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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 13, 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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#De Marchi T, Liu NQ, Stingl C, Timmermans MA, Smid M, Look MP, Tjoa M, Braakman RB, Opdam M, Linn SC, Sweep FC, Span PN, Kliffen M, Luider TM, Foekens JA, Martens JW, Umar A, (2016) "4-protein signature predicting tamoxifen treatment outcome in recurrent breast cancer." <i>Mol Oncol</i> <b>10</b>(1):24–39; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26285647 26285647]; doi: [https://dx.doi.org/10.1016/j.molonc.2015.07.004 10.1016/j.molonc.2015.07.004]; GPMDB: [http://gpmdb.org/data/keyword/26285647 112]. | #De Marchi T, Liu NQ, Stingl C, Timmermans MA, Smid M, Look MP, Tjoa M, Braakman RB, Opdam M, Linn SC, Sweep FC, Span PN, Kliffen M, Luider TM, Foekens JA, Martens JW, Umar A, (2016) "4-protein signature predicting tamoxifen treatment outcome in recurrent breast cancer." <i>Mol Oncol</i> <b>10</b>(1):24–39; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26285647 26285647]; doi: [https://dx.doi.org/10.1016/j.molonc.2015.07.004 10.1016/j.molonc.2015.07.004]; GPMDB: [http://gpmdb.org/data/keyword/26285647 112]. | ||
#Haas S, Hansson J, Klimmeck D, Loeffler D, Velten L, Uckelmann H, Wurzer S, Prendergast ÁM, Schnell A, Hexel K, Santarella-Mellwig R, Blaszkiewicz S, Kuck A, Geiger H, Milsom MD, Steinmetz LM, Schroeder T, Trumpp A, Krijgsveld J, Essers MA, (2015) "Inflammation-Induced Emergency Megakaryopoiesis Driven by Hematopoietic Stem Cell-like Megakaryocyte Progenitors." <i>Cell Stem Cell</i> <b>17</b>(4):422–34; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26299573 26299573]; doi: [https://dx.doi.org/10.1016/j.stem.2015.07.007 10.1016/j.stem.2015.07.007]; GPMDB: [http://gpmdb.org/data/keyword/26299573 240]. | #Haas S, Hansson J, Klimmeck D, Loeffler D, Velten L, Uckelmann H, Wurzer S, Prendergast ÁM, Schnell A, Hexel K, Santarella-Mellwig R, Blaszkiewicz S, Kuck A, Geiger H, Milsom MD, Steinmetz LM, Schroeder T, Trumpp A, Krijgsveld J, Essers MA, (2015) "Inflammation-Induced Emergency Megakaryopoiesis Driven by Hematopoietic Stem Cell-like Megakaryocyte Progenitors." <i>Cell Stem Cell</i> <b>17</b>(4):422–34; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26299573 26299573]; doi: [https://dx.doi.org/10.1016/j.stem.2015.07.007 10.1016/j.stem.2015.07.007]; GPMDB: [http://gpmdb.org/data/keyword/26299573 240]. | ||
+ | #Payne SH, Monroe ME, Overall CC, Kiebel GR, Degan M, Gibbons BC, Fujimoto GM, Purvine SO, Adkins JN, Lipton MS, Smith RD, (2015) "The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity." <i>Sci Data</i> <b>2</b>:150041; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26306205 26306205]; doi: [https://dx.doi.org/10.1038/sdata.2015.41 10.1038/sdata.2015.41]; GPMDB: [http://gpmdb.org/data/keyword/26306205 19590]. | ||
