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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 Mar. | + | 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 Mar. 18, 2018. |
#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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#Xu B, Gao Y, Zhan S, Ge W, (2017) "Quantitative proteomic profiling for clarification of the crucial roles of lysosomes in microbial infections." <i>Mol Immunol</i> <b>87</b>:122–131; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28433889 28433889]; doi: [https://dx.doi.org/10.1016/j.molimm.2017.04.002 10.1016/j.molimm.2017.04.002]; GPMDB: [http://gpmdb.org/data/keyword/28433889 2]. | #Xu B, Gao Y, Zhan S, Ge W, (2017) "Quantitative proteomic profiling for clarification of the crucial roles of lysosomes in microbial infections." <i>Mol Immunol</i> <b>87</b>:122–131; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28433889 28433889]; doi: [https://dx.doi.org/10.1016/j.molimm.2017.04.002 10.1016/j.molimm.2017.04.002]; GPMDB: [http://gpmdb.org/data/keyword/28433889 2]. | ||
#Clulow JA, Storck EM, Lanyon-Hogg T, Kalesh KA, Jones LH, Tate EW, (2017) "Competition-based, quantitative chemical proteomics in breast cancer cells identifies new target profiles for sulforaphane." <i>Chem Commun (Camb)</i> <b>53</b>(37):5182–5185; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28439590 28439590]; doi: [https://dx.doi.org/10.1039/c6cc08797c 10.1039/c6cc08797c]; GPMDB: [http://gpmdb.org/data/keyword/28439590 32]. | #Clulow JA, Storck EM, Lanyon-Hogg T, Kalesh KA, Jones LH, Tate EW, (2017) "Competition-based, quantitative chemical proteomics in breast cancer cells identifies new target profiles for sulforaphane." <i>Chem Commun (Camb)</i> <b>53</b>(37):5182–5185; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28439590 28439590]; doi: [https://dx.doi.org/10.1039/c6cc08797c 10.1039/c6cc08797c]; GPMDB: [http://gpmdb.org/data/keyword/28439590 32]. | ||
+ | #Yeung ATY, Hale C, Lee AH, Gill EE, Bushell W, Parry-Smith D, Goulding D, Pickard D, Roumeliotis T, Choudhary J, Thomson N, Skarnes WC, Dougan G, Hancock REW, (2017) "Exploiting induced pluripotent stem cell-derived macrophages to unravel host factors influencing Chlamydia trachomatis pathogenesis." <i>Nat Commun</i> <b>8</b>:15013; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28440293 28440293]; doi: [https://dx.doi.org/10.1038/ncomms15013 10.1038/ncomms15013]; GPMDB: [http://gpmdb.org/data/keyword/28440293 1]. | ||
#Arntzen MØ, Várnai A, Mackie RI, Eijsink VGH, Pope PB, (2017) "Outer membrane vesicles from Fibrobacter succinogenes S85 contain an array of carbohydrate-active enzymes with versatile polysaccharide-degrading capacity." <i>Environ Microbiol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28447389 28447389]; doi: [https://dx.doi.org/10.1111/1462-2920.13770 10.1111/1462-2920.13770]; GPMDB: [http://gpmdb.org/data/keyword/28447389 20]. | #Arntzen MØ, Várnai A, Mackie RI, Eijsink VGH, Pope PB, (2017) "Outer membrane vesicles from Fibrobacter succinogenes S85 contain an array of carbohydrate-active enzymes with versatile polysaccharide-degrading capacity." <i>Environ Microbiol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28447389 28447389]; doi: [https://dx.doi.org/10.1111/1462-2920.13770 10.1111/1462-2920.13770]; GPMDB: [http://gpmdb.org/data/keyword/28447389 20]. | ||
#Nguyen EV, Huhtinen K, Goo YA, Kaipio K, Andersson N, Rantanen V, Hynninen J, Lahesmaa R, Carpen O, Goodlett DR, (2017) "Hyper-phosphorylation of Sequestosome-1 distinguishes resistance to cisplatin in patient derived high grade serous ovarian cancer cells." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28455291 28455291]; doi: [https://dx.doi.org/10.1074/mcp.M116.058321 10.1074/mcp.M116.058321]; GPMDB: [http://gpmdb.org/data/keyword/28455291 60]. | #Nguyen EV, Huhtinen K, Goo YA, Kaipio K, Andersson N, Rantanen V, Hynninen J, Lahesmaa R, Carpen O, Goodlett DR, (2017) "Hyper-phosphorylation of Sequestosome-1 distinguishes resistance to cisplatin in patient derived high grade serous ovarian cancer cells." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28455291 28455291]; doi: [https://dx.doi.org/10.1074/mcp.M116.058321 10.1074/mcp.M116.058321]; GPMDB: [http://gpmdb.org/data/keyword/28455291 60]. | ||
