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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 October | + | 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 October 16, 2016. |
#Scott N, Sutton J, Gray C, (1989) "Morphometric diagnosis of serous effusions: refinement of differences between benign and malignant cases by use of outlying values and larger sample size." <i>J Clin Pathol</i> <b>42</b>(6):607–12; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/2738165 2738165]; GPMDB: [http://gpmdb.org/data/keyword/2738165 1]. | #Scott N, Sutton J, Gray C, (1989) "Morphometric diagnosis of serous effusions: refinement of differences between benign and malignant cases by use of outlying values and larger sample size." <i>J Clin Pathol</i> <b>42</b>(6):607–12; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/2738165 2738165]; GPMDB: [http://gpmdb.org/data/keyword/2738165 1]. | ||
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#Mitchell CJ, Getnet D, Kim MS, Manda SS, Kumar P, Huang TC, Pinto SM, Nirujogi RS, Iwasaki M, Shaw PG, Wu X, Zhong J, Chaerkady R, Marimuthu A, Muthusamy B, Sahasrabuddhe NA, Raju R, Bowman C, Danilova L, Cutler J, Kelkar DS, Drake CG, Prasad TS, Marchionni L, Murakami PN, Scott AF, Shi L, Thierry-Mieg J, Thierry-Mieg D, Irizarry R, Cope L, Ishihama Y, Wang C, Gowda H, Pandey A, (2015) "A multi-omic analysis of human naïve CD4+ T cells." <i>BMC Syst Biol</i> <b>9</b>:75; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26542228 26542228]; doi: [https://dx.doi.org/10.1186/s12918-015-0225-4 10.1186/s12918-015-0225-4]; GPMDB: [http://gpmdb.org/data/keyword/26542228 14]. | #Mitchell CJ, Getnet D, Kim MS, Manda SS, Kumar P, Huang TC, Pinto SM, Nirujogi RS, Iwasaki M, Shaw PG, Wu X, Zhong J, Chaerkady R, Marimuthu A, Muthusamy B, Sahasrabuddhe NA, Raju R, Bowman C, Danilova L, Cutler J, Kelkar DS, Drake CG, Prasad TS, Marchionni L, Murakami PN, Scott AF, Shi L, Thierry-Mieg J, Thierry-Mieg D, Irizarry R, Cope L, Ishihama Y, Wang C, Gowda H, Pandey A, (2015) "A multi-omic analysis of human naïve CD4+ T cells." <i>BMC Syst Biol</i> <b>9</b>:75; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26542228 26542228]; doi: [https://dx.doi.org/10.1186/s12918-015-0225-4 10.1186/s12918-015-0225-4]; GPMDB: [http://gpmdb.org/data/keyword/26542228 14]. | ||
#Aurass P, Gerlach T, Becher D, Voigt B, Karste S, Bernhardt J, Riedel K, Hecker M, Flieger A, (2016) "Life Stage-specific Proteomes of Legionella pneumophila Reveal a Highly Differential Abundance of Virulence-associated Dot/Icm effectors." <i>Mol Cell Proteomics</i> <b>15</b>(1):177–200; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26545400 26545400]; doi: [https://dx.doi.org/10.1074/mcp.M115.053579 10.1074/mcp.M115.053579]; GPMDB: [http://gpmdb.org/data/keyword/26545400 209]. | #Aurass P, Gerlach T, Becher D, Voigt B, Karste S, Bernhardt J, Riedel K, Hecker M, Flieger A, (2016) "Life Stage-specific Proteomes of Legionella pneumophila Reveal a Highly Differential Abundance of Virulence-associated Dot/Icm effectors." <i>Mol Cell Proteomics</i> <b>15</b>(1):177–200; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26545400 26545400]; doi: [https://dx.doi.org/10.1074/mcp.M115.053579 10.1074/mcp.M115.053579]; GPMDB: [http://gpmdb.org/data/keyword/26545400 209]. | ||
