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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 August | + | 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 August 27, 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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#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]. | ||
+ | #Chatterjee S, Stupp GS, Park SK, Ducom JC, Yates JR 3rd, Su AI, Wolan DW, (2016) "A comprehensive and scalable database search system for metaproteomics." <i>BMC Genomics</i> <b>17</b>(1):642; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27528457 27528457]; doi: [https://dx.doi.org/10.1186/s12864-016-2855-3 10.1186/s12864-016-2855-3]; GPMDB: [http://gpmdb.org/data/keyword/27528457 19]. | ||
#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]. | #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]. | ||
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#Poppleton DI, Duchateau M, Hourdel V, Matondo M, Flechsler J, Klingl A, Beloin C, Gribaldo S, (2017) "Outer Membrane Proteome of <i>Veillonella parvula:</i> A Diderm Firmicute of the Human Microbiome." <i>Front Microbiol</i> <b>8</b>:1215; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28713344 28713344]; doi: [https://dx.doi.org/10.3389/fmicb.2017.01215 10.3389/fmicb.2017.01215]; GPMDB: [http://gpmdb.org/data/keyword/28713344 16]. | #Poppleton DI, Duchateau M, Hourdel V, Matondo M, Flechsler J, Klingl A, Beloin C, Gribaldo S, (2017) "Outer Membrane Proteome of <i>Veillonella parvula:</i> A Diderm Firmicute of the Human Microbiome." <i>Front Microbiol</i> <b>8</b>:1215; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28713344 28713344]; doi: [https://dx.doi.org/10.3389/fmicb.2017.01215 10.3389/fmicb.2017.01215]; GPMDB: [http://gpmdb.org/data/keyword/28713344 16]. | ||
#Lee HJ, Jedrychowski MP, Vinayagam A, Wu N, Shyh-Chang N, Hu Y, Min-Wen C, Moore JK, Asara JM, Lyssiotis CA, Perrimon N, Gygi SP, Cantley LC, Kirschner MW, (2017) "Proteomic and Metabolomic Characterization of a Mammalian Cellular Transition from Quiescence to Proliferation." <i>Cell Rep</i> <b>20</b>(3):721–736; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28723573 28723573]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.06.074 10.1016/j.celrep.2017.06.074]; GPMDB: [http://gpmdb.org/data/keyword/28723573 2]. | #Lee HJ, Jedrychowski MP, Vinayagam A, Wu N, Shyh-Chang N, Hu Y, Min-Wen C, Moore JK, Asara JM, Lyssiotis CA, Perrimon N, Gygi SP, Cantley LC, Kirschner MW, (2017) "Proteomic and Metabolomic Characterization of a Mammalian Cellular Transition from Quiescence to Proliferation." <i>Cell Rep</i> <b>20</b>(3):721–736; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28723573 28723573]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.06.074 10.1016/j.celrep.2017.06.074]; GPMDB: [http://gpmdb.org/data/keyword/28723573 2]. | ||
- | #La Barbera G, Capriotti AL, Michelini E, Piovesana S, Calabretta MM, Chiozzi RZ, Roda A, Laganà A, (2017) "Proteomic analysis and bioluminescent reporter gene assays to investigate effects of simulated microgravity on Caco-2 cells." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28727291 28727291]; doi: [https://dx.doi.org/10.1002/pmic.201700081 10.1002/pmic.201700081]; GPMDB: [http://gpmdb.org/data/keyword/28727291 | + | #La Barbera G, Capriotti AL, Michelini E, Piovesana S, Calabretta MM, Chiozzi RZ, Roda A, Laganà A, (2017) "Proteomic analysis and bioluminescent reporter gene assays to investigate effects of simulated microgravity on Caco-2 cells." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28727291 28727291]; doi: [https://dx.doi.org/10.1002/pmic.201700081 10.1002/pmic.201700081]; GPMDB: [http://gpmdb.org/data/keyword/28727291 13]. |
#Hau AC, Grebbin BM, Agoston Z, Anders-Maurer M, Müller T, Groß A, Kolb J, Langer JD, Döring C, Schulte D, (2017) "MEIS homeodomain proteins facilitate PARP1/ARTD1-mediated eviction of histone H1." <i>J Cell Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28739678 28739678]; doi: [https://dx.doi.org/10.1083/jcb.201701154 10.1083/jcb.201701154]; GPMDB: [http://gpmdb.org/data/keyword/28739678 6]. | #Hau AC, Grebbin BM, Agoston Z, Anders-Maurer M, Müller T, Groß A, Kolb J, Langer JD, Döring C, Schulte D, (2017) "MEIS homeodomain proteins facilitate PARP1/ARTD1-mediated eviction of histone H1." <i>J Cell Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28739678 28739678]; doi: [https://dx.doi.org/10.1083/jcb.201701154 10.1083/jcb.201701154]; GPMDB: [http://gpmdb.org/data/keyword/28739678 6]. | ||
