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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 Oct. 8, 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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#Ayre DC, Chute IC, Joy AP, Barnett DA, Hogan AM, Grüll MP, Peña-Castillo L, Lang AS, Lewis SM, Christian SL, (2017) "CD24 induces changes to the surface receptors of B cell microvesicles with variable effects on their RNA and protein cargo." <i>Sci Rep</i> <b>7</b>(1):8642; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28819186 28819186]; doi: [https://dx.doi.org/10.1038/s41598-017-08094-8 10.1038/s41598-017-08094-8]; GPMDB: [http://gpmdb.org/data/keyword/28819186 146]. | #Ayre DC, Chute IC, Joy AP, Barnett DA, Hogan AM, Grüll MP, Peña-Castillo L, Lang AS, Lewis SM, Christian SL, (2017) "CD24 induces changes to the surface receptors of B cell microvesicles with variable effects on their RNA and protein cargo." <i>Sci Rep</i> <b>7</b>(1):8642; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28819186 28819186]; doi: [https://dx.doi.org/10.1038/s41598-017-08094-8 10.1038/s41598-017-08094-8]; GPMDB: [http://gpmdb.org/data/keyword/28819186 146]. | ||
#Hung CL, Pan SH, Han CL, Chang CW, Hsu YL, Su CH, Shih SC, Lai YJ, Chiang Chiau JS, Yeh HI, Liu CY, Lee HC, Lam CSP, (2017) "Membrane Proteomics of Impaired Energetics and Cytoskeletal Disorganization in Elderly Diet-Induced Diabetic Mice." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28823169 28823169]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00148 10.1021/acs.jproteome.7b00148]; GPMDB: [http://gpmdb.org/data/keyword/28823169 14]. | #Hung CL, Pan SH, Han CL, Chang CW, Hsu YL, Su CH, Shih SC, Lai YJ, Chiang Chiau JS, Yeh HI, Liu CY, Lee HC, Lam CSP, (2017) "Membrane Proteomics of Impaired Energetics and Cytoskeletal Disorganization in Elderly Diet-Induced Diabetic Mice." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28823169 28823169]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00148 10.1021/acs.jproteome.7b00148]; GPMDB: [http://gpmdb.org/data/keyword/28823169 14]. | ||
- | #Fu L, Liu KK, Sun MA, Tian CP, Sun R, Morales Betanzos C, Tallman KA, Porter NA, Yang Y, Guo DJ, Liebler DC, Yang J, (2017) "Systematic and quantitative assessment of hydrogen peroxide reactivity with cysteines across human proteomes." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28827280 28827280]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000108 10.1074/mcp.RA117.000108]; GPMDB: [http://gpmdb.org/data/keyword/28827280 | + | #Fu L, Liu KK, Sun MA, Tian CP, Sun R, Morales Betanzos C, Tallman KA, Porter NA, Yang Y, Guo DJ, Liebler DC, Yang J, (2017) "Systematic and quantitative assessment of hydrogen peroxide reactivity with cysteines across human proteomes." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28827280 28827280]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000108 10.1074/mcp.RA117.000108]; GPMDB: [http://gpmdb.org/data/keyword/28827280 12]. |