+ | #Hwang H, Park GW, Kim KH, Lee JY, Lee HK, Ji ES, Park SK, Xu T, Yates JR 3rd, Kwon KH, Park YM, Lee HJ, Paik YK, Kim JY, Yoo JS, (2015) "Chromosome-Based Proteomic Study for Identifying Novel Protein Variants from Human Hippocampal Tissue Using Customized neXtProt and GENCODE Databases." <i>J Proteome Res</i> <b>14</b>(12):5028–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26549206 26549206]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00472 10.1021/acs.jproteome.5b00472]; GPMDB: [http://gpmdb.org/data/keyword/26549206 1]. | ||
#Bensaddek D, Narayan V, Nicolas A, Murillo AB, Gartner A, Kenyon CJ, Lamond AI, (2016) "Micro-proteomics with iterative data analysis: Proteome analysis in C. elegans at the single worm level." <i>Proteomics</i> <b>16</b>(3):381–92; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26552604 26552604]; doi: [https://dx.doi.org/10.1002/pmic.201500264 10.1002/pmic.201500264]; GPMDB: [http://gpmdb.org/data/keyword/26552604 40]. | #Bensaddek D, Narayan V, Nicolas A, Murillo AB, Gartner A, Kenyon CJ, Lamond AI, (2016) "Micro-proteomics with iterative data analysis: Proteome analysis in C. elegans at the single worm level." <i>Proteomics</i> <b>16</b>(3):381–92; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26552604 26552604]; doi: [https://dx.doi.org/10.1002/pmic.201500264 10.1002/pmic.201500264]; GPMDB: [http://gpmdb.org/data/keyword/26552604 40]. | ||
#Dimayacyac-Esleta BR, Tsai CF, Kitata RB, Lin PY, Choong WK, Lin TD, Wang YT, Weng SH, Yang PC, Arco SD, Sung TY, Chen YJ, (2015) "Rapid High-pH Reverse Phase StageTip for Sensitive Small-Scale Membrane Proteomic Profiling." <i>Anal Chem</i> <b>87</b>(24):12016–23; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26554430 26554430]; doi: [https://dx.doi.org/10.1021/acs.analchem.5b03639 10.1021/acs.analchem.5b03639]; GPMDB: [http://gpmdb.org/data/keyword/26554430 14]. | #Dimayacyac-Esleta BR, Tsai CF, Kitata RB, Lin PY, Choong WK, Lin TD, Wang YT, Weng SH, Yang PC, Arco SD, Sung TY, Chen YJ, (2015) "Rapid High-pH Reverse Phase StageTip for Sensitive Small-Scale Membrane Proteomic Profiling." <i>Anal Chem</i> <b>87</b>(24):12016–23; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26554430 26554430]; doi: [https://dx.doi.org/10.1021/acs.analchem.5b03639 10.1021/acs.analchem.5b03639]; GPMDB: [http://gpmdb.org/data/keyword/26554430 14]. | ||
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#Locard-Paulet M, Lim L, Veluscek G, McMahon K, Sinclair J, van Weverwijk A, Worboys JD, Yuan Y, Isacke CM, Jørgensen C, (2016) "Phosphoproteomic analysis of interacting tumor and endothelial cells identifies regulatory mechanisms of transendothelial migration." <i>Sci Signal</i> <b>9</b>(414):ra15; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26861043 26861043]; doi: [https://dx.doi.org/10.1126/scisignal.aac5820 10.1126/scisignal.aac5820]; GPMDB: [http://gpmdb.org/data/keyword/26861043 76]. | #Locard-Paulet M, Lim L, Veluscek G, McMahon K, Sinclair J, van Weverwijk A, Worboys JD, Yuan Y, Isacke CM, Jørgensen C, (2016) "Phosphoproteomic analysis of interacting tumor and endothelial cells identifies regulatory mechanisms of transendothelial migration." <i>Sci Signal</i> <b>9</b>(414):ra15; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26861043 26861043]; doi: [https://dx.doi.org/10.1126/scisignal.aac5820 10.1126/scisignal.aac5820]; GPMDB: [http://gpmdb.org/data/keyword/26861043 76]. | ||
