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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 | + | 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 Dec. 3, 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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#Hou J, Li Z, Zhong W, Hao Q, Lei L, Wang L, Zhao D, Xu P, Zhou Y, Wang Y, Xu T, (2017) "Temporal Transcriptomic and Proteomic Landscapes of Deteriorating Pancreatic Islets in Type 2 Diabetic Rats." <i>Diabetes</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28559245 28559245]; doi: [https://dx.doi.org/10.2337/db16-1305 10.2337/db16-1305]; GPMDB: [http://gpmdb.org/data/keyword/28559245 12]. | #Hou J, Li Z, Zhong W, Hao Q, Lei L, Wang L, Zhao D, Xu P, Zhou Y, Wang Y, Xu T, (2017) "Temporal Transcriptomic and Proteomic Landscapes of Deteriorating Pancreatic Islets in Type 2 Diabetic Rats." <i>Diabetes</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28559245 28559245]; doi: [https://dx.doi.org/10.2337/db16-1305 10.2337/db16-1305]; GPMDB: [http://gpmdb.org/data/keyword/28559245 12]. | ||
#Sanchez-Quiles V, Akimov V, Osinalde N, Francavilla C, Puglia M, Barrio-Hernandez I, Kratchmarova I, Olsen JV, Blagoev B, (2017) "CYLD deubiquitinase is necessary for proper ubiquitination and degradation of the epidermal growth factor receptor." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28572092 28572092]; doi: [https://dx.doi.org/10.1074/mcp.M116.066423 10.1074/mcp.M116.066423]; GPMDB: [http://gpmdb.org/data/keyword/28572092 108]. | #Sanchez-Quiles V, Akimov V, Osinalde N, Francavilla C, Puglia M, Barrio-Hernandez I, Kratchmarova I, Olsen JV, Blagoev B, (2017) "CYLD deubiquitinase is necessary for proper ubiquitination and degradation of the epidermal growth factor receptor." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28572092 28572092]; doi: [https://dx.doi.org/10.1074/mcp.M116.066423 10.1074/mcp.M116.066423]; GPMDB: [http://gpmdb.org/data/keyword/28572092 108]. | ||
+ | #Bj Rås KØ, Sousa MML, Sharma A, Fonseca DM, S Gaard CK, Bj Rås M, Otterlei M, (2017) "Monitoring of the spatial and temporal dynamics of BER/SSBR pathway proteins, including MYH, UNG2, MPG, NTH1 and NEIL1-3, during DNA replication." <i>Nucleic Acids Res</i> <b>45</b>(14):8291–8301; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28575236 28575236]; doi: [https://dx.doi.org/10.1093/nar/gkx476 10.1093/nar/gkx476]; GPMDB: [http://gpmdb.org/data/keyword/28575236 31]. | ||
#Obermann J, Priglinger CS, Merl-Pham J, Geerlof A, Priglinger S, Götz M, Hauck SM, (2017) "Proteome-wide identification of glycosylation-dependent interactors of Galectin-1 and Galectin-3 on mesenchymal retinal pigment epithelial cells." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28576849 28576849]; doi: [https://dx.doi.org/10.1074/mcp.M116.066381 10.1074/mcp.M116.066381]; GPMDB: [http://gpmdb.org/data/keyword/28576849 193]. | #Obermann J, Priglinger CS, Merl-Pham J, Geerlof A, Priglinger S, Götz M, Hauck SM, (2017) "Proteome-wide identification of glycosylation-dependent interactors of Galectin-1 and Galectin-3 on mesenchymal retinal pigment epithelial cells." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28576849 28576849]; doi: [https://dx.doi.org/10.1074/mcp.M116.066381 10.1074/mcp.M116.066381]; GPMDB: [http://gpmdb.org/data/keyword/28576849 193]. | ||
