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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 Apr. | + | 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 Apr. 8, 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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#Topf U, Suppanz I, Samluk L, Wrobel L, Böser A, Sakowska P, Knapp B, Pietrzyk MK, Chacinska A, Warscheid B, (2018) "Quantitative proteomics identifies redox switches for global translation modulation by mitochondrially produced reactive oxygen species." <i>Nat Commun</i> <b>9</b>(1):324; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29358734 29358734]; doi: [https://dx.doi.org/10.1038/s41467-017-02694-8 10.1038/s41467-017-02694-8]; GPMDB: [http://gpmdb.org/data/keyword/29358734 96]. | #Topf U, Suppanz I, Samluk L, Wrobel L, Böser A, Sakowska P, Knapp B, Pietrzyk MK, Chacinska A, Warscheid B, (2018) "Quantitative proteomics identifies redox switches for global translation modulation by mitochondrially produced reactive oxygen species." <i>Nat Commun</i> <b>9</b>(1):324; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29358734 29358734]; doi: [https://dx.doi.org/10.1038/s41467-017-02694-8 10.1038/s41467-017-02694-8]; GPMDB: [http://gpmdb.org/data/keyword/29358734 96]. | ||
#Walheim E, Wiśniewski JR, Jastroch M, (2018) "Respiromics - An integrative analysis linking mitochondrial bioenergetics to molecular signatures." <i>Mol Metab</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29361498 29361498]; doi: [https://dx.doi.org/10.1016/j.molmet.2018.01.002 10.1016/j.molmet.2018.01.002]; GPMDB: [http://gpmdb.org/data/keyword/29361498 32]. | #Walheim E, Wiśniewski JR, Jastroch M, (2018) "Respiromics - An integrative analysis linking mitochondrial bioenergetics to molecular signatures." <i>Mol Metab</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29361498 29361498]; doi: [https://dx.doi.org/10.1016/j.molmet.2018.01.002 10.1016/j.molmet.2018.01.002]; GPMDB: [http://gpmdb.org/data/keyword/29361498 32]. | ||
+ | #Kosicek M, Gudelj I, Horvatic A, Jovic T, Vuckovic F, Lauc G, Hecimovic S, (2018) "N-glycome of the Lysosomal Glycocalyx is Altered in Niemann-Pick Type C Disease (NPC) Model Cells." <i>Mol Cell Proteomics</i> <b>17</b>(4):631–642; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29367433 29367433]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000129 10.1074/mcp.RA117.000129]; GPMDB: [http://gpmdb.org/data/keyword/29367433 6]. | ||
#Johnston HE, Carter MJ, Larrayoz M, Clarke J, Garbis SD, Oscier D, Strefford JC, Steele AJ, Walewska R, Cragg MS, (2018) "Proteomics profiling of CLL versus healthy B-cells identifies putative therapeutic targets and a subtype-independent signature of spliceosome dysregulation." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29367434 29367434]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000539 10.1074/mcp.RA117.000539]; GPMDB: [http://gpmdb.org/data/keyword/29367434 2]. | #Johnston HE, Carter MJ, Larrayoz M, Clarke J, Garbis SD, Oscier D, Strefford JC, Steele AJ, Walewska R, Cragg MS, (2018) "Proteomics profiling of CLL versus healthy B-cells identifies putative therapeutic targets and a subtype-independent signature of spliceosome dysregulation." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29367434 29367434]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000539 10.1074/mcp.RA117.000539]; GPMDB: [http://gpmdb.org/data/keyword/29367434 2]. | ||
