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==Data from publications== | ==Data from publications== | ||
- | The following is a 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 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 May 1, 2016. |
#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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#Chen Y, Li Y, Zhong J, Zhang J, Chen Z, Yang L, Cao X, He QY, Zhang G, Wang T, (2015) "Identification of Missing Proteins Defined by Chromosome-Centric Proteome Project in the Cytoplasmic Detergent-Insoluble Proteins." <i>J Proteome Res</i> <b>14</b>(9):3693–709; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26108252 26108252]; doi: [https://dx.doi.org/10.1021/pr501103r 10.1021/pr501103r]; GPMDB: [http://gpmdb.org/data/keyword/26108252 46]. | #Chen Y, Li Y, Zhong J, Zhang J, Chen Z, Yang L, Cao X, He QY, Zhang G, Wang T, (2015) "Identification of Missing Proteins Defined by Chromosome-Centric Proteome Project in the Cytoplasmic Detergent-Insoluble Proteins." <i>J Proteome Res</i> <b>14</b>(9):3693–709; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26108252 26108252]; doi: [https://dx.doi.org/10.1021/pr501103r 10.1021/pr501103r]; GPMDB: [http://gpmdb.org/data/keyword/26108252 46]. | ||
#Uebbing S, Konzer A, Xu L, Backström N, Brunström B, Bergquist J, Ellegren H, (2015) "Quantitative Mass Spectrometry Reveals Partial Translational Regulation for Dosage Compensation in Chicken." <i>Mol Biol Evol</i> <b>32</b>(10):2716–25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26108680 26108680]; doi: [https://dx.doi.org/10.1093/molbev/msv147 10.1093/molbev/msv147]; GPMDB: [http://gpmdb.org/data/keyword/26108680 30]. | #Uebbing S, Konzer A, Xu L, Backström N, Brunström B, Bergquist J, Ellegren H, (2015) "Quantitative Mass Spectrometry Reveals Partial Translational Regulation for Dosage Compensation in Chicken." <i>Mol Biol Evol</i> <b>32</b>(10):2716–25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26108680 26108680]; doi: [https://dx.doi.org/10.1093/molbev/msv147 10.1093/molbev/msv147]; GPMDB: [http://gpmdb.org/data/keyword/26108680 30]. | ||
+ | #Inácio P, Zuzarte-Luís V, Ruivo MT, Falkard B, Nagaraj N, Rooijers K, Mann M, Mair G, Fidock DA, Mota MM, (2015) "Parasite-induced ER stress response in hepatocytes facilitates Plasmodium liver stage infection." <i>EMBO Rep</i> <b>16</b>(8):955–64; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26113366 26113366]; doi: [https://dx.doi.org/10.15252/embr.201439979 10.15252/embr.201439979]; GPMDB: [http://gpmdb.org/data/keyword/26113366 16]. | ||
#Zhu M, Wu G, Li YX, Stevens JK, Fan CX, Spang A, Dong MQ, (2015) "Serum- and Glucocorticoid-Inducible Kinase-1 (SGK-1) Plays a Role in Membrane Trafficking in Caenorhabditis elegans." <i>PLoS One</i> <b>10</b>(6):e0130778; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26115433 26115433]; doi: [https://dx.doi.org/10.1371/journal.pone.0130778 10.1371/journal.pone.0130778]; GPMDB: [http://gpmdb.org/data/keyword/26115433 2]. | #Zhu M, Wu G, Li YX, Stevens JK, Fan CX, Spang A, Dong MQ, (2015) "Serum- and Glucocorticoid-Inducible Kinase-1 (SGK-1) Plays a Role in Membrane Trafficking in Caenorhabditis elegans." <i>PLoS One</i> <b>10</b>(6):e0130778; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26115433 26115433]; doi: [https://dx.doi.org/10.1371/journal.pone.0130778 10.1371/journal.pone.0130778]; GPMDB: [http://gpmdb.org/data/keyword/26115433 2]. | ||
#Marcon E, Jain H, Bhattacharya A, Guo H, Phanse S, Pu S, Byram G, Collins BC, Dowdell E, Fenner M, Guo X, Hutchinson A, Kennedy JJ, Krastins B, Larsen B, Lin ZY, Lopez MF, Loppnau P, Miersch S, Nguyen T, Olsen JB, Paduch M, Ravichandran M, Seitova A, Vadali G, Vogelsang MS, Whiteaker JR, Zhong G, Zhong N, Zhao L, Aebersold R, Arrowsmith CH, Emili A, Frappier L, Gingras AC, Gstaiger M, Paulovich AG, Koide S, Kossiakoff AA, Sidhu SS, Wodak SJ, Gräslund S, Greenblatt JF, Edwards AM, (2015) "Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation." <i>Nat Methods</i> <b>12</b>(8):725–31; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26121405 