#Phillips TJ, Scott H, Menassa DA, Bignell AL, Sood A, Morton JS, Akagi T, Azuma K, Rogers MF, Gilmore CE, Inman GJ, Grant S, Chung Y, Aljunaidy MM, Cooke CL, Steinkraus BR, Pocklington A, Logan A, Collett GP, Kemp H, Holmans PA, Murphy MP, Fulga TA, Coney AM, Akashi M, Davidge ST, Case CP, (2017) "Treating the placenta to prevent adverse effects of gestational hypoxia on fetal brain development." <i>Sci Rep</i> <b>7</b>(1):9079; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28831049 28831049]; doi: [https://dx.doi.org/10.1038/s41598-017-06300-1 10.1038/s41598-017-06300-1]; GPMDB: [http://gpmdb.org/data/keyword/28831049 1]. | #Phillips TJ, Scott H, Menassa DA, Bignell AL, Sood A, Morton JS, Akagi T, Azuma K, Rogers MF, Gilmore CE, Inman GJ, Grant S, Chung Y, Aljunaidy MM, Cooke CL, Steinkraus BR, Pocklington A, Logan A, Collett GP, Kemp H, Holmans PA, Murphy MP, Fulga TA, Coney AM, Akashi M, Davidge ST, Case CP, (2017) "Treating the placenta to prevent adverse effects of gestational hypoxia on fetal brain development." <i>Sci Rep</i> <b>7</b>(1):9079; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28831049 28831049]; doi: [https://dx.doi.org/10.1038/s41598-017-06300-1 10.1038/s41598-017-06300-1]; GPMDB: [http://gpmdb.org/data/keyword/28831049 1]. | ||
#Vyse S, McCarthy F, Broncel M, Paul A, Wong JP, Bhamra A, Huang PH, (2017) "Quantitative phosphoproteomic analysis of acquired cancer drug resistance to pazopanib and dasatinib." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28842319 28842319]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.08.015 10.1016/j.jprot.2017.08.015]; GPMDB: [http://gpmdb.org/data/keyword/28842319 42]. | #Vyse S, McCarthy F, Broncel M, Paul A, Wong JP, Bhamra A, Huang PH, (2017) "Quantitative phosphoproteomic analysis of acquired cancer drug resistance to pazopanib and dasatinib." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28842319 28842319]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.08.015 10.1016/j.jprot.2017.08.015]; GPMDB: [http://gpmdb.org/data/keyword/28842319 42]. | ||
Line 1,641: | Line 1,641: | ||
#Andersen PR, Tirian L, Vunjak M, Brennecke J, (2017) "A heterochromatin-dependent transcription machinery drives piRNA expression." <i>Nature</i> <b>549</b>(7670):54–59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28847004 28847004]; doi: [https://dx.doi.org/10.1038/nature23482 10.1038/nature23482]; GPMDB: [http://gpmdb.org/data/keyword/28847004 46]. | #Andersen PR, Tirian L, Vunjak M, Brennecke J, (2017) "A heterochromatin-dependent transcription machinery drives piRNA expression." <i>Nature</i> <b>549</b>(7670):54–59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28847004 28847004]; doi: [https://dx.doi.org/10.1038/nature23482 10.1038/nature23482]; GPMDB: [http://gpmdb.org/data/keyword/28847004 46]. | ||
#Mohl BP, Emmott E, Roy P, (2017) "Phosphoproteomic analysis reveals the importance of kinase regulation during orbivirus infection." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28851738 28851738]; doi: [https://dx.doi.org/10.1074/mcp.M117.067355 10.1074/mcp.M117.067355]; GPMDB: [http://gpmdb.org/data/keyword/28851738 6]. | #Mohl BP, Emmott E, Roy P, (2017) "Phosphoproteomic analysis reveals the importance of kinase regulation during orbivirus infection." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28851738 28851738]; doi: [https://dx.doi.org/10.1074/mcp.M117.067355 10.1074/mcp.M117.067355]; GPMDB: [http://gpmdb.org/data/keyword/28851738 6]. | ||
