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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 September 2, 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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.org/data/keyword/12177431 498]. | ||
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#Chamrád I, Rix U, Stukalov A, Gridling M, Parapatics K, Müller AC, Altiok S, Colinge J, Superti-Furga G, Haura EB, Bennett KL, (2013) "A miniaturized chemical proteomic approach for target profiling of clinical kinase inhibitors in tumor biopsies." <i>J Proteome Res</i> <b>12</b>(9):4005–17; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23901793 23901793]; doi: [https://dx.doi.org/10.1021/pr400309p 10.1021/pr400309p]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/23901793 56]. | #Chamrád I, Rix U, Stukalov A, Gridling M, Parapatics K, Müller AC, Altiok S, Colinge J, Superti-Furga G, Haura EB, Bennett KL, (2013) "A miniaturized chemical proteomic approach for target profiling of clinical kinase inhibitors in tumor biopsies." <i>J Proteome Res</i> <b>12</b>(9):4005–17; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23901793 23901793]; doi: [https://dx.doi.org/10.1021/pr400309p 10.1021/pr400309p]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/23901793 56]. | ||
#Oosterkamp MJ, Boeren S, Plugge CM, Schaap PJ, Stams AJ, (2013) "Metabolic response of Alicycliphilus denitrificans strain BC toward electron acceptor variation." <i>Proteomics</i> <b>13</b>(18-19):2886–94; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23907812 23907812]; doi: [https://dx.doi.org/10.1002/pmic.201200571 10.1002/pmic.201200571]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/23907812 16]. | #Oosterkamp MJ, Boeren S, Plugge CM, Schaap PJ, Stams AJ, (2013) "Metabolic response of Alicycliphilus denitrificans strain BC toward electron acceptor variation." <i>Proteomics</i> <b>13</b>(18-19):2886–94; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23907812 23907812]; doi: [https://dx.doi.org/10.1002/pmic.201200571 10.1002/pmic.201200571]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/23907812 16]. | ||
+ | #Kwon SC, Yi H, Eichelbaum K, Föhr S, Fischer B, You KT, Castello A, Krijgsveld J, Hentze MW, Kim VN, (2013) "The RNA-binding protein repertoire of embryonic stem cells." <i>Nat Struct Mol Biol</i> <b>20</b>(9):1122–30; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23912277 23912277]; doi: [https://dx.doi.org/10.1038/nsmb.2638 10.1038/nsmb.2638]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/23912277 36]. | ||
#Gholami AM, Hahne H, Wu Z, Auer FJ, Meng C, Wilhelm M, Kuster B, (2013) "Global proteome analysis of the NCI-60 cell line panel." <i>Cell Rep</i> <b>4</b>(3):609–20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23933261 23933261]; doi: [https://dx.doi.org/10.1016/j.celrep.2013.07.018 10.1016/j.celrep.2013.07.018]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/23933261 899]. | #Gholami AM, Hahne H, Wu Z, Auer FJ, Meng C, Wilhelm M, Kuster B, (2013) "Global proteome analysis of the NCI-60 cell line panel." <i>Cell Rep</i> <b>4</b>(3):609–20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23933261 23933261]; doi: [https://dx.doi.org/10.1016/j.celrep.2013.07.018 10.1016/j.celrep.2013.07.018]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/23933261 899]. | ||
#Krishnappa L, Dreisbach A, Otto A, Goosens VJ, Cranenburgh RM, Harwood CR, Becher D, van Dijl JM, (2013) "Extracytoplasmic proteases determining the cleavage and release of secreted proteins, lipoproteins, and membrane proteins in Bacillus subtilis." <i>J Proteome Res</i> <b>12</b>(9):4101–10; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23937099 23937099]; doi: [https://dx.doi.org/10.1021/pr400433h 10.1021/pr400433h]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/23937099 112]. | #Krishnappa L, Dreisbach A, Otto A, Goosens VJ, Cranenburgh RM, Harwood CR, Becher D, van Dijl JM, (2013) "Extracytoplasmic proteases determining the cleavage and release of secreted proteins, lipoproteins, and membrane proteins in Bacillus subtilis." <i>J Proteome Res</i> <b>12</b>(9):4101–10; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23937099 23937099]; doi: [https://dx.doi.org/10.1021/pr400433h 10.1021/pr400433h]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/23937099 112]. | ||