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#Awazawa M, Gabel P, Tsaousidou E, Nolte H, Krüger M, Schmitz J, Ackermann PJ, Brandt C, Altmüller J, Motameny S, Wunderlich FT, Kornfeld JW, Blüher M, Brüning JC, (2017) "A microRNA screen reveals that elevated hepatic ectodysplasin A expression contributes to obesity-induced insulin resistance in skeletal muscle." <i>Nat Med</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29106399 29106399]; doi: [https://dx.doi.org/10.1038/nm.4420 10.1038/nm.4420]; GPMDB: [http://gpmdb.org/data/keyword/29106399 8]. | #Awazawa M, Gabel P, Tsaousidou E, Nolte H, Krüger M, Schmitz J, Ackermann PJ, Brandt C, Altmüller J, Motameny S, Wunderlich FT, Kornfeld JW, Blüher M, Brüning JC, (2017) "A microRNA screen reveals that elevated hepatic ectodysplasin A expression contributes to obesity-induced insulin resistance in skeletal muscle." <i>Nat Med</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29106399 29106399]; doi: [https://dx.doi.org/10.1038/nm.4420 10.1038/nm.4420]; GPMDB: [http://gpmdb.org/data/keyword/29106399 8]. | ||
#Alvarez-Castelao B, Schanzenbächer CT, Hanus C, Glock C, Tom Dieck S, Dörrbaum AR, Bartnik I, Nassim-Assir B, Ciirdaeva E, Mueller A, Dieterich DC, Tirrell DA, Langer JD, Schuman EM, (2017) "Cell-type-specific metabolic labeling of nascent proteomes in vivo." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29106408 29106408]; doi: [https://dx.doi.org/10.1038/nbt.4016 10.1038/nbt.4016]; GPMDB: [http://gpmdb.org/data/keyword/29106408 98]. | #Alvarez-Castelao B, Schanzenbächer CT, Hanus C, Glock C, Tom Dieck S, Dörrbaum AR, Bartnik I, Nassim-Assir B, Ciirdaeva E, Mueller A, Dieterich DC, Tirrell DA, Langer JD, Schuman EM, (2017) "Cell-type-specific metabolic labeling of nascent proteomes in vivo." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29106408 29106408]; doi: [https://dx.doi.org/10.1038/nbt.4016 10.1038/nbt.4016]; GPMDB: [http://gpmdb.org/data/keyword/29106408 98]. | ||
+ | #Gialitakis M, Tolaini M, Li Y, Pardo M, Yu L, Toribio A, Choudhary JS, Niakan K, Papayannopoulos V, Stockinger B, (2017) "Activation of the Aryl Hydrocarbon Receptor Interferes with Early Embryonic Development." <i>Stem Cell Reports</i> <b>9</b>(5):1377–1386; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29107595 29107595]; doi: [https://dx.doi.org/10.1016/j.stemcr.2017.09.025 10.1016/j.stemcr.2017.09.025]; GPMDB: [http://gpmdb.org/data/keyword/29107595 108]. | ||
#Nielsen M, Connelley T, Ternette N, (2017) "Improved Prediction of Bovine Leucocyte Antigens (BoLA) Presented Ligands by Use of Mass-Spectrometry-Determined Ligand and in Vitro Binding Data." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29115832 29115832]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00675 10.1021/acs.jproteome.7b00675]; GPMDB: [http://gpmdb.org/data/keyword/29115832 10]. | #Nielsen M, Connelley T, Ternette N, (2017) "Improved Prediction of Bovine Leucocyte Antigens (BoLA) Presented Ligands by Use of Mass-Spectrometry-Determined Ligand and in Vitro Binding Data." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29115832 29115832]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00675 10.1021/acs.jproteome.7b00675]; GPMDB: [http://gpmdb.org/data/keyword/29115832 10]. | ||
#van der Wal L, Bezstarosti K, Sap KA, Dekkers DHW, Rijkers E, Mientjes E, Elgersma Y, Demmers JAA, (2017) "Improvement of ubiquitylation site detection by Orbitrap mass spectrometry." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29122726 29122726]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.10.014 10.1016/j.jprot.2017.10.014]; GPMDB: [http://gpmdb.org/data/keyword/29122726 86]. | #van der Wal L, Bezstarosti K, Sap KA, Dekkers DHW, Rijkers E, Mientjes E, Elgersma Y, Demmers JAA, (2017) "Improvement of ubiquitylation site detection by Orbitrap mass spectrometry." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29122726 29122726]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.10.014 10.1016/j.jprot.2017.10.014]; GPMDB: [http://gpmdb.org/data/keyword/29122726 86]. | ||