#Prior KK, Wittig I, Leisegang MS, Groenendyk J, Weissmann N, Michalak M, Jansen-Dürr P, Shah AM, Brandes RP, (2016) "The Endoplasmic Reticulum Chaperone Calnexin Is a NADPH Oxidase NOX4 Interacting Protein." <i>J Biol Chem</i> <b>291</b>(13):7045–59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26861875 26861875]; doi: [https://dx.doi.org/10.1074/jbc.M115.710772 10.1074/jbc.M115.710772]; GPMDB: [http://gpmdb.org/data/keyword/26861875 80]. | #Prior KK, Wittig I, Leisegang MS, Groenendyk J, Weissmann N, Michalak M, Jansen-Dürr P, Shah AM, Brandes RP, (2016) "The Endoplasmic Reticulum Chaperone Calnexin Is a NADPH Oxidase NOX4 Interacting Protein." <i>J Biol Chem</i> <b>291</b>(13):7045–59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26861875 26861875]; doi: [https://dx.doi.org/10.1074/jbc.M115.710772 10.1074/jbc.M115.710772]; GPMDB: [http://gpmdb.org/data/keyword/26861875 80]. | ||
+ | #Ramus C, Hovasse A, Marcellin M, Hesse AM, Mouton-Barbosa E, Bouyssié D, Vaca S, Carapito C, Chaoui K, Bruley C, Garin J, Cianférani S, Ferro M, Dorssaeler AV, Burlet-Schiltz O, Schaeffer C, Couté Y, Gonzalez de Peredo A, (2016) "Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods." <i>Data Brief</i> <b>6</b>:286–94; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26862574 26862574]; doi: [https://dx.doi.org/10.1016/j.dib.2015.11.063 10.1016/j.dib.2015.11.063]; GPMDB: [http://gpmdb.org/data/keyword/26862574 27]. | ||
#Sahebekhtiari N, Thomsen MM, Sloth JJ, Stenbroen V, Zeviani M, Gregersen N, Viscomi C, Palmfeldt J, (2016) "Quantitative proteomics suggests metabolic reprogramming during ETHE1 deficiency." <i>Proteomics</i> <b>16</b>(7):1166–76; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26867521 26867521]; doi: [https://dx.doi.org/10.1002/pmic.201500336 10.1002/pmic.201500336]; GPMDB: [http://gpmdb.org/data/keyword/26867521 50]. | #Sahebekhtiari N, Thomsen MM, Sloth JJ, Stenbroen V, Zeviani M, Gregersen N, Viscomi C, Palmfeldt J, (2016) "Quantitative proteomics suggests metabolic reprogramming during ETHE1 deficiency." <i>Proteomics</i> <b>16</b>(7):1166–76; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26867521 26867521]; doi: [https://dx.doi.org/10.1002/pmic.201500336 10.1002/pmic.201500336]; GPMDB: [http://gpmdb.org/data/keyword/26867521 50]. | ||
#Lamberti Y, Cafiero JH, Surmann K, Valdez H, Holubova J, Večerek B, Sebo P, Schmidt F, Völker U, Rodriguez ME, (2016) "Proteome analysis of Bordetella pertussis isolated from human macrophages." <i>J Proteomics</i> <b>136</b>:55–67; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26873878 26873878]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.02.002 10.1016/j.jprot.2016.02.002]; GPMDB: [http://gpmdb.org/data/keyword/26873878 9]. | #Lamberti Y, Cafiero JH, Surmann K, Valdez H, Holubova J, Večerek B, Sebo P, Schmidt F, Völker U, Rodriguez ME, (2016) "Proteome analysis of Bordetella pertussis isolated from human macrophages." <i>J Proteomics</i> <b>136</b>:55–67; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26873878 26873878]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.02.002 10.1016/j.jprot.2016.02.002]; GPMDB: [http://gpmdb.org/data/keyword/26873878 9]. | ||
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#Petrone A, Adamo ME, Cheng C, Kettenbach AN, (2016) "Identification of Candidate Cyclin-dependent kinase 1 (Cdk1) Substrates in Mitosis by Quantitative Phosphoproteomics." <i>Mol Cell Proteomics</i> <b>15</b>(7):2448–61; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27134283 27134283]; doi: [https://dx.doi.org/10.1074/mcp.M116.059394 10.1074/mcp.M116.059394]; GPMDB: [http://gpmdb.org/data/keyword/27134283 90]. | #Petrone A, Adamo ME, Cheng C, Kettenbach AN, (2016) "Identification of Candidate Cyclin-dependent kinase 1 (Cdk1) Substrates in Mitosis by Quantitative Phosphoproteomics." <i>Mol Cell Proteomics</i> <b>15</b>(7):2448–61; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27134283 27134283]; doi: [https://dx.doi.org/10.1074/mcp.M116.059394 10.1074/mcp.M116.059394]; GPMDB: [http://gpmdb.org/data/keyword/27134283 90]. | ||
#Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer MW, Beck M, (2015) "Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats." <i>Cell Syst</i> <b>1</b>(3):224–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27135913 27135913]; doi: [https://dx.doi.org/10.1016/j.cels.2015.08.012 10.1016/j.cels.2015.08.012]; GPMDB: [http://gpmdb.org/data/keyword/27135913 190]. | #Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer MW, Beck M, (2015) "Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats." <i>Cell Syst</i> <b>1</b>(3):224–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27135913 27135913]; doi: [https://dx.doi.org/10.1016/j.cels.2015.08.012 10.1016/j.cels.2015.08.012]; GPMDB: [http://gpmdb.org/data/keyword/27135913 190]. | ||
+ | #Francavilla C, Papetti M, Rigbolt KT, Pedersen AK, Sigurdsson JO, Cazzamali G, Karemore G, Blagoev B, Olsen JV, (2016) "Multilayered proteomics reveals molecular switches dictating ligand-dependent EGFR trafficking." <i>Nat Struct Mol Biol</i> <b>23</b>(6):608–18; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27136326 27136326]; doi: [https://dx.doi.org/10.1038/nsmb.3218 10.1038/nsmb.3218]; GPMDB: [http://gpmdb.org/data/keyword/27136326 19]. | ||
#Ulrich V, Rotllan N, Araldi E, Luciano A, Skroblin P, Abonnenc M, Perrotta P, Yin X, Bauer A, Leslie KL, Zhang P, Aryal B, Montgomery RL, Thum T, Martin K, Suarez Y, Mayr M, Fernandez-Hernando C, Sessa WC, (2016) "Chronic miR-29 antagonism promotes favorable plaque remodeling in atherosclerotic mice." <i>EMBO Mol Med</i> <b>8</b>(6):643–53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27137489 27137489]; doi: [https://dx.doi.org/10.15252/emmm.201506031 10.15252/emmm.201506031]; GPMDB: [http://gpmdb.org/data/keyword/27137489 120]. | #Ulrich V, Rotllan N, Araldi E, Luciano A, Skroblin P, Abonnenc M, Perrotta P, Yin X, Bauer A, Leslie KL, Zhang P, Aryal B, Montgomery RL, Thum T, Martin K, Suarez Y, Mayr M, Fernandez-Hernando C, Sessa WC, (2016) "Chronic miR-29 antagonism promotes favorable plaque remodeling in atherosclerotic mice." <i>EMBO Mol Med</i> <b>8</b>(6):643–53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27137489 27137489]; doi: [https://dx.doi.org/10.15252/emmm.201506031 10.15252/emmm.201506031]; GPMDB: [http://gpmdb.org/data/keyword/27137489 120]. | ||
#Zielke RA, Wierzbicki IH, Baarda BI, Gafken PR, Soge OO, Holmes KK, Jerse AE, Unemo M, Sikora AE, (2016) "Proteomics-driven Antigen Discovery for Development of Vaccines Against Gonorrhea." <i>Mol Cell Proteomics</i> <b>15</b>(7):2338–55; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27141096 27141096]; doi: [https://dx.doi.org/10.1074/mcp.M116.058800 10.1074/mcp.M116.058800]; GPMDB: [http://gpmdb.org/data/keyword/27141096 3]. | #Zielke RA, Wierzbicki IH, Baarda BI, Gafken PR, Soge OO, Holmes KK, Jerse AE, Unemo M, Sikora AE, (2016) "Proteomics-driven Antigen Discovery for Development of Vaccines Against Gonorrhea." <i>Mol Cell Proteomics</i> <b>15</b>(7):2338–55; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27141096 27141096]; doi: [https://dx.doi.org/10.1074/mcp.M116.058800 10.1074/mcp.M116.058800]; GPMDB: [http://gpmdb.org/data/keyword/27141096 3]. | ||
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#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 8004]. |
#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]. | ||
