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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 April | + | 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 April 23, 2017. |
#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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#Higgins R, Gendron JM, Rising L, Mak R, Webb K, Kaiser SE, Zuzow N, Riviere P, Yang B, Fenech E, Tang X, Lindsay SA, Christianson JC, Hampton RY, Wasserman SA, Bennett EJ, (2015) "The Unfolded Protein Response Triggers Site-Specific Regulatory Ubiquitylation of 40S Ribosomal Proteins." <i>Mol Cell</i> <b>59</b>(1):35–49; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26051182 26051182]; doi: [https://dx.doi.org/10.1016/j.molcel.2015.04.026 10.1016/j.molcel.2015.04.026]; GPMDB: [http://gpmdb.org/data/keyword/26051182 54]. | #Higgins R, Gendron JM, Rising L, Mak R, Webb K, Kaiser SE, Zuzow N, Riviere P, Yang B, Fenech E, Tang X, Lindsay SA, Christianson JC, Hampton RY, Wasserman SA, Bennett EJ, (2015) "The Unfolded Protein Response Triggers Site-Specific Regulatory Ubiquitylation of 40S Ribosomal Proteins." <i>Mol Cell</i> <b>59</b>(1):35–49; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26051182 26051182]; doi: [https://dx.doi.org/10.1016/j.molcel.2015.04.026 10.1016/j.molcel.2015.04.026]; GPMDB: [http://gpmdb.org/data/keyword/26051182 54]. | ||
#Sethi MK, Thaysen-Andersen M, Kim H, Park CK, Baker MS, Packer NH, Paik YK, Hancock WS, Fanayan S, (2015) "Quantitative proteomic analysis of paired colorectal cancer and non-tumorigenic tissues reveals signature proteins and perturbed pathways involved in CRC progression and metastasis." <i>J Proteomics</i> <b>126</b>:54–67; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26054784 26054784]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.05.037 10.1016/j.jprot.2015.05.037]; GPMDB: [http://gpmdb.org/data/keyword/26054784 15]. | #Sethi MK, Thaysen-Andersen M, Kim H, Park CK, Baker MS, Packer NH, Paik YK, Hancock WS, Fanayan S, (2015) "Quantitative proteomic analysis of paired colorectal cancer and non-tumorigenic tissues reveals signature proteins and perturbed pathways involved in CRC progression and metastasis." <i>J Proteomics</i> <b>126</b>:54–67; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26054784 26054784]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.05.037 10.1016/j.jprot.2015.05.037]; GPMDB: [http://gpmdb.org/data/keyword/26054784 15]. | ||
- | #Cifani P, Kirik U, Waldemarson S, James P, (2015) "Molecular Portrait of Breast-Cancer-Derived Cell Lines Reveals Poor Similarity with Tumors." <i>J Proteome Res</i> <b>14</b>(7):2819–27; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26055192 26055192]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00375 10.1021/acs.jproteome.5b00375]; GPMDB: [http://gpmdb.org/data/keyword/26055192 | + | #Cifani P, Kirik U, Waldemarson S, James P, (2015) "Molecular Portrait of Breast-Cancer-Derived Cell Lines Reveals Poor Similarity with Tumors." <i>J Proteome Res</i> <b>14</b>(7):2819–27; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26055192 26055192]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00375 10.1021/acs.jproteome.5b00375]; GPMDB: [http://gpmdb.org/data/keyword/26055192 439]. |
#McCloy RA, Parker BL, Rogers S, Chaudhuri R, Gayevskiy V, Hoffman NJ, Ali N, Watkins DN, Daly RJ, James DE, Lorca T, Castro A, Burgess A, (2015) "Global Phosphoproteomic Mapping of Early Mitotic Exit in Human Cells Identifies Novel Substrate Dephosphorylation Motifs." <i>Mol Cell Proteomics</i> <b>14</b>(8):2194–212; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26055452 26055452]; doi: [https://dx.doi.org/10.1074/mcp.M114.046938 10.1074/mcp.M114.046938]; GPMDB: [http://gpmdb.org/data/keyword/26055452 29]. | #McCloy RA, Parker BL, Rogers S, Chaudhuri R, Gayevskiy V, Hoffman NJ, Ali N, Watkins DN, Daly RJ, James DE, Lorca T, Castro A, Burgess A, (2015) "Global Phosphoproteomic Mapping of Early Mitotic Exit in Human Cells Identifies Novel Substrate Dephosphorylation Motifs." <i>Mol Cell Proteomics</i> <b>14</b>(8):2194–212; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26055452 26055452]; doi: [https://dx.doi.org/10.1074/mcp.M114.046938 10.1074/mcp.M114.046938]; GPMDB: [http://gpmdb.org/data/keyword/26055452 29]. | ||