#Kostas M, Haugsten EM, Zhen Y, Sorensen V, Szybowska P, Fiorito E, Lorenz S, de Souza GA, Wiedlocha A, Wesche J, (2018) "The phosphatase PTPRG controls FGFR1 activity and influences sensitivity to FGFR kinase inhibitors." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29371290 29371290]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000538 10.1074/mcp.RA117.000538]; GPMDB: [http://gpmdb.org/data/keyword/29371290 54]. | #Kostas M, Haugsten EM, Zhen Y, Sorensen V, Szybowska P, Fiorito E, Lorenz S, de Souza GA, Wiedlocha A, Wesche J, (2018) "The phosphatase PTPRG controls FGFR1 activity and influences sensitivity to FGFR kinase inhibitors." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29371290 29371290]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000538 10.1074/mcp.RA117.000538]; GPMDB: [http://gpmdb.org/data/keyword/29371290 54]. | ||
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#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]. | #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]. | ||
#Smestad J, Hamidi O, Wang L, Holte MN, Khazal FA, Erber L, Chen Y, Maher LJ 3rd, (2018) "Characterization and metabolic synthetic lethal testing in a new model of SDH-loss familial pheochromocytoma and paraganglioma." <i>Oncotarget</i> <b>9</b>(5):6109–6127; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29464059 29464059]; doi: [https://dx.doi.org/10.18632/oncotarget.23639 10.18632/oncotarget.23639]; GPMDB: [http://gpmdb.org/data/keyword/29464059 20]. | #Smestad J, Hamidi O, Wang L, Holte MN, Khazal FA, Erber L, Chen Y, Maher LJ 3rd, (2018) "Characterization and metabolic synthetic lethal testing in a new model of SDH-loss familial pheochromocytoma and paraganglioma." <i>Oncotarget</i> <b>9</b>(5):6109–6127; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29464059 29464059]; doi: [https://dx.doi.org/10.18632/oncotarget.23639 10.18632/oncotarget.23639]; GPMDB: [http://gpmdb.org/data/keyword/29464059 20]. | ||
+ | #Laria AE, Messineo S, Arcidiacono B, Varano M, Chiefari E, Semple RK, Rocha N, Russo D, Cuda G, Gaspari M, Brunetti A, Foti DP, (2018) "Secretome Analysis of Hypoxia-Induced 3T3-L1 Adipocytes Uncovers Novel Proteins Potentially Involved in Obesity." <i>Proteomics</i> <b>18</b>(7):e1700260; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29466620 29466620]; doi: [https://dx.doi.org/10.1002/pmic.201700260 10.1002/pmic.201700260]; GPMDB: [http://gpmdb.org/data/keyword/29466620 8]. | ||
#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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#Lanoix J, Durette C, Courcelles M, Cossette É, Comtois-Marotte S, Hardy MP, Côté C, Perreault C, Thibault P, (2018) "Comparison of the MHC I Immunopeptidome Repertoire of B-Cell Lymphoblasts using Two Isolation Methods." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29508533 29508533]; doi: [https://dx.doi.org/10.1002/pmic.201700251 10.1002/pmic.201700251]; GPMDB: [http://gpmdb.org/data/keyword/29508533 48]. | #Lanoix J, Durette C, Courcelles M, Cossette É, Comtois-Marotte S, Hardy MP, Côté C, Perreault C, Thibault P, (2018) "Comparison of the MHC I Immunopeptidome Repertoire of B-Cell Lymphoblasts using Two Isolation Methods." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29508533 29508533]; doi: [https://dx.doi.org/10.1002/pmic.201700251 10.1002/pmic.201700251]; GPMDB: [http://gpmdb.org/data/keyword/29508533 48]. | ||
#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]. | #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 | + | #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 111]. |
#Ojalill M, Rappu P, Siljamäki E, Taimen P, Boström P, Heino J, (2018) "The composition of prostate core matrisome in vivo and in vitro unveiled by mass spectrometric analysis." <i>Prostate</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29520855 29520855]; doi: [https://dx.doi.org/10.1002/pros.23503 10.1002/pros.23503]; GPMDB: [http://gpmdb.org/data/keyword/29520855 62]. | #Ojalill M, Rappu P, Siljamäki E, Taimen P, Boström P, Heino J, (2018) "The composition of prostate core matrisome in vivo and in vitro unveiled by mass spectrometric analysis." <i>Prostate</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29520855 29520855]; doi: [https://dx.doi.org/10.1002/pros.23503 10.1002/pros.23503]; GPMDB: [http://gpmdb.org/data/keyword/29520855 62]. | ||