#Sun C, De Mello V, Mohamed A, Ortuste Quiroga HP, Garcia-Munoz A, Al Bloshi A, Tremblay AM, von Kriegsheim A, Collie-Duguid E, Vargesson N, Matallanas D, Wackerhage H, Zammit PS, (2017) "Common and Distinctive Functions of the Hippo Effectors Taz and Yap in Skeletal Muscle Stem Cell Function." <i>Stem Cells</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28589555 28589555]; doi: [https://dx.doi.org/10.1002/stem.2652 10.1002/stem.2652]; GPMDB: [http://gpmdb.org/data/keyword/28589555 36]. | #Sun C, De Mello V, Mohamed A, Ortuste Quiroga HP, Garcia-Munoz A, Al Bloshi A, Tremblay AM, von Kriegsheim A, Collie-Duguid E, Vargesson N, Matallanas D, Wackerhage H, Zammit PS, (2017) "Common and Distinctive Functions of the Hippo Effectors Taz and Yap in Skeletal Muscle Stem Cell Function." <i>Stem Cells</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28589555 28589555]; doi: [https://dx.doi.org/10.1002/stem.2652 10.1002/stem.2652]; GPMDB: [http://gpmdb.org/data/keyword/28589555 36]. | ||
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#Dittus L, Werner T, Muelbaier M, Bantscheff M, (2017) "Differential Kinobeads Profiling for Target Identification of Irreversible Kinase Inhibitors." <i>ACS Chem Biol</i> <b>12</b>(10):2515–2521; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28876896 28876896]; doi: [https://dx.doi.org/10.1021/acschembio.7b00617 10.1021/acschembio.7b00617]; GPMDB: [http://gpmdb.org/data/keyword/28876896 154]. | #Dittus L, Werner T, Muelbaier M, Bantscheff M, (2017) "Differential Kinobeads Profiling for Target Identification of Irreversible Kinase Inhibitors." <i>ACS Chem Biol</i> <b>12</b>(10):2515–2521; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28876896 28876896]; doi: [https://dx.doi.org/10.1021/acschembio.7b00617 10.1021/acschembio.7b00617]; GPMDB: [http://gpmdb.org/data/keyword/28876896 154]. | ||
#Kälin S, Becker M, Ott VB, Serr I, Hosp F, Mollah MMH, Keipert S, Lamp D, Rohner-Jeanrenaud F, Flynn VK, Scherm MG, Nascimento LFR, Gerlach K, Popp V, Dietzen S, Bopp T, Krishnamurthy P, Kaplan MH, Serrano M, Woods SC, Tripal P, Palmisano R, Jastroch M, Blüher M, Wolfrum C, Weigmann B, Ziegler AG, Mann M, Tschöp MH, Daniel C, (2017) "A Stat6/Pten Axis Links Regulatory T Cells with Adipose Tissue Function." <i>Cell Metab</i> <b>26</b>(3):475–492.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28877454 28877454]; doi: [https://dx.doi.org/10.1016/j.cmet.2017.08.008 10.1016/j.cmet.2017.08.008]; GPMDB: [http://gpmdb.org/data/keyword/28877454 31]. | #Kälin S, Becker M, Ott VB, Serr I, Hosp F, Mollah MMH, Keipert S, Lamp D, Rohner-Jeanrenaud F, Flynn VK, Scherm MG, Nascimento LFR, Gerlach K, Popp V, Dietzen S, Bopp T, Krishnamurthy P, Kaplan MH, Serrano M, Woods SC, Tripal P, Palmisano R, Jastroch M, Blüher M, Wolfrum C, Weigmann B, Ziegler AG, Mann M, Tschöp MH, Daniel C, (2017) "A Stat6/Pten Axis Links Regulatory T Cells with Adipose Tissue Function." <i>Cell Metab</i> <b>26</b>(3):475–492.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28877454 28877454]; doi: [https://dx.doi.org/10.1016/j.cmet.2017.08.008 10.1016/j.cmet.2017.08.008]; GPMDB: [http://gpmdb.org/data/keyword/28877454 31]. | ||