#Titz B, Sewer A, Schneider T, Elamin A, Martin F, Dijon S, Luettich K, Guedj E, Vuillaume G, Ivanov NV, Peck MJ, Chaudhary NI, Hoeng J, Peitsch MC, (2015) "Alterations in the sputum proteome and transcriptome in smokers and early-stage COPD subjects." <i>J Proteomics</i> <b>128</b>:306–20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26306861 26306861]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.08.009 10.1016/j.jprot.2015.08.009]; GPMDB: [http://gpmdb.org/data/keyword/26306861 120]. | #Titz B, Sewer A, Schneider T, Elamin A, Martin F, Dijon S, Luettich K, Guedj E, Vuillaume G, Ivanov NV, Peck MJ, Chaudhary NI, Hoeng J, Peitsch MC, (2015) "Alterations in the sputum proteome and transcriptome in smokers and early-stage COPD subjects." <i>J Proteomics</i> <b>128</b>:306–20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26306861 26306861]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.08.009 10.1016/j.jprot.2015.08.009]; GPMDB: [http://gpmdb.org/data/keyword/26306861 120]. | ||
#Yang CR, Raghuram V, Emamian M, Sandoval PC, Knepper MA, (2015) "Deep proteomic profiling of vasopressin-sensitive collecting duct cells. II. Bioinformatic analysis of vasopressin signaling." <i>Am J Physiol Cell Physiol</i> <b>309</b>(12):C799–812; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26310817 26310817]; doi: [https://dx.doi.org/10.1152/ajpcell.00214.2015 10.1152/ajpcell.00214.2015]; GPMDB: [http://gpmdb.org/data/keyword/26310817 257]. | #Yang CR, Raghuram V, Emamian M, Sandoval PC, Knepper MA, (2015) "Deep proteomic profiling of vasopressin-sensitive collecting duct cells. II. Bioinformatic analysis of vasopressin signaling." <i>Am J Physiol Cell Physiol</i> <b>309</b>(12):C799–812; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26310817 26310817]; doi: [https://dx.doi.org/10.1152/ajpcell.00214.2015 10.1152/ajpcell.00214.2015]; GPMDB: [http://gpmdb.org/data/keyword/26310817 257]. | ||
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#Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyö D, Ellis MJ, Carr SA, NCI CPTAC., (2016) "Proteogenomics connects somatic mutations to signalling in breast cancer." <i>Nature</i> <b>534</b>(7605):55–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27251275 27251275]; doi: [https://dx.doi.org/10.1038/nature18003 10.1038/nature18003]; GPMDB: [http://gpmdb.org/data/keyword/27251275 1265]. | #Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyö D, Ellis MJ, Carr SA, NCI CPTAC., (2016) "Proteogenomics connects somatic mutations to signalling in breast cancer." <i>Nature</i> <b>534</b>(7605):55–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27251275 27251275]; doi: [https://dx.doi.org/10.1038/nature18003 10.1038/nature18003]; GPMDB: [http://gpmdb.org/data/keyword/27251275 1265]. | ||
#Humphrey ES, Su SP, Nagrial AM, Hochgräfe F, Pajic M, Lehrbach GM, Parton RG, Yap AS, Horvath LG, Chang DK, Biankin AV, Wu J, Daly RJ, (2016) "Resolution of Novel Pancreatic Ductal Adenocarcinoma Subtypes by Global Phosphotyrosine Profiling." <i>Mol Cell Proteomics</i> <b>15</b>(8):2671–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27259358 27259358]; doi: [https://dx.doi.org/10.1074/mcp.M116.058313 10.1074/mcp.M116.058313]; GPMDB: [http://gpmdb.org/data/keyword/27259358 112]. | #Humphrey ES, Su SP, Nagrial AM, Hochgräfe F, Pajic M, Lehrbach GM, Parton RG, Yap AS, Horvath LG, Chang DK, Biankin AV, Wu J, Daly RJ, (2016) "Resolution of Novel Pancreatic Ductal Adenocarcinoma Subtypes by Global Phosphotyrosine Profiling." <i>Mol Cell Proteomics</i> <b>15</b>(8):2671–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27259358 27259358]; doi: [https://dx.doi.org/10.1074/mcp.M116.058313 10.1074/mcp.M116.058313]; GPMDB: [http://gpmdb.org/data/keyword/27259358 112]. | ||