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#Grossegesse M, Doellinger J, Fritsch A, Laue M, Piesker J, Schaade L, Nitsche A, (2018) "Global ubiquitination analysis reveals extensive modification and proteasomal degradation of cowpox virus proteins, but preservation of viral cores." <i>Sci Rep</i> <b>8</b>(1):1807; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29379051 29379051]; doi: [https://dx.doi.org/10.1038/s41598-018-20130-9 10.1038/s41598-018-20130-9]; GPMDB: [http://gpmdb.org/data/keyword/29379051 16]. | #Grossegesse M, Doellinger J, Fritsch A, Laue M, Piesker J, Schaade L, Nitsche A, (2018) "Global ubiquitination analysis reveals extensive modification and proteasomal degradation of cowpox virus proteins, but preservation of viral cores." <i>Sci Rep</i> <b>8</b>(1):1807; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29379051 29379051]; doi: [https://dx.doi.org/10.1038/s41598-018-20130-9 10.1038/s41598-018-20130-9]; GPMDB: [http://gpmdb.org/data/keyword/29379051 16]. | ||
#Hawkins AG, Basrur V, da Veiga Leprevost F, Pedersen E, Sperring C, Nesvizhskii AI, Lawlor ER, (2018) "The Ewing sarcoma secretome and its response to activation of Wnt/beta-catenin signaling." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29386236 29386236]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000596 10.1074/mcp.RA118.000596]; GPMDB: [http://gpmdb.org/data/keyword/29386236 12]. | #Hawkins AG, Basrur V, da Veiga Leprevost F, Pedersen E, Sperring C, Nesvizhskii AI, Lawlor ER, (2018) "The Ewing sarcoma secretome and its response to activation of Wnt/beta-catenin signaling." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29386236 29386236]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000596 10.1074/mcp.RA118.000596]; GPMDB: [http://gpmdb.org/data/keyword/29386236 12]. | ||
+ | #Sandow JJ, Rainczuk A, Infusini G, Makanji M, Bilandzic M, Wilson AL, Fairweather N, Stanton PG, Garama D, Gough D, Jobling TW, Webb AI, Stephens AN, (2018) "Discovery and Validation of Novel Protein Biomarkers in Ovarian Cancer Patient Urine." <i>Proteomics Clin Appl</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29426060 29426060]; doi: [https://dx.doi.org/10.1002/prca.201700135 10.1002/prca.201700135]; GPMDB: [http://gpmdb.org/data/keyword/29426060 10]. | ||
#Schanzenbächer CT, Langer JD, Schuman EM, (2018) "Time- and polarity-dependent proteomic changes associated with homeostatic scaling at central synapses." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29447110 29447110]; doi: [https://dx.doi.org/10.7554/eLife.33322 10.7554/eLife.33322]; GPMDB: [http://gpmdb.org/data/keyword/29447110 78]. | #Schanzenbächer CT, Langer JD, Schuman EM, (2018) "Time- and polarity-dependent proteomic changes associated with homeostatic scaling at central synapses." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29447110 29447110]; doi: [https://dx.doi.org/10.7554/eLife.33322 10.7554/eLife.33322]; GPMDB: [http://gpmdb.org/data/keyword/29447110 78]. | ||
#Lan J, Núñez Galindo A, Doecke J, Fowler C, Martins RN, Rainey-Smith SR, Cominetti O, Dayon L, (2018) "Systematic Evaluation of the Use of Human Plasma and Serum for Mass-Spectrometry-Based Shotgun Proteomics." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29451788 29451788]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00788 10.1021/acs.jproteome.7b00788]; GPMDB: [http://gpmdb.org/data/keyword/29451788 36]. | #Lan J, Núñez Galindo A, Doecke J, Fowler C, Martins RN, Rainey-Smith SR, Cominetti O, Dayon L, (2018) "Systematic Evaluation of the Use of Human Plasma and Serum for Mass-Spectrometry-Based Shotgun Proteomics." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29451788 29451788]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00788 10.1021/acs.jproteome.7b00788]; GPMDB: [http://gpmdb.org/data/keyword/29451788 36]. | ||