#Viktorovskaya OV, Greco TM, Cristea IM, Thompson SR, (2016) "Identification of RNA Binding Proteins Associated with Dengue Virus RNA in Infected Cells Reveals Temporally Distinct Host Factor Requirements." <i>PLoS Negl Trop Dis</i> <b>10</b>(8):e0004921; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27556644 27556644]; doi: [https://dx.doi.org/10.1371/journal.pntd.0004921 10.1371/journal.pntd.0004921]; GPMDB: [http://gpmdb.org/data/keyword/27556644 7]. | #Viktorovskaya OV, Greco TM, Cristea IM, Thompson SR, (2016) "Identification of RNA Binding Proteins Associated with Dengue Virus RNA in Infected Cells Reveals Temporally Distinct Host Factor Requirements." <i>PLoS Negl Trop Dis</i> <b>10</b>(8):e0004921; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27556644 27556644]; doi: [https://dx.doi.org/10.1371/journal.pntd.0004921 10.1371/journal.pntd.0004921]; GPMDB: [http://gpmdb.org/data/keyword/27556644 7]. | ||
#Cassidy L, Prasse D, Linke D, Schmitz RA, Tholey A, (2016) "Combination of Bottom-up 2D-LC-MS and Semi-top-down GelFree-LC-MS Enhances Coverage of Proteome and Low Molecular Weight Short Open Reading Frame Encoded Peptides of the Archaeon Methanosarcina mazei." <i>J Proteome Res</i> <b>15</b>(10):3773–3783; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27557128 27557128]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00569 10.1021/acs.jproteome.6b00569]; GPMDB: [http://gpmdb.org/data/keyword/27557128 6]. | #Cassidy L, Prasse D, Linke D, Schmitz RA, Tholey A, (2016) "Combination of Bottom-up 2D-LC-MS and Semi-top-down GelFree-LC-MS Enhances Coverage of Proteome and Low Molecular Weight Short Open Reading Frame Encoded Peptides of the Archaeon Methanosarcina mazei." <i>J Proteome Res</i> <b>15</b>(10):3773–3783; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27557128 27557128]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00569 10.1021/acs.jproteome.6b00569]; GPMDB: [http://gpmdb.org/data/keyword/27557128 6]. | ||
+ | #Häupl B, Ihling CH, Sinz A, (2016) "Protein Interaction Network of Human Protein Kinase D2 Revealed by Chemical Cross-Linking/Mass Spectrometry." <i>J Proteome Res</i> <b>15</b>(10):3686–3699; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27559607 27559607]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00513 10.1021/acs.jproteome.6b00513]; GPMDB: [http://gpmdb.org/data/keyword/27559607 81]. | ||
+ | #Jiang Y, Lee J, Lee JH, Lee JW, Kim JH, Choi WH, Yoo YD, Cha-Molstad H, Kim BY, Kwon YT, Noh SA, Kim KP, Lee MJ, (2016) "The arginylation branch of the N-end rule pathway positively regulates cellular autophagic flux and clearance of proteotoxic proteins." <i>Autophagy</i> <b></b>:1–16; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27560450 27560450]; doi: [https://dx.doi.org/10.1080/15548627.2016.1222991 10.1080/15548627.2016.1222991]; GPMDB: [http://gpmdb.org/data/keyword/27560450 2]. | ||
#Ross SH, Rollings C, Anderson KE, Hawkins PT, Stephens LR, Cantrell DA, (2016) "Phosphoproteomic Analyses of Interleukin 2 Signaling Reveal Integrated JAK Kinase-Dependent and -Independent Networks in CD8(+) T Cells." <i>Immunity</i> <b>45</b>(3):685–700; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27566939 27566939]; doi: [https://dx.doi.org/10.1016/j.immuni.2016.07.022 10.1016/j.immuni.2016.07.022]; GPMDB: [http://gpmdb.org/data/keyword/27566939 208]. | #Ross SH, Rollings C, Anderson KE, Hawkins PT, Stephens LR, Cantrell DA, (2016) "Phosphoproteomic Analyses of Interleukin 2 Signaling Reveal Integrated JAK Kinase-Dependent and -Independent Networks in CD8(+) T Cells." <i>Immunity</i> <b>45</b>(3):685–700; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27566939 27566939]; doi: [https://dx.doi.org/10.1016/j.immuni.2016.07.022 10.1016/j.immuni.2016.07.022]; GPMDB: [http://gpmdb.org/data/keyword/27566939 208]. | ||