- | #Xu L, Gao Y, Chen Y, Xiao Y, He Q, Qiu H, Ge W, (2016) "Quantitative proteomics reveals that distant recurrence-associated protein R-Ras and Transgelin predict post-surgical survival in patients with Stage III colorectal cancer." <i>Oncotarget</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27270312 27270312]; doi: [https://dx.doi.org/10.18632/oncotarget.9701 10.18632/oncotarget.9701]; GPMDB: [http://gpmdb.org/data/keyword/27270312 2]. | + | #Xu L, Gao Y, Chen Y, Xiao Y, He Q, Qiu H, Ge W, (2016) "Quantitative proteomics reveals that distant recurrence-associated protein R-Ras and Transgelin predict post-surgical survival in patients with Stage III colorectal cancer." <i>Oncotarget</i> <b>7</b>(28):43868–43893; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27270312 27270312]; doi: [https://dx.doi.org/10.18632/oncotarget.9701 10.18632/oncotarget.9701]; GPMDB: [http://gpmdb.org/data/keyword/27270312 2]. |
#Gnad F, Doll S, Song K, Stokes MP, Moffat J, Liu B, Arnott D, Wallin J, Friedman LS, Hatzivassiliou G, Belvin M, (2016) "Phosphoproteome analysis of the MAPK pathway reveals previously undetected feedback mechanisms." <i>Proteomics</i> <b>16</b>(14):1998–2004; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27273156 27273156]; doi: [https://dx.doi.org/10.1002/pmic.201600119 10.1002/pmic.201600119]; GPMDB: [http://gpmdb.org/data/keyword/27273156 56]. | #Gnad F, Doll S, Song K, Stokes MP, Moffat J, Liu B, Arnott D, Wallin J, Friedman LS, Hatzivassiliou G, Belvin M, (2016) "Phosphoproteome analysis of the MAPK pathway reveals previously undetected feedback mechanisms." <i>Proteomics</i> <b>16</b>(14):1998–2004; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27273156 27273156]; doi: [https://dx.doi.org/10.1002/pmic.201600119 10.1002/pmic.201600119]; GPMDB: [http://gpmdb.org/data/keyword/27273156 56]. | ||
#Gnad F, Wallin J, Edgar K, Doll S, Arnott D, Robillard L, Kirkpatrick DS, Stokes MP, Vijapurkar U, Hatzivassiliou G, Friedman LS, Belvin M, (2016) "Quantitative phosphoproteomic analysis of the PI3K-regulated signaling network." <i>Proteomics</i> <b>16</b>(14):1992–7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27282143 27282143]; doi: [https://dx.doi.org/10.1002/pmic.201600118 10.1002/pmic.201600118]; GPMDB: [http://gpmdb.org/data/keyword/27282143 72]. | #Gnad F, Wallin J, Edgar K, Doll S, Arnott D, Robillard L, Kirkpatrick DS, Stokes MP, Vijapurkar U, Hatzivassiliou G, Friedman LS, Belvin M, (2016) "Quantitative phosphoproteomic analysis of the PI3K-regulated signaling network." <i>Proteomics</i> <b>16</b>(14):1992–7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27282143 27282143]; doi: [https://dx.doi.org/10.1002/pmic.201600118 10.1002/pmic.201600118]; GPMDB: [http://gpmdb.org/data/keyword/27282143 72]. | ||
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#Carrier M, Joint M, Lutzing R, Page A, Rochette-Egly C, (2016) "Phosphoproteome and Transcriptome of RA-Responsive and RA-Resistant Breast Cancer Cell Lines." <i>PLoS One</i> <b>11</b>(6):e0157290; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27362937 27362937]; doi: [https://dx.doi.org/10.1371/journal.pone.0157290 10.1371/journal.pone.0157290]; GPMDB: [http://gpmdb.org/data/keyword/27362937 6]. | #Carrier M, Joint M, Lutzing R, Page A, Rochette-Egly C, (2016) "Phosphoproteome and Transcriptome of RA-Responsive and RA-Resistant Breast Cancer Cell Lines." <i>PLoS One</i> <b>11</b>(6):e0157290; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27362937 27362937]; doi: [https://dx.doi.org/10.1371/journal.pone.0157290 10.1371/journal.pone.0157290]; GPMDB: [http://gpmdb.org/data/keyword/27362937 6]. | ||