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#Kelstrup CD, Bekker-Jensen DB, Arrey TN, Hogrebe A, Harder A, Olsen JV, (2018) "Performance Evaluation of the Q Exactive HF-X for Shotgun Proteomics." <i>J Proteome Res</i> <b>17</b>(1):727–738; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29183128 29183128]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00602 10.1021/acs.jproteome.7b00602]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29183128 107]. | #Kelstrup CD, Bekker-Jensen DB, Arrey TN, Hogrebe A, Harder A, Olsen JV, (2018) "Performance Evaluation of the Q Exactive HF-X for Shotgun Proteomics." <i>J Proteome Res</i> <b>17</b>(1):727–738; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29183128 29183128]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00602 10.1021/acs.jproteome.7b00602]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29183128 107]. | ||
#Winter DL, Hart-Smith G, Wilkins MR, (2018) "Characterization of Protein Methyltransferases Rkm1, Rkm4, Efm4, Efm7, Set5 and Hmt1 Reveals Extensive Post-Translational Modification." <i>J Mol Biol</i> <b>430</b>(1):102–118; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29183786 29183786]; doi: [https://dx.doi.org/10.1016/j.jmb.2017.11.009 10.1016/j.jmb.2017.11.009]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29183786 18]. | #Winter DL, Hart-Smith G, Wilkins MR, (2018) "Characterization of Protein Methyltransferases Rkm1, Rkm4, Efm4, Efm7, Set5 and Hmt1 Reveals Extensive Post-Translational Modification." <i>J Mol Biol</i> <b>430</b>(1):102–118; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29183786 29183786]; doi: [https://dx.doi.org/10.1016/j.jmb.2017.11.009 10.1016/j.jmb.2017.11.009]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29183786 18]. | ||
+ | #Carlyle BC, Kitchen RR, Kanyo JE, Voss EZ, Pletikos M, Sousa AMM, Lam TT, Gerstein MB, Sestan N, Nairn AC, (2017) "A multiregional proteomic survey of the postnatal human brain." <i>Nat Neurosci</i> <b>20</b>(12):1787–1795; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29184206 29184206]; doi: [https://dx.doi.org/10.1038/s41593-017-0011-2 10.1038/s41593-017-0011-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29184206 196]. | ||
#Lacombe M, Marie-Desvergne C, Combes F, Kraut A, Bruley C, Vandenbrouck Y, Chamel Mossuz V, Couté Y, Brun V, (2017) "Proteomic characterization of human exhaled breath condensate." <i>J Breath Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29189203 29189203]; doi: [https://dx.doi.org/10.1088/1752-7163/aa9e71 10.1088/1752-7163/aa9e71]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29189203 4]. | #Lacombe M, Marie-Desvergne C, Combes F, Kraut A, Bruley C, Vandenbrouck Y, Chamel Mossuz V, Couté Y, Brun V, (2017) "Proteomic characterization of human exhaled breath condensate." <i>J Breath Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29189203 29189203]; doi: [https://dx.doi.org/10.1088/1752-7163/aa9e71 10.1088/1752-7163/aa9e71]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29189203 4]. | ||
#Klaeger S, Heinzlmeir S, Wilhelm M, Polzer H, Vick B, Koenig PA, Reinecke M, Ruprecht B, Petzoldt S, Meng C, Zecha J, Reiter K, Qiao H, Helm D, Koch H, Schoof M, Canevari G, Casale E, Depaolini SR, Feuchtinger A, Wu Z, Schmidt T, Rueckert L, Becker W, Huenges J, Garz AK, Gohlke BO, Zolg DP, Kayser G, Vooder T, Preissner R, Hahne H, Tõnisson N, Kramer K, Götze K, Bassermann F, Schlegl J, Ehrlich HC, Aiche S, Walch A, Greif PA, Schneider S, Felder ER, Ruland J, Médard G, Jeremias I, Spiekermann K, Kuster B, (2017) "The target landscape of clinical kinase drugs." <i>Science</i> <b>358</b>(6367):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29191878 29191878]; doi: [https://dx.doi.org/10.1126/science.aan4368 