that reanalyzed results from all data sources are made available within 48 hours of their being released. In addition, data from lab web sites, ftp sites and direct contributions through the GPM sites made available to researchers are imported into GPMDB as part of a daily incremental update process.
GPMDB has been in operation since Jan. 1, 2004. Several large data source repositories have come into existence and ceased activity in the period since that time. All of the data from those repositories (e.g., TRANCHE, Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.
Simply because data is made available does not mean that it will be included in GPMDB. The data must pass our internal automated quality control tests for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of November 20, 2016.