#Pettersen VK, Mosevoll KA, Lindemann PC, Wiker HG, (2016) "Coordination of Metabolism and Virulence Factors Expression of Extraintestinal Pathogenic Escherichia coli Purified from Blood Cultures of Patients with Sepsis." <i>Mol Cell Proteomics</i> <b>15</b>(9):2890–907; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27364158 27364158]; doi: [https://dx.doi.org/10.1074/mcp.M116.060582 10.1074/mcp.M116.060582]; GPMDB: [http://gpmdb.org/data/keyword/27364158 90]. | #Pettersen VK, Mosevoll KA, Lindemann PC, Wiker HG, (2016) "Coordination of Metabolism and Virulence Factors Expression of Extraintestinal Pathogenic Escherichia coli Purified from Blood Cultures of Patients with Sepsis." <i>Mol Cell Proteomics</i> <b>15</b>(9):2890–907; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27364158 27364158]; doi: [https://dx.doi.org/10.1074/mcp.M116.060582 10.1074/mcp.M116.060582]; GPMDB: [http://gpmdb.org/data/keyword/27364158 90]. | ||
+ | #Zhang H, Liu T, Zhang Z, Payne SH, Zhang B, McDermott JE, Zhou JY, Petyuk VA, Chen L, Ray D, Sun S, Yang F, Chen L, Wang J, Shah P, Cha SW, Aiyetan P, Woo S, Tian Y, Gritsenko MA, Clauss TR, Choi C, Monroe ME, Thomas S, Nie S, Wu C, Moore RJ, Yu KH, Tabb DL, Fenyö D, Bafna V, Wang Y, Rodriguez H, Boja ES, Hiltke T, Rivers RC, Sokoll L, Zhu H, Shih IeM, Cope L, Pandey A, Zhang B, Snyder MP, Levine DA, Smith RD, Chan DW, Rodland KD, CPTAC Investigators., (2016) "Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer." <i>Cell</i> <b>166</b>(3):755–65; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27372738 27372738]; doi: [https://dx.doi.org/10.1016/j.cell.2016.05.069 10.1016/j.cell.2016.05.069]; GPMDB: [http://gpmdb.org/data/keyword/27372738 1996]. | ||
#Luo Y, Jacobs EY, Greco TM, Mohammed KD, Tong T, Keegan S, Binley JM, Cristea IM, Fenyö D, Rout MP, Chait BT, Muesing MA, (2016) "HIV-host interactome revealed directly from infected cells." <i>Nat Microbiol</i> <b>1</b>(7):16068; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27375898 27375898]; doi: [https://dx.doi.org/10.1038/nmicrobiol.2016.68 10.1038/nmicrobiol.2016.68]; GPMDB: [http://gpmdb.org/data/keyword/27375898 53]. | #Luo Y, Jacobs EY, Greco TM, Mohammed KD, Tong T, Keegan S, Binley JM, Cristea IM, Fenyö D, Rout MP, Chait BT, Muesing MA, (2016) "HIV-host interactome revealed directly from infected cells." <i>Nat Microbiol</i> <b>1</b>(7):16068; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27375898 27375898]; doi: [https://dx.doi.org/10.1038/nmicrobiol.2016.68 10.1038/nmicrobiol.2016.68]; GPMDB: [http://gpmdb.org/data/keyword/27375898 53]. | ||
#Carabetta VJ, Greco TM, Tanner AW, Cristea IM, Dubnau D, (2016) "Temporal Regulation of the <i>Bacillus subtilis</i> Acetylome and Evidence for a Role of MreB Acetylation in Cell Wall Growth." <i>mSystems</i> <b>1</b>(3):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27376153 27376153]; doi: [https://dx.doi.org/10.1128/mSystems.00005-16 10.1128/mSystems.00005-16]; GPMDB: [http://gpmdb.org/data/keyword/27376153 30]. | #Carabetta VJ, Greco TM, Tanner AW, Cristea IM, Dubnau D, (2016) "Temporal Regulation of the <i>Bacillus subtilis</i> Acetylome and Evidence for a Role of MreB Acetylation in Cell Wall Growth." <i>mSystems</i> <b>1</b>(3):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27376153 27376153]; doi: [https://dx.doi.org/10.1128/mSystems.00005-16 10.1128/mSystems.00005-16]; GPMDB: [http://gpmdb.org/data/keyword/27376153 30]. | ||