10.1126/science.aan4368]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29191878 3032]. | #Klaeger S, Heinzlmeir S, Wilhelm M, Polzer H, Vick B, Koenig PA, Reinecke M, Ruprecht B, Petzoldt S, Meng C, Zecha J, Reiter K, Qiao H, Helm D, Koch H, Schoof M, Canevari G, Casale E, Depaolini SR, Feuchtinger A, Wu Z, Schmidt T, Rueckert L, Becker W, Huenges J, Garz AK, Gohlke BO, Zolg DP, Kayser G, Vooder T, Preissner R, Hahne H, Tõnisson N, Kramer K, Götze K, Bassermann F, Schlegl J, Ehrlich HC, Aiche S, Walch A, Greif PA, Schneider S, Felder ER, Ruland J, Médard G, Jeremias I, Spiekermann K, Kuster B, (2017) "The target landscape of clinical kinase drugs." <i>Science</i> <b>358</b>(6367):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29191878 29191878]; doi: [https://dx.doi.org/10.1126/science.aan4368 10.1126/science.aan4368]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29191878 3032]. | ||
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#Duda P, Wójcicka O, Wiśniewski JR, Rakus D, (2018) "Global quantitative TPA-based proteomics of mouse brain structures reveals significant alterations in expression of proteins involved in neuronal plasticity during aging." <i>Aging (Albany NY)</i> <b>10</b>(7):1682–1697; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30026405 30026405]; doi: [https://dx.doi.org/10.18632/aginh.101501 10.18632/aginh.101501]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30026405 59]. | #Duda P, Wójcicka O, Wiśniewski JR, Rakus D, (2018) "Global quantitative TPA-based proteomics of mouse brain structures reveals significant alterations in expression of proteins involved in neuronal plasticity during aging." <i>Aging (Albany NY)</i> <b>10</b>(7):1682–1697; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30026405 30026405]; doi: [https://dx.doi.org/10.18632/aginh.101501 10.18632/aginh.101501]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30026405 59]. | ||
#Evans J, Infusini G, McGovern J, Cuttle L, Webb A, Nebl T, Milla L, Kimble R, Kempf M, Andrews CJ, Leavesley D, Salamonsen LA, (2018) "Menstrual fluid factors facilitate tissue repair: identification and functional action in endometrial and skin repair." <i>FASEB J</i> <b></b>:fj201800086R; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30036086 30036086]; doi: [https://dx.doi.org/10.1096/fj.201800086R 10.1096/fj.201800086R]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30036086 46]. | #Evans J, Infusini G, McGovern J, Cuttle L, Webb A, Nebl T, Milla L, Kimble R, Kempf M, Andrews CJ, Leavesley D, Salamonsen LA, (2018) "Menstrual fluid factors facilitate tissue repair: identification and functional action in endometrial and skin repair." <i>FASEB J</i> <b></b>:fj201800086R; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30036086 30036086]; doi: [https://dx.doi.org/10.1096/fj.201800086R 10.1096/fj.201800086R]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30036086 46]. | ||
- | #Iglesias-Gato D, Thysell E, Tyanova S, Crnalic S, Santos A, Lima TS, Geiger T, Cox J, Widmark A, Bergh A, Mann M, Flores-Morales A, Wikström P, (2018) "The proteome of prostate cancer bone metastasis reveals heterogeneity with prognostic implications." <i>Clin Cancer Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30042207 30042207]; doi: [https://dx.doi.org/10.1158/1078-0432.CCR-18-1229 10.1158/1078-0432.CCR-18-1229]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30042207 | + | #Iglesias-Gato D, Thysell E, Tyanova S, Crnalic S, Santos A, Lima TS, Geiger T, Cox J, Widmark A, Bergh A, Mann M, Flores-Morales A, Wikström P, (2018) "The proteome of prostate cancer bone metastasis reveals heterogeneity with prognostic implications." <i>Clin Cancer Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30042207 30042207]; doi: [https://dx.doi.org/10.1158/1078-0432.CCR-18-1229 10.1158/1078-0432.CCR-18-1229]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30042207 21]. |