+ | #Merkley ED, Sego LH, Lin A, Leiser OP, Kaiser BLD, Adkins JN, Keim PS, Wagner DM, Kreuzer HW, (2017) "Protein abundances can distinguish between naturally-occurring and laboratory strains of Yersinia pestis, the causative agent of plague." <i>PLoS One</i> <b>12</b>(8):e0183478; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28854255 28854255]; doi: [https://dx.doi.org/10.1371/journal.pone.0183478 10.1371/journal.pone.0183478]; GPMDB: [http://gpmdb.org/data/keyword/28854255 343]. | ||
#Peng X, Xu F, Liu S, Li S, Huang Q, Chang L, Wang L, Ma X, He F, Xu P, (2017) "Identification of Missing Proteins in the Phosphoproteome of Kidney Cancer." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28857561 28857561]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00332 10.1021/acs.jproteome.7b00332]; GPMDB: [http://gpmdb.org/data/keyword/28857561 17]. | #Peng X, Xu F, Liu S, Li S, Huang Q, Chang L, Wang L, Ma X, He F, Xu P, (2017) "Identification of Missing Proteins in the Phosphoproteome of Kidney Cancer." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28857561 28857561]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00332 10.1021/acs.jproteome.7b00332]; GPMDB: [http://gpmdb.org/data/keyword/28857561 17]. | ||
#Subramanian K, Rauniyar N, Lavalleé-Adam M, Yates JR 3rd, Balch WE, (2017) "Quantitative Analysis of the Proteome Response to the Histone Deacetylase Inhibitor (HDACi) Vorinostat in Niemann-Pick Type C1 disease." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28860124 28860124]; doi: [https://dx.doi.org/10.1074/mcp.M116.064949 10.1074/mcp.M116.064949]; GPMDB: [http://gpmdb.org/data/keyword/28860124 7]. | #Subramanian K, Rauniyar N, Lavalleé-Adam M, Yates JR 3rd, Balch WE, (2017) "Quantitative Analysis of the Proteome Response to the Histone Deacetylase Inhibitor (HDACi) Vorinostat in Niemann-Pick Type C1 disease." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28860124 28860124]; doi: [https://dx.doi.org/10.1074/mcp.M116.064949 10.1074/mcp.M116.064949]; GPMDB: [http://gpmdb.org/data/keyword/28860124 7]. | ||
#Rossello J, Lima A, Gil M, Rodríguez Duarte J, Correa A, Carvalho PC, Kierbel A, Durán R, (2017) "The EAL-domain protein FcsR regulates flagella, chemotaxis and type III secretion system in Pseudomonas aeruginosa by a phosphodiesterase independent mechanism." <i>Sci Rep</i> <b>7</b>(1):10281; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28860517 28860517]; doi: [https://dx.doi.org/10.1038/s41598-017-09926-3 10.1038/s41598-017-09926-3]; GPMDB: [http://gpmdb.org/data/keyword/28860517 21]. | #Rossello J, Lima A, Gil M, Rodríguez Duarte J, Correa A, Carvalho PC, Kierbel A, Durán R, (2017) "The EAL-domain protein FcsR regulates flagella, chemotaxis and type III secretion system in Pseudomonas aeruginosa by a phosphodiesterase independent mechanism." <i>Sci Rep</i> <b>7</b>(1):10281; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28860517 28860517]; doi: [https://dx.doi.org/10.1038/s41598-017-09926-3 10.1038/s41598-017-09926-3]; GPMDB: [http://gpmdb.org/data/keyword/28860517 21]. | ||