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#Naboulsi W, Bracht T, Megger DA, Reis H, Ahrens M, Turewicz M, Eisenacher M, Tautges S, Canbay AE, Meyer HE, Weber F, Baba HA, Sitek B, (2016) "Quantitative proteome analysis reveals the correlation between endocytosis-associated proteins and hepatocellular carcinoma dedifferentiation." <i>Biochim Biophys Acta</i> <b>1864</b>(11):1579–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27519163 27519163]; doi: [https://dx.doi.org/10.1016/j.bbapap.2016.08.005 10.1016/j.bbapap.2016.08.005]; GPMDB: [http://gpmdb.org/data/keyword/27519163 36]. | #Naboulsi W, Bracht T, Megger DA, Reis H, Ahrens M, Turewicz M, Eisenacher M, Tautges S, Canbay AE, Meyer HE, Weber F, Baba HA, Sitek B, (2016) "Quantitative proteome analysis reveals the correlation between endocytosis-associated proteins and hepatocellular carcinoma dedifferentiation." <i>Biochim Biophys Acta</i> <b>1864</b>(11):1579–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27519163 27519163]; doi: [https://dx.doi.org/10.1016/j.bbapap.2016.08.005 10.1016/j.bbapap.2016.08.005]; GPMDB: [http://gpmdb.org/data/keyword/27519163 36]. | ||
#Rasmussen MH, Lyskjær I, Jersie-Christensen RR, Tarpgaard LS, Primdal-Bengtson B, Nielsen MM, Pedersen JS, Hansen TP, Hansen F, Olsen JV, Pfeiffer P, Ørntoft TF, Andersen CL, (2016) "miR-625-3p regulates oxaliplatin resistance by targeting MAP2K6-p38 signalling in human colorectal adenocarcinoma cells." <i>Nat Commun</i> <b>7</b>:12436; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27526785 27526785]; doi: [https://dx.doi.org/10.1038/ncomms12436 10.1038/ncomms12436]; GPMDB: [http://gpmdb.org/data/keyword/27526785 24]. | #Rasmussen MH, Lyskjær I, Jersie-Christensen RR, Tarpgaard LS, Primdal-Bengtson B, Nielsen MM, Pedersen JS, Hansen TP, Hansen F, Olsen JV, Pfeiffer P, Ørntoft TF, Andersen CL, (2016) "miR-625-3p regulates oxaliplatin resistance by targeting MAP2K6-p38 signalling in human colorectal adenocarcinoma cells." <i>Nat Commun</i> <b>7</b>:12436; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27526785 27526785]; doi: [https://dx.doi.org/10.1038/ncomms12436 10.1038/ncomms12436]; GPMDB: [http://gpmdb.org/data/keyword/27526785 24]. | ||
- | #Liu L, Phua YW, Lee RS, Ma X, Jenkins Y, Novy K, Humphrey ES, Chan H, Shearer R, Ong PC, Dai W, Saunders DN, Lucet IS, Daly RJ, (2016) "Homo- and Heterotypic Association Regulates | + | #Liu L, Phua YW, Lee RS, Ma X, Jenkins Y, Novy K, Humphrey ES, Chan H, Shearer R, Ong PC, Dai W, Saunders DN, Lucet IS, Daly RJ, (2016) "Homo- and Heterotypic Association Regulates Signaling by the SgK269/PEAK1 and SgK223 Pseudokinases." <i>J Biol Chem</i> <b>291</b>(41):21571–21583; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27531744 27531744]; doi: [https://dx.doi.org/10.1074/jbc.M116.748897 10.1074/jbc.M116.748897]; GPMDB: [http://gpmdb.org/data/keyword/27531744 6]. |