+ | #Larsen SC, Sylvestersen KB, Mund A, Lyon D, Mullari M, Madsen MV, Daniel JA, Jensen LJ, Nielsen ML, (2016) "Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cells." <i>Sci Signal</i> <b>9</b>(443):rs9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27577262 27577262]; doi: [https://dx.doi.org/10.1126/scisignal.aaf7329 10.1126/scisignal.aaf7329]; GPMDB: [http://gpmdb.org/data/keyword/27577262 1]. | ||
#Delaveau T, Davoine D, Jolly A, Vallot A, Rouvière JO, Gerber A, Brochet S, Plessis M, Roquigny R, Merhej J, Leger T, Garcia C, Lelandais G, Laine E, Palancade B, Devaux F, Garcia M, (2016) "Tma108, a putative M1 aminopeptidase, is a specific nascent chain-associated protein in Saccharomyces cerevisiae." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27580715 27580715]; doi: [https://dx.doi.org/10.1093/nar/gkw732 10.1093/nar/gkw732]; GPMDB: [http://gpmdb.org/data/keyword/27580715 19]. | #Delaveau T, Davoine D, Jolly A, Vallot A, Rouvière JO, Gerber A, Brochet S, Plessis M, Roquigny R, Merhej J, Leger T, Garcia C, Lelandais G, Laine E, Palancade B, Devaux F, Garcia M, (2016) "Tma108, a putative M1 aminopeptidase, is a specific nascent chain-associated protein in Saccharomyces cerevisiae." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27580715 27580715]; doi: [https://dx.doi.org/10.1093/nar/gkw732 10.1093/nar/gkw732]; GPMDB: [http://gpmdb.org/data/keyword/27580715 19]. | ||
#Lee H, Chae S, Park J, Bae J, Go EB, Kim SJ, Kim H, Hwang D, Lee SW, Lee SY, (2016) "Comprehensive proteome profiling of platelet identified a protein profile predictive of responses to an antiplatelet agent sarpogrelate." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27601597 27601597]; doi: [https://dx.doi.org/10.1074/mcp.M116.059154 10.1074/mcp.M116.059154]; GPMDB: [http://gpmdb.org/data/keyword/27601597 96]. | #Lee H, Chae S, Park J, Bae J, Go EB, Kim SJ, Kim H, Hwang D, Lee SW, Lee SY, (2016) "Comprehensive proteome profiling of platelet identified a protein profile predictive of responses to an antiplatelet agent sarpogrelate." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27601597 27601597]; doi: [https://dx.doi.org/10.1074/mcp.M116.059154 10.1074/mcp.M116.059154]; GPMDB: [http://gpmdb.org/data/keyword/27601597 96]. | ||
#Lee J, McKinney KQ, Pavlopoulos AJ, Han MH, Kim SH, Kim HJ, Hwang S, (2016) "Exosomal proteome analysis of cerebrospinal fluid detects biosignatures of neuromyelitis optica and multiple sclerosis." <i>Clin Chim Acta</i> <b>462</b>:118–126; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27609124 27609124]; doi: [https://dx.doi.org/10.1016/j.cca.2016.09.001 10.1016/j.cca.2016.09.001]; GPMDB: [http://gpmdb.org/data/keyword/27609124 24]. | #Lee J, McKinney KQ, Pavlopoulos AJ, Han MH, Kim SH, Kim HJ, Hwang S, (2016) "Exosomal proteome analysis of cerebrospinal fluid detects biosignatures of neuromyelitis optica and multiple sclerosis." <i>Clin Chim Acta</i> <b>462</b>:118–126; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27609124 27609124]; doi: [https://dx.doi.org/10.1016/j.cca.2016.09.001 10.1016/j.cca.2016.09.001]; GPMDB: [http://gpmdb.org/data/keyword/27609124 24]. | ||