#Bergmann TJ, Fregno I, Fumagalli F, Rinaldi A, Bertoni F, Boersema PJ, Picotti P, Molinari M, (2018) "Chemical stresses fail to mimic the unfolded protein response resulting from luminal load with unfolded polypeptides." <i>J Biol Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29453283 29453283]; doi: [https://dx.doi.org/10.1074/jbc.RA117.001484 10.1074/jbc.RA117.001484]; GPMDB: [http://gpmdb.org/data/keyword/29453283 39]. | #Bergmann TJ, Fregno I, Fumagalli F, Rinaldi A, Bertoni F, Boersema PJ, Picotti P, Molinari M, (2018) "Chemical stresses fail to mimic the unfolded protein response resulting from luminal load with unfolded polypeptides." <i>J Biol Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29453283 29453283]; doi: [https://dx.doi.org/10.1074/jbc.RA117.001484 10.1074/jbc.RA117.001484]; GPMDB: [http://gpmdb.org/data/keyword/29453283 39]. | ||
+ | #Das CK, Linder B, Bonn F, Rothweiler F, Dikic I, Michaelis M, Cinatl J, Mandal M, Kögel D, (2018) "BAG3 Overexpression and Cytoprotective Autophagy Mediate Apoptosis Resistance in Chemoresistant Breast Cancer Cells." <i>Neoplasia</i> <b>20</b>(3):263–279; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29462756 29462756]; doi: [https://dx.doi.org/10.1016/j.neo.2018.01.001 10.1016/j.neo.2018.01.001]; GPMDB: [http://gpmdb.org/data/keyword/29462756 12]. | ||
#O'Loughlin T, Masters TA, Buss F, (2018) "The MYO6 interactome reveals adaptor complexes coordinating early endosome and cytoskeletal dynamics." <i>EMBO Rep</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29467281 29467281]; doi: [https://dx.doi.org/10.15252/embr.201744884 10.15252/embr.201744884]; GPMDB: [http://gpmdb.org/data/keyword/29467281 34]. | #O'Loughlin T, Masters TA, Buss F, (2018) "The MYO6 interactome reveals adaptor complexes coordinating early endosome and cytoskeletal dynamics." <i>EMBO Rep</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29467281 29467281]; doi: [https://dx.doi.org/10.15252/embr.201744884 10.15252/embr.201744884]; GPMDB: [http://gpmdb.org/data/keyword/29467281 34]. | ||
#Di Costanzo A, Del Gaudio N, Conte L, Dell'Aversana C, Vermeulen M, de Thé H, Migliaccio A, Nebbioso A, Altucci L, (2018) "The HDAC inhibitor SAHA regulates CBX2 stability via a SUMO-triggered ubiquitin-mediated pathway in leukemia." <i>Oncogene</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29467492 29467492]; doi: [https://dx.doi.org/10.1038/s41388-018-0143-1 10.1038/s41388-018-0143-1]; GPMDB: [http://gpmdb.org/data/keyword/29467492 6]. | #Di Costanzo A, Del Gaudio N, Conte L, Dell'Aversana C, Vermeulen M, de Thé H, Migliaccio A, Nebbioso A, Altucci L, (2018) "The HDAC inhibitor SAHA regulates CBX2 stability via a SUMO-triggered ubiquitin-mediated pathway in leukemia." <i>Oncogene</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29467492 29467492]; doi: [https://dx.doi.org/10.1038/s41388-018-0143-1 10.1038/s41388-018-0143-1]; GPMDB: [http://gpmdb.org/data/keyword/29467492 6]. | ||
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#Zeiner PS, Zinke J, Kowalewski DJ, Bernatz S, Tichy J, Ronellenfitsch MW, Thorsen F, Berger A, Forster MT, Muller A, Steinbach JP, Beschorner R, Wischhusen J, Kvasnicka HM, Plate KH, Stefanović S, Weide B, Mittelbronn M, Harter PN, (2018) "CD74 regulates complexity of tumor cell HLA class II peptidome in brain metastasis and is a positive prognostic marker for patient survival." <i>Acta Neuropathol Commun</i> <b>6</b>(1):18; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29490700 29490700]; doi: [https://dx.doi.org/10.1186/s40478-018-0521-5 10.1186/s40478-018-0521-5]; GPMDB: [http://gpmdb.org/data/keyword/29490700 20]. | #Zeiner PS, Zinke J, Kowalewski DJ, Bernatz S, Tichy J, Ronellenfitsch MW, Thorsen F, Berger A, Forster MT, Muller A, Steinbach JP, Beschorner R, Wischhusen J, Kvasnicka HM, Plate KH, Stefanović S, Weide B, Mittelbronn M, Harter PN, (2018) "CD74 regulates complexity of tumor cell HLA class II peptidome in brain metastasis and is a positive prognostic marker for patient survival." <i>Acta Neuropathol Commun</i> <b>6</b>(1):18; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29490700 29490700]; doi: [https://dx.doi.org/10.1186/s40478-018-0521-5 10.1186/s40478-018-0521-5]; GPMDB: [http://gpmdb.org/data/keyword/29490700 20]. | ||