#Mattei B, Spinelli F, Pontiggia D, De Lorenzo G, (2016) "Comprehensive Analysis of the Membrane Phosphoproteome Regulated by Oligogalacturonides in Arabidopsis thaliana." <i>Front Plant Sci</i> <b>7</b>:1107; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27532006 27532006]; doi: [https://dx.doi.org/10.3389/fpls.2016.01107 10.3389/fpls.2016.01107]; GPMDB: [http://gpmdb.org/data/keyword/27532006 12]. | #Mattei B, Spinelli F, Pontiggia D, De Lorenzo G, (2016) "Comprehensive Analysis of the Membrane Phosphoproteome Regulated by Oligogalacturonides in Arabidopsis thaliana." <i>Front Plant Sci</i> <b>7</b>:1107; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27532006 27532006]; doi: [https://dx.doi.org/10.3389/fpls.2016.01107 10.3389/fpls.2016.01107]; GPMDB: [http://gpmdb.org/data/keyword/27532006 12]. | ||
#Solari FA, Mattheij NJ, Burkhart JM, Swieringa F, Collins PW, Cosemans JM, Sickmann A, Heemskerk JW, Zahedi RP, (2016) "Combined Quantification of the Global Proteome, Phosphoproteome, and Proteolytic Cleavage to Characterize Altered Platelet Functions in the Human Scott Syndrome." <i>Mol Cell Proteomics</i> <b>15</b>(10):3154–3169; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27535140 27535140]; doi: [https://dx.doi.org/10.1074/mcp.M116.060368 10.1074/mcp.M116.060368]; GPMDB: [http://gpmdb.org/data/keyword/27535140 23]. | #Solari FA, Mattheij NJ, Burkhart JM, Swieringa F, Collins PW, Cosemans JM, Sickmann A, Heemskerk JW, Zahedi RP, (2016) "Combined Quantification of the Global Proteome, Phosphoproteome, and Proteolytic Cleavage to Characterize Altered Platelet Functions in the Human Scott Syndrome." <i>Mol Cell Proteomics</i> <b>15</b>(10):3154–3169; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27535140 27535140]; doi: [https://dx.doi.org/10.1074/mcp.M116.060368 10.1074/mcp.M116.060368]; GPMDB: [http://gpmdb.org/data/keyword/27535140 23]. | ||
#Dobó J, Szakács D, Oroszlán G, Kortvely E, Kiss B, Boros E, Szász R, Závodszky P, Gál P, Pál G, (2016) "MASP-3 is the exclusive pro-factor D activator in resting blood: the lectin and the alternative complement pathways are fundamentally linked." <i>Sci Rep</i> <b>6</b>:31877; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27535802 27535802]; doi: [https://dx.doi.org/10.1038/srep31877 10.1038/srep31877]; GPMDB: [http://gpmdb.org/data/keyword/27535802 6]. | #Dobó J, Szakács D, Oroszlán G, Kortvely E, Kiss B, Boros E, Szász R, Závodszky P, Gál P, Pál G, (2016) "MASP-3 is the exclusive pro-factor D activator in resting blood: the lectin and the alternative complement pathways are fundamentally linked." <i>Sci Rep</i> <b>6</b>:31877; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27535802 27535802]; doi: [https://dx.doi.org/10.1038/srep31877 10.1038/srep31877]; GPMDB: [http://gpmdb.org/data/keyword/27535802 6]. | ||
#Zhang P, Karani R, Turner RL, Dufresne C, Ferri S, Van Eyk JE, Semba RD, (2016) "The proteome of normal human retrobulbar optic nerve and sclera." <i>Proteomics</i> <b>16</b>(19):2592–2596; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27538499 27538499]; doi: [https://dx.doi.org/10.1002/pmic.201600229 10.1002/pmic.201600229]; GPMDB: [http://gpmdb.org/data/keyword/27538499 60]. | #Zhang P, Karani R, Turner RL, Dufresne C, Ferri S, Van Eyk JE, Semba RD, (2016) "The proteome of normal human retrobulbar optic nerve and sclera." <i>Proteomics</i> <b>16</b>(19):2592–2596; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27538499 27538499]; doi: [https://dx.doi.org/10.1002/pmic.201600229 10.1002/pmic.201600229]; GPMDB: [http://gpmdb.org/data/keyword/27538499 60]. | ||