+ | #Bennike TB, Ellingsen T, Glerup H, Bonderup OK, Carlsen TG, Meyer MK, Bøgsted M, Christiansen G, Birkelund S, Andersen V, Stensballe A, (2016) "Proteome Analysis of Rheumatoid Arthritis Gut Mucosa." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27627584 27627584]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00598 10.1021/acs.jproteome.6b00598]; GPMDB: [http://gpmdb.org/data/keyword/27627584 33]. | ||
+ | #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]. | ||
+ | #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>; 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>; 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]. | ||
#Radzikowski JL, Vedelaar S, Siegel D, Ortega ÁD, Schmidt A, Heinemann M, (2016) "Bacterial persistence is an active σS stress response to metabolic flux limitation." <i>Mol Syst Biol</i> <b>12</b>(9):882; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27655400 27655400]; GPMDB: [http://gpmdb.org/data/keyword/27655400 30]. | #Radzikowski JL, Vedelaar S, Siegel D, Ortega ÁD, Schmidt A, Heinemann M, (2016) "Bacterial persistence is an active σS stress response to metabolic flux limitation." <i>Mol Syst Biol</i> <b>12</b>(9):882; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27655400 27655400]; GPMDB: [http://gpmdb.org/data/keyword/27655400 30]. | ||
#Lee A, Miller D, Henry R, Paruchuri VD, O'Meally RN, Boronina T, Cole RN, Zachara NE, (2016) "Combined Antibody/Lectin-Enrichment Identifies Extensive Changes in the O-GlcNAc Sub-proteome Upon Oxidative Stress." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27669760 27669760]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00369 10.1021/acs.jproteome.6b00369]; GPMDB: [http://gpmdb.org/data/keyword/27669760 14]. | #Lee A, Miller D, Henry R, Paruchuri VD, O'Meally RN, Boronina T, Cole RN, Zachara NE, (2016) "Combined Antibody/Lectin-Enrichment Identifies Extensive Changes in the O-GlcNAc Sub-proteome Upon Oxidative Stress." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27669760 27669760]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00369 10.1021/acs.jproteome.6b00369]; GPMDB: [http://gpmdb.org/data/keyword/27669760 14]. | ||
- | #Lyon SM, Mayampurath A, Rogers MR, Wolfgeher DJ, Fisher SM, Volchenboum SL, He TC, Reid RR, (2016) "A method for whole protein isolation from human cranial bone." <i>Anal Biochem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27677936 27677936]; doi: [https://dx.doi.org/10.1016/j.ab.2016.09.021 10.1016/j.ab.2016.09.021]; GPMDB: [http://gpmdb.org/data/keyword/27677936 | + | #Lyon SM, Mayampurath A, Rogers MR, Wolfgeher DJ, Fisher SM, Volchenboum SL, He TC, Reid RR, (2016) "A method for whole protein isolation from human cranial bone." <i>Anal Biochem</i> <b>515</b>:33–39; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27677936 27677936]; doi: [https://dx.doi.org/10.1016/j.ab.2016.09.021 10.1016/j.ab.2016.09.021]; GPMDB: [http://gpmdb.org/data/keyword/27677936 10]. |
+ | #Gautier V, Cayrol C, Farache D, Roga S, Monsarrat B, Burlet-Schiltz O, Gonzalez de Peredo A, Girard JP, (2016) "Extracellular IL-33 cytokine, but not endogenous nuclear IL-33, regulates protein expression in endothelial cells." <i>Sci Rep</i> <b>6</b>:34255; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27694941 27694941]; doi: [https://dx.doi.org/10.1038/srep34255 10.1038/srep34255]; GPMDB: [http://gpmdb.org/data/keyword/27694941 70]. | ||
+ | #Kwon OK, Kim SJ, 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]. | ||
+ | #Baas R, Sijm A, van Teeffelen HA, van Es R, Vos HR, 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>; 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]. |
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 October 16, 2016.