- | #Chen TW, Lee CC, Liu H, Wu CS, Pickering CR, Huang PJ, Wang J, Chang IY, Yeh YM, Chen CD, Li HP, Luo JD, Tan BC, Chan TEH, Hsueh C, Chu LJ, Chen YT, Zhang B, Yang CY, Wu CC, Hsu CW, See LC, Tang P, Yu JS, Liao WC, Chiang WF, Rodriguez H, Myers JN, Chang KP, Chang YS, (2017) "APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism." <i>Nat Commun</i> <b>8</b>(1):465; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28878238 28878238]; doi: [https://dx.doi.org/10.1038/s41467-017-00493-9 10.1038/s41467-017-00493-9]; GPMDB: [http://gpmdb.org/data/keyword/28878238 | + | #Chen TW, Lee CC, Liu H, Wu CS, Pickering CR, Huang PJ, Wang J, Chang IY, Yeh YM, Chen CD, Li HP, Luo JD, Tan BC, Chan TEH, Hsueh C, Chu LJ, Chen YT, Zhang B, Yang CY, Wu CC, Hsu CW, See LC, Tang P, Yu JS, Liao WC, Chiang WF, Rodriguez H, Myers JN, Chang KP, Chang YS, (2017) "APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism." <i>Nat Commun</i> <b>8</b>(1):465; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28878238 28878238]; doi: [https://dx.doi.org/10.1038/s41467-017-00493-9 10.1038/s41467-017-00493-9]; GPMDB: [http://gpmdb.org/data/keyword/28878238 13]. |
#Han B, Fang Y, Feng M, Hu H, Hao Y, Ma C, Huo X, Meng L, Zhang X, Wu F, Li J, (2017) "Brain Membrane Proteome and Phosphoproteome Reveal Molecular Basis Associating with Nursing and Foraging Behaviors of Honeybee Workers." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28879772 28879772]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00371 10.1021/acs.jproteome.7b00371]; GPMDB: [http://gpmdb.org/data/keyword/28879772 47]. | #Han B, Fang Y, Feng M, Hu H, Hao Y, Ma C, Huo X, Meng L, Zhang X, Wu F, Li J, (2017) "Brain Membrane Proteome and Phosphoproteome Reveal Molecular Basis Associating with Nursing and Foraging Behaviors of Honeybee Workers." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28879772 28879772]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00371 10.1021/acs.jproteome.7b00371]; GPMDB: [http://gpmdb.org/data/keyword/28879772 47]. | ||
#Phillips B, Titz B, Kogel U, Sharma D, Leroy P, Xiang Y, Vuillaume G, Lebrun S, Sciuscio D, Ho J, Nury C, Guedj E, Elamin A, Esposito M, Krishnan S, Schlage WK, Veljkovic E, Ivanov NV, Martin F, Peitsch MC, Hoeng J, Vanscheeuwijck P, (2017) "Toxicity of the main electronic cigarette components, propylene glycol, glycerin, and nicotine, in Sprague-Dawley rats in a 90-day OECD inhalation study complemented by molecular endpoints." <i>Food Chem Toxicol</i> <b>109</b>(Pt 1):315–332; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28882640 28882640]; doi: [https://dx.doi.org/10.1016/j.fct.2017.09.001 10.1016/j.fct.2017.09.001]; GPMDB: [http://gpmdb.org/data/keyword/28882640 36]. | #Phillips B, Titz B, Kogel U, Sharma D, Leroy P, Xiang Y, Vuillaume G, Lebrun S, Sciuscio D, Ho J, Nury C, Guedj E, Elamin A, Esposito M, Krishnan S, Schlage WK, Veljkovic E, Ivanov NV, Martin F, Peitsch MC, Hoeng J, Vanscheeuwijck P, (2017) "Toxicity of the main electronic cigarette components, propylene glycol, glycerin, and nicotine, in Sprague-Dawley rats in a 90-day OECD inhalation study complemented by molecular endpoints." <i>Food Chem Toxicol</i> <b>109</b>(Pt 1):315–332; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28882640 28882640]; doi: [https://dx.doi.org/10.1016/j.fct.2017.09.001 10.1016/j.fct.2017.09.001]; GPMDB: [http://gpmdb.org/data/keyword/28882640 36]. | ||
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#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]. | ||
#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]. | ||
+ | #Steger M, Diez F, Dhekne HS, Lis P, Nirujogi RS, Karayel O, Tonelli F, Martinez TN, Lorentzen E, Pfeffer SR, Alessi DR, Mann M, (2017) "Systematic proteomic analysis of LRRK2-mediated Rab GTPase phosphorylation establishes a connection to ciliogenesis." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29125462 29125462]; doi: [https://dx.doi.org/10.7554/eLife.31012 10.7554/eLife.31012]; GPMDB: [http://gpmdb.org/data/keyword/29125462 458]. | ||