#Mulvey CM, Schröter C, Gatto L, Dikicioglu D, Fidaner IB, Christoforou A, Deery MJ, Cho LT, Niakan KK, Martinez-Arias A, Lilley KS, (2015) "Dynamic Proteomic Profiling of Extra-Embryonic Endoderm Differentiation in Mouse Embryonic Stem Cells." <i>Stem Cells</i> <b>33</b>(9):2712–25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26059426 26059426]; doi: [https://dx.doi.org/10.1002/stem.2067 10.1002/stem.2067]; GPMDB: [http://gpmdb.org/data/keyword/26059426 7]. | #Mulvey CM, Schröter C, Gatto L, Dikicioglu D, Fidaner IB, Christoforou A, Deery MJ, Cho LT, Niakan KK, Martinez-Arias A, Lilley KS, (2015) "Dynamic Proteomic Profiling of Extra-Embryonic Endoderm Differentiation in Mouse Embryonic Stem Cells." <i>Stem Cells</i> <b>33</b>(9):2712–25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26059426 26059426]; doi: [https://dx.doi.org/10.1002/stem.2067 10.1002/stem.2067]; GPMDB: [http://gpmdb.org/data/keyword/26059426 7]. | ||
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#O'Neill JR, Pak HS, Pairo-Castineira E, Save V, Paterson-Brown S, Nenutil R, Vojtěšek B, Overton I, Scherl A, Hupp TR, (2017) "Quantitative shotgun proteomics unveils candidate novel oesophageal adenocarcinoma-specific proteins." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28336725 28336725]; doi: [https://dx.doi.org/10.1074/mcp.M116.065078 10.1074/mcp.M116.065078]; GPMDB: [http://gpmdb.org/data/keyword/28336725 7]. | #O'Neill JR, Pak HS, Pairo-Castineira E, Save V, Paterson-Brown S, Nenutil R, Vojtěšek B, Overton I, Scherl A, Hupp TR, (2017) "Quantitative shotgun proteomics unveils candidate novel oesophageal adenocarcinoma-specific proteins." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28336725 28336725]; doi: [https://dx.doi.org/10.1074/mcp.M116.065078 10.1074/mcp.M116.065078]; GPMDB: [http://gpmdb.org/data/keyword/28336725 7]. | ||
#Francavilla C, Lupia M, Tsafou K, Villa A, Kowalczyk K, Rakownikow Jersie-Christensen R, Bertalot G, Confalonieri S, Brunak S, Jensen LJ, Cavallaro U, Olsen JV, (2017) "Phosphoproteomics of Primary Cells Reveals Druggable Kinase Signatures in Ovarian Cancer." <i>Cell Rep</i> <b>18</b>(13):3242–3256; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28355574 28355574]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.03.015 10.1016/j.celrep.2017.03.015]; GPMDB: [http://gpmdb.org/data/keyword/28355574 59]. | #Francavilla C, Lupia M, Tsafou K, Villa A, Kowalczyk K, Rakownikow Jersie-Christensen R, Bertalot G, Confalonieri S, Brunak S, Jensen LJ, Cavallaro U, Olsen JV, (2017) "Phosphoproteomics of Primary Cells Reveals Druggable Kinase Signatures in Ovarian Cancer." <i>Cell Rep</i> <b>18</b>(13):3242–3256; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28355574 28355574]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.03.015 10.1016/j.celrep.2017.03.015]; GPMDB: [http://gpmdb.org/data/keyword/28355574 59]. | ||
+ | #Chatzinikolaou G, Apostolou Z, Aid-Pavlidis T, Ioannidou A, Karakasilioti I, Papadopoulos GL, Aivaliotis M, Tsekrekou M, Strouboulis J, Kosteas T, Garinis GA, (2017) "ERCC1-XPF cooperates with CTCF and cohesin to facilitate the developmental silencing of imprinted genes." <i>Nat Cell Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28368372 28368372]; doi: [https://dx.doi.org/10.1038/ncb3499 10.1038/ncb3499]; GPMDB: [http://gpmdb.org/data/keyword/28368372 146]. | ||