- | #Mendes M, Peláez-García A, López-Lucendo M, Bartolomé RA, Calviño E, Barderas R, Casal JI, (2017) "Mapping the spatial proteome of metastatic cells in colorectal cancer." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28861940 28861940]; doi: [https://dx.doi.org/10.1002/pmic.201700094 10.1002/pmic.201700094]; GPMDB: [http://gpmdb.org/data/keyword/28861940 | + | #Mendes M, Peláez-García A, López-Lucendo M, Bartolomé RA, Calviño E, Barderas R, Casal JI, (2017) "Mapping the spatial proteome of metastatic cells in colorectal cancer." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28861940 28861940]; doi: [https://dx.doi.org/10.1002/pmic.201700094 10.1002/pmic.201700094]; GPMDB: [http://gpmdb.org/data/keyword/28861940 200]. |
#Tanabe Y, Naito Y, Vasuta C, Lee AK, Soumounou Y, Linhoff MW, Takahashi H, (2017) "IgSF21 promotes differentiation of inhibitory synapses via binding to neurexin2α." <i>Nat Commun</i> <b>8</b>(1):408; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28864826 28864826]; doi: [https://dx.doi.org/10.1038/s41467-017-00333-w 10.1038/s41467-017-00333-w]; GPMDB: [http://gpmdb.org/data/keyword/28864826 32]. | #Tanabe Y, Naito Y, Vasuta C, Lee AK, Soumounou Y, Linhoff MW, Takahashi H, (2017) "IgSF21 promotes differentiation of inhibitory synapses via binding to neurexin2α." <i>Nat Commun</i> <b>8</b>(1):408; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28864826 28864826]; doi: [https://dx.doi.org/10.1038/s41467-017-00333-w 10.1038/s41467-017-00333-w]; GPMDB: [http://gpmdb.org/data/keyword/28864826 32]. | ||
- | #Edupuganti RR, Geiger S, Lindeboom RGH, Shi H, Hsu PJ, Lu Z, Wang SY, Baltissen MPA, Jansen PWTC, Rossa M, Müller M, Stunnenberg HG, He C, Carell T, Vermeulen M, (2017) "N<sup>6</sup>-methyladenosine (m<sup>6</sup>A) recruits and repels proteins to regulate mRNA homeostasis." <i>Nat Struct Mol Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28869609 28869609]; doi: [https://dx.doi.org/10.1038/nsmb.3462 10.1038/nsmb.3462]; GPMDB: [http://gpmdb.org/data/keyword/28869609 | + | #Kraner ME, Müller C, Sonnewald U, (2017) "Comparative proteomic profiling of the Choline transporter-like1 (CHER1) mutant provides insights into plasmodesmata composition of fully developed Arabidopsis thaliana leaves." <i>Plant J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28865150 28865150]; doi: [https://dx.doi.org/10.1111/tpj.13702 10.1111/tpj.13702]; GPMDB: [http://gpmdb.org/data/keyword/28865150 1]. |
+ | #Edupuganti RR, Geiger S, Lindeboom RGH, Shi H, Hsu PJ, Lu Z, Wang SY, Baltissen MPA, Jansen PWTC, Rossa M, Müller M, Stunnenberg HG, He C, Carell T, Vermeulen M, (2017) "N<sup>6</sup>-methyladenosine (m<sup>6</sup>A) recruits and repels proteins to regulate mRNA homeostasis." <i>Nat Struct Mol Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28869609 28869609]; doi: [https://dx.doi.org/10.1038/nsmb.3462 10.1038/nsmb.3462]; GPMDB: [http://gpmdb.org/data/keyword/28869609 40]. | ||
#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]. | ||
+ | #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]. | ||
+ | #Pawellek A, Ryder U, Tammsalu T, King LJ, Kreinin H, Ly T, Hay RT, Hartley RC, Lamond AI, (2017) "Characterisation of the biflavonoid hinokiflavone as a pre-mRNA splicing modulator that inhibits SENP." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28884683 28884683]; doi: [https://dx.doi.org/10.7554/eLife.27402 10.7554/eLife.27402]; GPMDB: [http://gpmdb.org/data/keyword/28884683 6]. | ||