#Negretti NM, Gourley CR, Clair G, Adkins JN, Konkel ME, (2017) "The food-borne pathogen Campylobacter jejuni responds to the bile salt deoxycholate with countermeasures to reactive oxygen species." <i>Sci Rep</i> <b>7</b>(1):15455; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29133896 29133896]; doi: [https://dx.doi.org/10.1038/s41598-017-15379-5 10.1038/s41598-017-15379-5]; GPMDB: [http://gpmdb.org/data/keyword/29133896 8]. | #Negretti NM, Gourley CR, Clair G, Adkins JN, Konkel ME, (2017) "The food-borne pathogen Campylobacter jejuni responds to the bile salt deoxycholate with countermeasures to reactive oxygen species." <i>Sci Rep</i> <b>7</b>(1):15455; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29133896 29133896]; doi: [https://dx.doi.org/10.1038/s41598-017-15379-5 10.1038/s41598-017-15379-5]; GPMDB: [http://gpmdb.org/data/keyword/29133896 8]. | ||
- | #Doll S, Dreßen M, Geyer PE, Itzhak DN, Braun C, Doppler SA, Meier F, Deutsch MA, Lahm H, Lange R, Krane M, Mann M, (2017) "Region and cell-type resolved quantitative proteomic map of the human heart." <i>Nat Commun</i> <b>8</b>(1):1469; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29133944 29133944]; doi: [https://dx.doi.org/10.1038/s41467-017-01747-2 10.1038/s41467-017-01747-2]; GPMDB: [http://gpmdb.org/data/keyword/29133944 | + | #Doll S, Dreßen M, Geyer PE, Itzhak DN, Braun C, Doppler SA, Meier F, Deutsch MA, Lahm H, Lange R, Krane M, Mann M, (2017) "Region and cell-type resolved quantitative proteomic map of the human heart." <i>Nat Commun</i> <b>8</b>(1):1469; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29133944 29133944]; doi: [https://dx.doi.org/10.1038/s41467-017-01747-2 10.1038/s41467-017-01747-2]; GPMDB: [http://gpmdb.org/data/keyword/29133944 149]. |
- | #Geis-Asteggiante L, Belew AT, Clements VK, Edwards NJ, Ostrand-Rosenberg S, El-Sayed NM, Fenselau C, (2017) "Differential content of proteins, mRNAs, and miRNAs suggests that MDSC and their exosomes may mediate distinct immune suppressive functions." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29139296 29139296]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00646 10.1021/acs.jproteome.7b00646]; GPMDB: [http://gpmdb.org/data/keyword/29139296 10]. | + | #Geis-Asteggiante L, Belew AT, Clements VK, Edwards NJ, Ostrand-Rosenberg S, El-Sayed NM, Fenselau C, (2017) "Differential content of proteins, mRNAs, and miRNAs suggests that MDSC and their exosomes may mediate distinct immune suppressive functions." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29139296 29139296]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00646 10.1021/acs.jproteome.7b00646]; GPMDB: [http://gpmdb.org/data/keyword/29139296 60]. |
+ | #Hosp F, Gutiérrez-Ángel S, Schaefer MH, Cox J, Meissner F, Hipp MS, Hartl FU, Klein R, Dudanova I, Mann M, (2017) "Spatiotemporal Proteomic Profiling of Huntington's Disease Inclusions Reveals Widespread Loss of Protein Function." <i>Cell Rep</i> <b>21</b>(8):2291–2303; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29166617 29166617]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.10.097 10.1016/j.celrep.2017.10.097]; GPMDB: [http://gpmdb.org/data/keyword/29166617 196]. |
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.
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 Dec. 3, 2017.