+ | #Duguet F, Locard-Paulet M, Marcellin M, Chaoui K, Bernard I, Andreoletti O, Lesourne R, Burlet-Schiltz O, Gonzalez de Peredo A, Saoudi A, (2017) "Proteomic analysis of regulatory T cells reveals the importance of Themis1 in the control of their suppressive function." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28373295 28373295]; doi: [https://dx.doi.org/10.1074/mcp.M116.062745 10.1074/mcp.M116.062745]; GPMDB: [http://gpmdb.org/data/keyword/28373295 26]. | ||
+ | #Namuduri AV, Heras G, Mi J, Cacciani N, Hörnaeus K, Konzer A, Bergström Lind S, Larsson L, Gastaldello S, (2017) "A proteomic approach to identify alterations in the SUMO network during controlled mechanical ventilation in rat diaphragm muscle." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28373296 28373296]; doi: [https://dx.doi.org/10.1074/mcp.M116.066159 10.1074/mcp.M116.066159]; GPMDB: [http://gpmdb.org/data/keyword/28373296 80]. | ||
+ | #Anderson KA, Huynh FK, Fisher-Wellman K, Stuart JD, Peterson BS, Douros JD, Wagner GR, Thompson JW, Madsen AS, Green MF, Sivley RM, Ilkayeva OR, Stevens RD, Backos DS, Capra JA, Olsen CA, Campbell JE, Muoio DM, Grimsrud PA, Hirschey MD, (2017) "SIRT4 Is a Lysine Deacylase that Controls Leucine Metabolism and Insulin Secretion." <i>Cell Metab</i> <b>25</b>(4):838–855.e15; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28380376 28380376]; doi: [https://dx.doi.org/10.1016/j.cmet.2017.03.003 10.1016/j.cmet.2017.03.003]; GPMDB: [http://gpmdb.org/data/keyword/28380376 4]. | ||
#Casas-Vila N, Bluhm A, Sayols S, Dinges N, Dejung M, Altenhein T, Kappei D, Altenhein B, Roignant JY, Butter F, (2017) "The developmental proteome of <i>Drosophila melanogaster</i>." <i>Genome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28381612 28381612]; doi: [https://dx.doi.org/10.1101/gr.213694.116 10.1101/gr.213694.116]; GPMDB: [http://gpmdb.org/data/keyword/28381612 124]. | #Casas-Vila N, Bluhm A, Sayols S, Dinges N, Dejung M, Altenhein T, Kappei D, Altenhein B, Roignant JY, Butter F, (2017) "The developmental proteome of <i>Drosophila melanogaster</i>." <i>Genome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28381612 28381612]; doi: [https://dx.doi.org/10.1101/gr.213694.116 10.1101/gr.213694.116]; GPMDB: [http://gpmdb.org/data/keyword/28381612 124]. | ||
- | #Chiang CK, Xu B, Mehta N, Mayne J, Sun WY, Cheng K, Ning Z, Dong J, Zou H, Cheng HM, Figeys D, (2017) "Phosphoproteome Profiling Reveals Circadian Clock Regulation of Posttranslational Modifications in the Murine Hippocampus." <i>Front Neurol</i> <b>8</b>:110; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28382018 28382018]; doi: [https://dx.doi.org/10.3389/fneur.2017.00110 10.3389/fneur.2017.00110]; GPMDB: [http://gpmdb.org/data/keyword/28382018 | + | #Chiang CK, Xu B, Mehta N, Mayne J, Sun WY, Cheng K, Ning Z, Dong J, Zou H, Cheng HM, Figeys D, (2017) "Phosphoproteome Profiling Reveals Circadian Clock Regulation of Posttranslational Modifications in the Murine Hippocampus." <i>Front Neurol</i> <b>8</b>:110; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28382018 28382018]; doi: [https://dx.doi.org/10.3389/fneur.2017.00110 10.3389/fneur.2017.00110]; GPMDB: [http://gpmdb.org/data/keyword/28382018 299]. |
+ | #Young C, Podtelejnikov AV, Nielsen ML, (2017) "Improved Reversed Phase Chromatography of Hydrophilic Peptides from Spatial and Temporal Changes in Column Temperature." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28387123 28387123]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b01055 10.1021/acs.jproteome.6b01055]; GPMDB: [http://gpmdb.org/data/keyword/28387123 12]. | ||
+ | #Beach RR, Ricci-Tam C, Brennan CM, Moomau CA, Hsu PH, Hua B, Silberman RE, Springer M, Amon A, (2017) "Aneuploidy Causes Non-genetic Individuality." <i>Cell</i> <b>169</b>(2):229–242.e21; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28388408 28388408]; doi: [https://dx.doi.org/10.1016/j.cell.2017.03.021 10.1016/j.cell.2017.03.021]; GPMDB: [http://gpmdb.org/data/keyword/28388408 3]. |
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 be approved our quality control AI 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 April 23, 2017.