#Rijkers M, van den Eshof BL, van der Meer PF, van Alphen FPJ, de Korte D, Leebeek FWG, Meijer AB, Voorberg J, Jansen AJG, (2017) "Monitoring storage induced changes in the platelet proteome employing label free quantitative mass spectrometry." <i>Sci Rep</i> <b>7</b>(1):11045; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28887518 28887518]; doi: [https://dx.doi.org/10.1038/s41598-017-11643-w 10.1038/s41598-017-11643-w]; GPMDB: [http://gpmdb.org/data/keyword/28887518 21]. | #Rijkers M, van den Eshof BL, van der Meer PF, van Alphen FPJ, de Korte D, Leebeek FWG, Meijer AB, Voorberg J, Jansen AJG, (2017) "Monitoring storage induced changes in the platelet proteome employing label free quantitative mass spectrometry." <i>Sci Rep</i> <b>7</b>(1):11045; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28887518 28887518]; doi: [https://dx.doi.org/10.1038/s41598-017-11643-w 10.1038/s41598-017-11643-w]; GPMDB: [http://gpmdb.org/data/keyword/28887518 21]. | ||
#Bachofner M, Speicher T, Bogorad RL, Muzumdar S, Derrer CP, Hürlimann F, Böhm F, Nanni P, Kockmann T, Kachaylo E, Meyer M, Padrissa-Altés S, Graf R, Anderson DG, Koteliansky V, Auf dem Keller U, Werner S, (2017) "Large-Scale Quantitative Proteomics Identifies the Ubiquitin Ligase Nedd4-1 as an Essential Regulator of Liver Regeneration." <i>Dev Cell</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28890072 28890072]; doi: [https://dx.doi.org/10.1016/j.devcel.2017.07.025 10.1016/j.devcel.2017.07.025]; GPMDB: [http://gpmdb.org/data/keyword/28890072 20]. | #Bachofner M, Speicher T, Bogorad RL, Muzumdar S, Derrer CP, Hürlimann F, Böhm F, Nanni P, Kockmann T, Kachaylo E, Meyer M, Padrissa-Altés S, Graf R, Anderson DG, Koteliansky V, Auf dem Keller U, Werner S, (2017) "Large-Scale Quantitative Proteomics Identifies the Ubiquitin Ligase Nedd4-1 as an Essential Regulator of Liver Regeneration." <i>Dev Cell</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28890072 28890072]; doi: [https://dx.doi.org/10.1016/j.devcel.2017.07.025 10.1016/j.devcel.2017.07.025]; GPMDB: [http://gpmdb.org/data/keyword/28890072 20]. | ||
+ | #Lapek JD Jr, Greninger P, Morris R, Amzallag A, Pruteanu-Malinici I, Benes CH, Haas W, (2017) "Detection of dysregulated protein-association networks by high-throughput proteomics predicts cancer vulnerabilities." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28892078 28892078]; doi: [https://dx.doi.org/10.1038/nbt.3955 10.1038/nbt.3955]; GPMDB: [http://gpmdb.org/data/keyword/28892078 11]. | ||
+ | #Bardot P, Vincent SD, Fournier M, Hubaud A, Joint M, Tora L, Pourquié O, (2017) "The TAF10-containing TFIID and SAGA transcriptional complexes are dispensable for early somitogenesis in the mouse embryo." <i>Development</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28893950 28893950]; doi: [https://dx.doi.org/10.1242/dev.146902 10.1242/dev.146902]; GPMDB: [http://gpmdb.org/data/keyword/28893950 30]. | ||
#Avenarius MR, Krey JF, Dumont RA, Morgan CP, Benson CB, Vijayakumar S, Cunningham CL, Scheffer DI, Corey DP, Müller U, Jones SM, Barr-Gillespie PG, (2017) "Heterodimeric capping protein is required for stereocilia length and width regulation." <i>J Cell Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28899994 28899994]; doi: [https://dx.doi.org/10.1083/jcb.201704171 10.1083/jcb.201704171]; GPMDB: [http://gpmdb.org/data/keyword/28899994 52]. | #Avenarius MR, Krey JF, Dumont RA, Morgan CP, Benson CB, Vijayakumar S, Cunningham CL, Scheffer DI, Corey DP, Müller U, Jones SM, Barr-Gillespie PG, (2017) "Heterodimeric capping protein is required for stereocilia length and width regulation." <i>J Cell Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28899994 28899994]; doi: [https://dx.doi.org/10.1083/jcb.201704171 10.1083/jcb.201704171]; GPMDB: [http://gpmdb.org/data/keyword/28899994 52]. | ||