- | #Deeke SA, Starr AE, Ning Z, Ahmadi S, Zhang X, Mayne J, Chiang CK, Singleton R, Benchimol EI, Mack DR, Stintzi A, Figeys D, (2018) "Mucosal-luminal interface proteomics reveals biomarkers of pediatric inflammatory bowel disease-associated colitis." <i>Am J Gastroenterol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29531307 29531307]; doi: [https://dx.doi.org/10.1038/s41395-018-0024-9 10.1038/s41395-018-0024-9]; GPMDB: [http://gpmdb.org/data/keyword/29531307 | + | #Deeke SA, Starr AE, Ning Z, Ahmadi S, Zhang X, Mayne J, Chiang CK, Singleton R, Benchimol EI, Mack DR, Stintzi A, Figeys D, (2018) "Mucosal-luminal interface proteomics reveals biomarkers of pediatric inflammatory bowel disease-associated colitis." <i>Am J Gastroenterol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29531307 29531307]; doi: [https://dx.doi.org/10.1038/s41395-018-0024-9 10.1038/s41395-018-0024-9]; GPMDB: [http://gpmdb.org/data/keyword/29531307 58]. |
#Zila N, Bileck A, Muqaku B, Janker L, Eichhoff OM, Cheng PF, Dummer R, Levesque MP, Gerner C, Paulitschke V, (2018) "Proteomics-based insights into mitogen-activated protein kinase inhibitor resistance of cerebral melanoma metastases." <i>Clin Proteomics</i> <b>15</b>:13; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29541007 29541007]; doi: [https://dx.doi.org/10.1186/s12014-018-9189-x 10.1186/s12014-018-9189-x]; GPMDB: [http://gpmdb.org/data/keyword/29541007 36]. | #Zila N, Bileck A, Muqaku B, Janker L, Eichhoff OM, Cheng PF, Dummer R, Levesque MP, Gerner C, Paulitschke V, (2018) "Proteomics-based insights into mitogen-activated protein kinase inhibitor resistance of cerebral melanoma metastases." <i>Clin Proteomics</i> <b>15</b>:13; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29541007 29541007]; doi: [https://dx.doi.org/10.1186/s12014-018-9189-x 10.1186/s12014-018-9189-x]; GPMDB: [http://gpmdb.org/data/keyword/29541007 36]. | ||
#Liang P, Zhu W, Lan T, Tao Q, (2018) "Detection of salivary protein biomarkers of saliva secretion disorder in a primary Sjögren syndrome murine model." <i>J Pharm Biomed Anal</i> <b>154</b>:252–262; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29558726 29558726]; doi: [https://dx.doi.org/10.1016/j.jpba.2018.03.023 10.1016/j.jpba.2018.03.023]; GPMDB: [http://gpmdb.org/data/keyword/29558726 2]. | #Liang P, Zhu W, Lan T, Tao Q, (2018) "Detection of salivary protein biomarkers of saliva secretion disorder in a primary Sjögren syndrome murine model." <i>J Pharm Biomed Anal</i> <b>154</b>:252–262; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29558726 29558726]; doi: [https://dx.doi.org/10.1016/j.jpba.2018.03.023 10.1016/j.jpba.2018.03.023]; GPMDB: [http://gpmdb.org/data/keyword/29558726 2]. | ||
+ | #Saei AA, Sabatier P, Güler Tokat Ü, Chernobrovkin A, Pirmoradian M, Zubarev RA, (2018) "Comparative proteomics of dying and surviving cancer cells improves the identification of drug targets and sheds light on cell life/death decisions." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29572246 29572246]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000610 10.1074/mcp.RA118.000610]; GPMDB: [http://gpmdb.org/data/keyword/29572246 90]. | ||
+ | #Haller C, Chaskar P, Piccand J, Cominetti O, Macron C, Dayon L, Kraus MR, (2018) "Insights into islet differentiation and maturation through proteomic characterization of a human iPSC-derived pancreatic endocrine model." <i>Proteomics Clin Appl</i> <b></b>:e1600173; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29578310 29578310]; doi: [https://dx.doi.org/10.1002/prca.201600173 10.1002/prca.201600173]; GPMDB: [http://gpmdb.org/data/keyword/29578310 34]. |
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 Apr. 8, 2018.