#Ghezraoui H, Oliveira C, Becker JR, Bilham K, Moralli D, Anzilotti C, Fischer R, Deobagkar-Lele M, Sanchiz-Calvo M, Fueyo-Marcos E, Bonham S, Kessler BM, Rottenberg S, Cornall RJ, Green CM, Chapman JR, (2018) "53BP1 cooperation with the REV7-shieldin complex underpins DNA structure-specific NHEJ." <i>Nature</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30046110 30046110]; doi: [https://dx.doi.org/10.1038/s41586-018-0362-1 10.1038/s41586-018-0362-1]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30046110 8]. | #Ghezraoui H, Oliveira C, Becker JR, Bilham K, Moralli D, Anzilotti C, Fischer R, Deobagkar-Lele M, Sanchiz-Calvo M, Fueyo-Marcos E, Bonham S, Kessler BM, Rottenberg S, Cornall RJ, Green CM, Chapman JR, (2018) "53BP1 cooperation with the REV7-shieldin complex underpins DNA structure-specific NHEJ." <i>Nature</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30046110 30046110]; doi: [https://dx.doi.org/10.1038/s41586-018-0362-1 10.1038/s41586-018-0362-1]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30046110 8]. | ||
#Nilsen BW, Simon-Santamaria J, Örtengren U, Jensen E, Bruun JA, Michelsen VB, Sørensen KK, (2018) "Dose- and time-dependent effects of triethylene glycol dimethacrylate on the proteome of human THP-1 monocytes." <i>Eur J Oral Sci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30051916 30051916]; doi: [https://dx.doi.org/10.1111/eos.12559 10.1111/eos.12559]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30051916 92]. | #Nilsen BW, Simon-Santamaria J, Örtengren U, Jensen E, Bruun JA, Michelsen VB, Sørensen KK, (2018) "Dose- and time-dependent effects of triethylene glycol dimethacrylate on the proteome of human THP-1 monocytes." <i>Eur J Oral Sci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30051916 30051916]; doi: [https://dx.doi.org/10.1111/eos.12559 10.1111/eos.12559]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30051916 92]. | ||
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#Schiza C, Korbakis D, Panteleli E, Jarvi K, Drabovich AP, Diamandis EP, (2018) "Discovery of a human testis-specific protein complex TEX101-DPEP3 and selection of its disrupting antibodies." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30097533 30097533]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000749 10.1074/mcp.RA118.000749]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30097533 44]. | #Schiza C, Korbakis D, Panteleli E, Jarvi K, Drabovich AP, Diamandis EP, (2018) "Discovery of a human testis-specific protein complex TEX101-DPEP3 and selection of its disrupting antibodies." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30097533 30097533]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000749 10.1074/mcp.RA118.000749]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30097533 44]. | ||
#Hwang H, Jeong JE, Lee HK, Yun KN, An HJ, Lee B, Paik YK, Jeong TS, Yee GT, Kim JY, Yoo JS, (2018) "Identification of Missing Proteins in Human Olfactory Epithelial Tissue by Liquid Chromatography-Tandem Mass Spectrometry." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30113170 30113170]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00408 10.1021/acs.jproteome.8b00408]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30113170 23]. | #Hwang H, Jeong JE, Lee HK, Yun KN, An HJ, Lee B, Paik YK, Jeong TS, Yee GT, Kim JY, Yoo JS, (2018) "Identification of Missing Proteins in Human Olfactory Epithelial Tissue by Liquid Chromatography-Tandem Mass Spectrometry." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30113170 30113170]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00408 10.1021/acs.jproteome.8b00408]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30113170 23]. | ||
+ | #Weßbecher IM, Hinrichsen I, Funke S, Oellerich T, Plotz G, Zeuzem S, Grus FH, Biondi RM, Brieger A, (2018) "DNA mismatch repair activity of MutLα is regulated by CK2-dependent phosphorylation of MLH1 (S477)." <i>Mol Carcinog</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30136313 30136313]; doi: [https://dx.doi.org/10.1002/mc.22892 10.1002/mc.22892]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30136313 2]. |
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 September 2, 2018.