- | #Hospital MA, Jacquel A, Mazed F, Saland E, Larrue C, Mondesir J, Birsen R, Green AS, Lambert M, Sujobert P, Gautier EF, Salnot V, Le Gall M, Decroocq J, Poulain L, Jacque N, Fontenay M, Kosmider O, Récher C, Auberger P, Mayeux P, Bouscary D, Sarry JE, Tamburini J, (2017) "RSK2 is a new Pim2 target with pro-survival functions in FLT3-ITD-positive acute myeloid leukemia." <i>Leukemia</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28914261 28914261]; doi: [https://dx.doi.org/10.1038/leu.2017.284 10.1038/leu.2017.284]; GPMDB: [http://gpmdb.org/data/keyword/28914261 | + | #Hospital MA, Jacquel A, Mazed F, Saland E, Larrue C, Mondesir J, Birsen R, Green AS, Lambert M, Sujobert P, Gautier EF, Salnot V, Le Gall M, Decroocq J, Poulain L, Jacque N, Fontenay M, Kosmider O, Récher C, Auberger P, Mayeux P, Bouscary D, Sarry JE, Tamburini J, (2017) "RSK2 is a new Pim2 target with pro-survival functions in FLT3-ITD-positive acute myeloid leukemia." <i>Leukemia</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28914261 28914261]; doi: [https://dx.doi.org/10.1038/leu.2017.284 10.1038/leu.2017.284]; GPMDB: [http://gpmdb.org/data/keyword/28914261 17]. |
#Tain LS, Sehlke R, Jain C, Chokkalingam M, Nagaraj N, Essers P, Rassner M, Grönke S, Froelich J, Dieterich C, Mann M, Alic N, Beyer A, Partridge L, (2017) "A proteomic atlas of insulin signalling reveals tissue-specific mechanisms of longevity assurance." <i>Mol Syst Biol</i> <b>13</b>(9):939; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28916541 28916541]; GPMDB: [http://gpmdb.org/data/keyword/28916541 92]. | #Tain LS, Sehlke R, Jain C, Chokkalingam M, Nagaraj N, Essers P, Rassner M, Grönke S, Froelich J, Dieterich C, Mann M, Alic N, Beyer A, Partridge L, (2017) "A proteomic atlas of insulin signalling reveals tissue-specific mechanisms of longevity assurance." <i>Mol Syst Biol</i> <b>13</b>(9):939; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28916541 28916541]; GPMDB: [http://gpmdb.org/data/keyword/28916541 92]. | ||
#Weber A, Elliott PR, Pinto-Fernandez A, Bonham S, Kessler BM, Komander D, El Oualid F, Krappmann D, (2017) "A Linear Diubiquitin-Based Probe for Efficient and Selective Detection of the Deubiquitinating Enzyme OTULIN." <i>Cell Chem Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28919039 28919039]; doi: [https://dx.doi.org/10.1016/j.chembiol.2017.08.006 10.1016/j.chembiol.2017.08.006]; GPMDB: [http://gpmdb.org/data/keyword/28919039 16]. | #Weber A, Elliott PR, Pinto-Fernandez A, Bonham S, Kessler BM, Komander D, El Oualid F, Krappmann D, (2017) "A Linear Diubiquitin-Based Probe for Efficient and Selective Detection of the Deubiquitinating Enzyme OTULIN." <i>Cell Chem Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28919039 28919039]; doi: [https://dx.doi.org/10.1016/j.chembiol.2017.08.006 10.1016/j.chembiol.2017.08.006]; GPMDB: [http://gpmdb.org/data/keyword/28919039 16]. | ||