#D'Angelo G, Chaerkady R, Yu W, Hizal DB, Hess S, Zhao W, Lekstrom K, Guo X, White WI, Roskos L, Bowen MA, Yang H, (2017) "Statistical models for the analysis of isobaric tags multiplexed quantitative proteomics." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28745510 28745510]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b01050 10.1021/acs.jproteome.6b01050]; GPMDB: [http://gpmdb.org/data/keyword/28745510 5]. | #D'Angelo G, Chaerkady R, Yu W, Hizal DB, Hess S, Zhao W, Lekstrom K, Guo X, White WI, Roskos L, Bowen MA, Yang H, (2017) "Statistical models for the analysis of isobaric tags multiplexed quantitative proteomics." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28745510 28745510]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b01050 10.1021/acs.jproteome.6b01050]; GPMDB: [http://gpmdb.org/data/keyword/28745510 5]. | ||
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#Gómez-Baena G, Bennett RJ, Martínez-Rodríguez C, Wnęk M, Laing G, Hickey G, McLean L, Beynon RJ, Carrol ED, (2017) "Quantitative Proteomics of Cerebrospinal Fluid in Paediatric Pneumococcal Meningitis." <i>Sci Rep</i> <b>7</b>(1):7042; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28765563 28765563]; doi: [https://dx.doi.org/10.1038/s41598-017-07127-6 10.1038/s41598-017-07127-6]; GPMDB: [http://gpmdb.org/data/keyword/28765563 28]. | #Gómez-Baena G, Bennett RJ, Martínez-Rodríguez C, Wnęk M, Laing G, Hickey G, McLean L, Beynon RJ, Carrol ED, (2017) "Quantitative Proteomics of Cerebrospinal Fluid in Paediatric Pneumococcal Meningitis." <i>Sci Rep</i> <b>7</b>(1):7042; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28765563 28765563]; doi: [https://dx.doi.org/10.1038/s41598-017-07127-6 10.1038/s41598-017-07127-6]; GPMDB: [http://gpmdb.org/data/keyword/28765563 28]. | ||
#Khan MH, Salomaa SI, Jacquemet G, Butt U, Miihkinen M, Deguchi T, Kremneva E, Lappalainen P, Humphries MJ, Pouwels J, (2017) "The Sharpin interactome reveals a role for Sharpin in lamellipodium formation via the Arp2/3 complex." <i>J Cell Sci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28775156 28775156]; doi: [https://dx.doi.org/10.1242/jcs.200329 10.1242/jcs.200329]; GPMDB: [http://gpmdb.org/data/keyword/28775156 51]. | #Khan MH, Salomaa SI, Jacquemet G, Butt U, Miihkinen M, Deguchi T, Kremneva E, Lappalainen P, Humphries MJ, Pouwels J, (2017) "The Sharpin interactome reveals a role for Sharpin in lamellipodium formation via the Arp2/3 complex." <i>J Cell Sci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28775156 28775156]; doi: [https://dx.doi.org/10.1242/jcs.200329 10.1242/jcs.200329]; GPMDB: [http://gpmdb.org/data/keyword/28775156 51]. | ||
- | #Woo J, Han D, Wang JI, Park J, Kim H, Kim Y, (2017) "Quantitative proteomics reveal temporal proteomic changes in signaling pathways during BV2 mouse microglial cell activation." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28777000 28777000]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00445 10.1021/acs.jproteome.7b00445]; GPMDB: [http://gpmdb.org/data/keyword/28777000 | + | #Woo J, Han D, Wang JI, Park J, Kim H, Kim Y, (2017) "Quantitative proteomics reveal temporal proteomic changes in signaling pathways during BV2 mouse microglial cell activation." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28777000 28777000]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00445 10.1021/acs.jproteome.7b00445]; GPMDB: [http://gpmdb.org/data/keyword/28777000 18]. |
+ | #Wang X, Mooradian AD, Erdmann-Gilmore P, Zhang Q, Viner R, Davies SR, Huang KL, Bomgarden R, Van Tine BA, Shao J, Ding L, Li S, Ellis MJ, Rogers JC, Townsend RR, Fenyö D, Held JM, (2017) "Breast tumors educate the proteome of stromal tissue in an individualized but coordinated manner." <i>Sci Signal</i> <b>10</b>(491):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28790197 28790197]; doi: [https://dx.doi.org/10.1126/scisignal.aam8065 10.1126/scisignal.aam8065]; GPMDB: [http://gpmdb.org/data/keyword/28790197 7]. |
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 August 27, 2017.