#Goel RK, Paczkowska M, Reimand J, Napper S, Lukong KE, (2018) "Phosphoproteomics analysis identifies novel candidate substrates of the non-receptor tyrosine kinase, SRMS." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29496907 29496907]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000643 10.1074/mcp.RA118.000643]; GPMDB: [http://gpmdb.org/data/keyword/29496907 4]. | #Goel RK, Paczkowska M, Reimand J, Napper S, Lukong KE, (2018) "Phosphoproteomics analysis identifies novel candidate substrates of the non-receptor tyrosine kinase, SRMS." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29496907 29496907]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000643 10.1074/mcp.RA118.000643]; GPMDB: [http://gpmdb.org/data/keyword/29496907 4]. | ||
- | #Ge S, Xia X, Ding C, Zhen B, Zhou Q, Feng J, Yuan J, Chen R, Li Y, Ge Z, Ji J, Zhang L, Wang J, Li Z, Lai Y, Hu Y, Li Y, Li Y, Gao J, Chen L, Xu J, Zhang C, Jung SY, Choi JM, Jain A, Liu M, Song L, Liu W, Guo G, Gong T, Huang Y, Qiu Y, Huang W, Shi T, Zhu W, Wang Y, He F, Shen L, Qin J, (2018) "A proteomic landscape of diffuse-type gastric cancer." <i>Nat Commun</i> <b>9</b>(1):1012; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29520031 29520031]; doi: [https://dx.doi.org/10.1038/s41467-018-03121-2 10.1038/s41467-018-03121-2]; GPMDB: [http://gpmdb.org/data/keyword/29520031 | + | #Azimi A, Caramuta S, Seashore-Ludlow B, Boström J, Robinson JL, Edfors F, Tuominen R, Kemper K, Krijgsman O, Peeper DS, Nielsen J, Hansson J, Egyhazi Brage S, Altun M, Uhlen M, Maddalo G, (2018) "Targeting CDK2 overcomes melanoma resistance against BRAF and Hsp90 inhibitors." <i>Mol Syst Biol</i> <b>14</b>(3):e7858; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29507054 29507054]; GPMDB: [http://gpmdb.org/data/keyword/29507054 16]. |
+ | #Carette X, Platig J, Young DC, Helmel M, Young AT, Wang Z, Potluri LP, Moody CS, Zeng J, Prisic S, Paulson JN, Muntel J, Madduri AVR, Velarde J, Mayfield JA, Locher C, Wang T, Quackenbush J, Rhee KY, Moody DB, Steen H, Husson RN, (2018) "Multisystem Analysis of <i>Mycobacterium tuberculosis</i> Reveals Kinase-Dependent Remodeling of the Pathogen-Environment Interface." <i>MBio</i> <b>9</b>(2):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29511081 29511081]; doi: [https://dx.doi.org/10.1128/mBio.02333-17 10.1128/mBio.02333-17]; GPMDB: [http://gpmdb.org/data/keyword/29511081 48]. | ||
+ | #Ge S, Xia X, Ding C, Zhen B, Zhou Q, Feng J, Yuan J, Chen R, Li Y, Ge Z, Ji J, Zhang L, Wang J, Li Z, Lai Y, Hu Y, Li Y, Li Y, Gao J, Chen L, Xu J, Zhang C, Jung SY, Choi JM, Jain A, Liu M, Song L, Liu W, Guo G, Gong T, Huang Y, Qiu Y, Huang W, Shi T, Zhu W, Wang Y, He F, Shen L, Qin J, (2018) "A proteomic landscape of diffuse-type gastric cancer." <i>Nat Commun</i> <b>9</b>(1):1012; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29520031 29520031]; doi: [https://dx.doi.org/10.1038/s41467-018-03121-2 10.1038/s41467-018-03121-2]; GPMDB: [http://gpmdb.org/data/keyword/29520031 66]. | ||
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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 be approved our quality control AI for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
CAUTION: Many papers contain serious errors in their Methods sections. When using data from the literature, it is important to be skeptical of any experimental parameter (cell line, tissue type, modification reagents, quantitation methoods, etc.) that may impact on your use of the data. We have tried to correct any obvious errors, but there is no way to guarantee that we found them all. When attempting to analyze or reproduce results, keep in mind the likelyhood that even key parts of the experiment methods may have been recorded incorrectly in the associated manuscript, as methods are rarely reviewed properly in the current journal publication process.
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 Mar. 18, 2018.