#Kuboniwa M, Houser JR, Hendrickson EL, Wang Q, Alghamdi SA, Sakanaka A, Miller DP, Hutcherson JA, Wang T, Beck DAC, Whiteley M, Amano A, Wang H, Marcotte EM, Hackett M, Lamont RJ, (2017) "Metabolic crosstalk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial infection." <i>Nat Microbiol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28924191 28924191]; doi: [https://dx.doi.org/10.1038/s41564-017-0021-6 10.1038/s41564-017-0021-6]; GPMDB: [http://gpmdb.org/data/keyword/28924191 15]. | #Kuboniwa M, Houser JR, Hendrickson EL, Wang Q, Alghamdi SA, Sakanaka A, Miller DP, Hutcherson JA, Wang T, Beck DAC, Whiteley M, Amano A, Wang H, Marcotte EM, Hackett M, Lamont RJ, (2017) "Metabolic crosstalk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial infection." <i>Nat Microbiol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28924191 28924191]; doi: [https://dx.doi.org/10.1038/s41564-017-0021-6 10.1038/s41564-017-0021-6]; GPMDB: [http://gpmdb.org/data/keyword/28924191 15]. | ||
+ | #Lum KM, Sato Y, Beyer BA, Plaisted WC, Anglin JL, Lairson LL, Cravatt BF, (2017) "Mapping Protein Targets of Bioactive Small Molecules Using Lipid-Based Chemical Proteomics." <i>ACS Chem Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28930429 28930429]; doi: [https://dx.doi.org/10.1021/acschembio.7b00581 10.1021/acschembio.7b00581]; GPMDB: [http://gpmdb.org/data/keyword/28930429 30]. | ||
#Whiteley AM, Prado MA, Peng I, Abbas AR, Haley B, Paulo JA, Reichelt M, Katakam A, Sagolla M, Modrusan Z, Lee DY, Roose-Girma M, Kirkpatrick DS, McKenzie BS, Gygi SP, Finley D, Brown EJ, (2017) "Ubiquilin1 promotes antigen-receptor mediated proliferation by eliminating mislocalized mitochondrial proteins." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28933694 28933694]; doi: [https://dx.doi.org/10.7554/eLife.26435 10.7554/eLife.26435]; GPMDB: [http://gpmdb.org/data/keyword/28933694 4]. | #Whiteley AM, Prado MA, Peng I, Abbas AR, Haley B, Paulo JA, Reichelt M, Katakam A, Sagolla M, Modrusan Z, Lee DY, Roose-Girma M, Kirkpatrick DS, McKenzie BS, Gygi SP, Finley D, Brown EJ, (2017) "Ubiquilin1 promotes antigen-receptor mediated proliferation by eliminating mislocalized mitochondrial proteins." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28933694 28933694]; doi: [https://dx.doi.org/10.7554/eLife.26435 10.7554/eLife.26435]; GPMDB: [http://gpmdb.org/data/keyword/28933694 4]. | ||
+ | #Triana S, de Cock H, Ohm RA, Danies G, Wösten HAB, Restrepo S, González Barrios AF, Celis A, (2017) "Lipid Metabolic Versatility in <i>Malassezia</i> spp. Yeasts Studied through Metabolic Modeling." <i>Front Microbiol</i> <b>8</b>:1772; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28959251 28959251]; doi: [https://dx.doi.org/10.3389/fmicb.2017.01772 10.3389/fmicb.2017.01772]; GPMDB: [http://gpmdb.org/data/keyword/28959251 37]. | ||
+ | #Stadlmann J, Taubenschmid J, Wenzel D, Gattinger A, Dürnberger G, Dusberger F, Elling U, Mach L, Mechtler K, Penninger JM, (2017) "Comparative glycoproteomics of stem cells identifies new players in ricin toxicity." <i>Nature</i> <b>549</b>(7673):538–542; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28959962 28959962]; doi: [https://dx.doi.org/10.1038/nature24015 10.1038/nature24015]; GPMDB: [http://gpmdb.org/data/keyword/28959962 1]. |
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 Oct. 8, 2017.