- | #Walley JW, Sartor RC, Shen Z, Schmitz RJ, Wu KJ, Urich MA, Nery JR, Smith LG, Schnable JC, Ecker JR, Briggs SP, (2016) "Integration of omic networks in a developmental atlas of maize." <i>Science</i> <b>353</b>(6301):814–8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27540173 27540173]; doi: [https://dx.doi.org/10.1126/science.aag1125 10.1126/science.aag1125]; GPMDB: [http://gpmdb.org/data/keyword/27540173 | + | #Walley JW, Sartor RC, Shen Z, Schmitz RJ, Wu KJ, Urich MA, Nery JR, Smith LG, Schnable JC, Ecker JR, Briggs SP, (2016) "Integration of omic networks in a developmental atlas of maize." <i>Science</i> <b>353</b>(6301):814–8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27540173 27540173]; doi: [https://dx.doi.org/10.1126/science.aag1125 10.1126/science.aag1125]; GPMDB: [http://gpmdb.org/data/keyword/27540173 10350]. |
#Xie Y, Wang J, Zhang Y, Liu X, Wang X, Liu K, Huang X, Wang Y, (2016) "Quantitative profiling of spreading-coupled protein tyrosine phosphorylation in migratory cells." <i>Sci Rep</i> <b>6</b>:31811; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27554326 27554326]; doi: [https://dx.doi.org/10.1038/srep31811 10.1038/srep31811]; GPMDB: [http://gpmdb.org/data/keyword/27554326 6]. | #Xie Y, Wang J, Zhang Y, Liu X, Wang X, Liu K, Huang X, Wang Y, (2016) "Quantitative profiling of spreading-coupled protein tyrosine phosphorylation in migratory cells." <i>Sci Rep</i> <b>6</b>:31811; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27554326 27554326]; doi: [https://dx.doi.org/10.1038/srep31811 10.1038/srep31811]; GPMDB: [http://gpmdb.org/data/keyword/27554326 6]. | ||
#He PH, Dong WX, Chu XL, Feng MG, Ying SH, (2016) "The cellular proteome is affected by a gelsolin (BbGEL1) during morphological transitions in aerobic surface versus liquid growth in the entomopathogenic fungus Beauveria bassiana." <i>Environ Microbiol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27554994 27554994]; doi: [https://dx.doi.org/10.1111/1462-2920.13500 10.1111/1462-2920.13500]; GPMDB: [http://gpmdb.org/data/keyword/27554994 34]. | #He PH, Dong WX, Chu XL, Feng MG, Ying SH, (2016) "The cellular proteome is affected by a gelsolin (BbGEL1) during morphological transitions in aerobic surface versus liquid growth in the entomopathogenic fungus Beauveria bassiana." <i>Environ Microbiol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27554994 27554994]; doi: [https://dx.doi.org/10.1111/1462-2920.13500 10.1111/1462-2920.13500]; GPMDB: [http://gpmdb.org/data/keyword/27554994 34]. | ||
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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 17]. | ||
#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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#Kwon OK, Kim S, Lee S, (2016) "Global proteomic analysis of lysine acetylation in zebrafish (Danio rerio) embryos." <i>Electrophoresis</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27696471 27696471]; doi: [https://dx.doi.org/10.1002/elps.201600210 10.1002/elps.201600210]; GPMDB: [http://gpmdb.org/data/keyword/27696471 2]. | #Kwon OK, Kim S, Lee S, (2016) "Global proteomic analysis of lysine acetylation in zebrafish (Danio rerio) embryos." <i>Electrophoresis</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27696471 27696471]; doi: [https://dx.doi.org/10.1002/elps.201600210 10.1002/elps.201600210]; GPMDB: [http://gpmdb.org/data/keyword/27696471 2]. | ||
#Witzke KE, Rosowski K, Müller C, Ahrens M, Eisenacher M, Megger DA, Knobloch J, Koch AR, Bracht T, Sitek B, (2016) "Quantitative Secretome Analysis of Activated Jurkat Cells using Click Chemistry-Based Enrichment of Secreted Glycoproteins." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27696881 27696881]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00575 10.1021/acs.jproteome.6b00575]; GPMDB: [http://gpmdb.org/data/keyword/27696881 82]. | #Witzke KE, Rosowski K, Müller C, Ahrens M, Eisenacher M, Megger DA, Knobloch J, Koch AR, Bracht T, Sitek B, (2016) "Quantitative Secretome Analysis of Activated Jurkat Cells using Click Chemistry-Based Enrichment of Secreted Glycoproteins." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27696881 27696881]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00575 10.1021/acs.jproteome.6b00575]; GPMDB: [http://gpmdb.org/data/keyword/27696881 82]. | ||
- | #Baas R, Sijm A, van Teeffelen HA, van Es R, Vos HR, Timmers HT, (2016) "Quantitative Proteomics of the SMAD (Suppressor of Mothers | + | #Baas R, Sijm A, van Teeffelen HA, van Es R, Vos HR, Marc Timmers HT, (2016) "Quantitative Proteomics of the SMAD (Suppressor of Mothers against Decapentaplegic) Transcription Factor Family Identifies Importin 5 as a Bone Morphogenic Protein Receptor SMAD-specific Importin." <i>J Biol Chem</i> <b>291</b>(46):24121–24132; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27703004 27703004]; doi: [https://dx.doi.org/10.1074/jbc.M116.748582 10.1074/jbc.M116.748582]; GPMDB: [http://gpmdb.org/data/keyword/27703004 108]. |
#Hughes CS, McConechy MK, Cochrane DR, Nazeran T, Karnezis AN, Huntsman DG, Morin GB, (2016) "Quantitative Profiling of Single Formalin Fixed Tumour Sections: proteomics for translational research." <i>Sci Rep</i> <b>6</b>:34949; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27713570 27713570]; doi: [https://dx.doi.org/10.1038/srep34949 10.1038/srep34949]; GPMDB: [http://gpmdb.org/data/keyword/27713570 172]. | #Hughes CS, McConechy MK, Cochrane DR, Nazeran T, Karnezis AN, Huntsman DG, Morin GB, (2016) "Quantitative Profiling of Single Formalin Fixed Tumour Sections: proteomics for translational research." <i>Sci Rep</i> <b>6</b>:34949; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27713570 27713570]; doi: [https://dx.doi.org/10.1038/srep34949 10.1038/srep34949]; GPMDB: [http://gpmdb.org/data/keyword/27713570 172]. | ||
#Sivadasan R, Hornburg D, Drepper C, Frank N, Jablonka S, Hansel A, Lojewski X, Sterneckert J, Hermann A, Shaw PJ, Ince PG, Mann M, Meissner F, Sendtner M, (2016) "C9ORF72 interaction with cofilin modulates actin dynamics in motor neurons." <i>Nat Neurosci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27723745 27723745]; doi: [https://dx.doi.org/10.1038/nn.4407 10.1038/nn.4407]; GPMDB: [http://gpmdb.org/data/keyword/27723745 6]. | #Sivadasan R, Hornburg D, Drepper C, Frank N, Jablonka S, Hansel A, Lojewski X, Sterneckert J, Hermann A, Shaw PJ, Ince PG, Mann M, Meissner F, Sendtner M, (2016) "C9ORF72 interaction with cofilin modulates actin dynamics in motor neurons." <i>Nat Neurosci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27723745 27723745]; doi: [https://dx.doi.org/10.1038/nn.4407 10.1038/nn.4407]; GPMDB: [http://gpmdb.org/data/keyword/27723745 6]. | ||
#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]. | ||
+ | #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.
Contents |
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 13, 2016.