26121405]; doi: [https://dx.doi.org/10.1038/nmeth.3472 10.1038/nmeth.3472]; GPMDB: [http://gpmdb.org/data/keyword/26121405 1220]. | #Marcon E, Jain H, Bhattacharya A, Guo H, Phanse S, Pu S, Byram G, Collins BC, Dowdell E, Fenner M, Guo X, Hutchinson A, Kennedy JJ, Krastins B, Larsen B, Lin ZY, Lopez MF, Loppnau P, Miersch S, Nguyen T, Olsen JB, Paduch M, Ravichandran M, Seitova A, Vadali G, Vogelsang MS, Whiteaker JR, Zhong G, Zhong N, Zhao L, Aebersold R, Arrowsmith CH, Emili A, Frappier L, Gingras AC, Gstaiger M, Paulovich AG, Koide S, Kossiakoff AA, Sidhu SS, Wodak SJ, Gräslund S, Greenblatt JF, Edwards AM, (2015) "Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation." <i>Nat Methods</i> <b>12</b>(8):725–31; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26121405 26121405]; doi: [https://dx.doi.org/10.1038/nmeth.3472 10.1038/nmeth.3472]; GPMDB: [http://gpmdb.org/data/keyword/26121405 1220]. | ||
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#White CH, Johnston HE, Moesker B, Manousopoulou A, Margolis DM, Richman DD, Spina CA, Garbis SD, Woelk CH, Beliakova-Bethell N, (2015) "Mixed effects of suberoylanilide hydroxamic acid (SAHA) on the host transcriptome and proteome and their implications for HIV reactivation from latency." <i>Antiviral Res</i> <b>123</b>:78–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26343910 26343910]; doi: [https://dx.doi.org/10.1016/j.antiviral.2015.09.002 10.1016/j.antiviral.2015.09.002]; GPMDB: [http://gpmdb.org/data/keyword/26343910 172]. | #White CH, Johnston HE, Moesker B, Manousopoulou A, Margolis DM, Richman DD, Spina CA, Garbis SD, Woelk CH, Beliakova-Bethell N, (2015) "Mixed effects of suberoylanilide hydroxamic acid (SAHA) on the host transcriptome and proteome and their implications for HIV reactivation from latency." <i>Antiviral Res</i> <b>123</b>:78–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26343910 26343910]; doi: [https://dx.doi.org/10.1016/j.antiviral.2015.09.002 10.1016/j.antiviral.2015.09.002]; GPMDB: [http://gpmdb.org/data/keyword/26343910 172]. | ||
#Wan C, Borgeson B, Phanse S, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, Babu M, Derry WB, Tillier ER, Wallingford JB, Parkinson J, Marcotte EM, Emili A, (2015) "Panorama of ancient metazoan macromolecular complexes." <i>Nature</i> <b>525</b>(7569):339–44; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26344197 26344197]; doi: [https://dx.doi.org/10.1038/nature14877 10.1038/nature14877]; GPMDB: [http://gpmdb.org/data/keyword/26344197 4066]. | #Wan C, Borgeson B, Phanse S, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, Babu M, Derry WB, Tillier ER, Wallingford JB, Parkinson J, Marcotte EM, Emili A, (2015) "Panorama of ancient metazoan macromolecular complexes." <i>Nature</i> <b>525</b>(7569):339–44; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26344197 26344197]; doi: [https://dx.doi.org/10.1038/nature14877 10.1038/nature14877]; GPMDB: [http://gpmdb.org/data/keyword/26344197 4066]. | ||
- | #Borgdorff H, Gautam R, Armstrong SD, Xia D, Ndayisaba GF, van Teijlingen NH, Geijtenbeek TB, Wastling JM, van de Wijgert JH, ( | + | #Borgdorff H, Gautam R, Armstrong SD, Xia D, Ndayisaba GF, van Teijlingen NH, Geijtenbeek TB, Wastling JM, van de Wijgert JH, (2016) "Cervicovaginal microbiome dysbiosis is associated with proteome changes related to alterations of the cervicovaginal mucosal barrier." <i>Mucosal Immunol</i> <b>9</b>(3):621–33; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26349657 26349657]; doi: [https://dx.doi.org/10.1038/mi.2015.86 10.1038/mi.2015.86]; GPMDB: [http://gpmdb.org/data/keyword/26349657 50]. |
#Weinert BT, Moustafa T, Iesmantavicius V, Zechner R, Choudhary C, (2015) "Analysis of acetylation stoichiometry suggests that SIRT3 repairs nonenzymatic acetylation lesions." <i>EMBO J</i> <b>34</b>(21):2620–32; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26358839 26358839]; doi: [https://dx.doi.org/10.15252/embj.201591271 10.15252/embj.201591271]; GPMDB: [http://gpmdb.org/data/keyword/26358839 142]. | #Weinert BT, Moustafa T, Iesmantavicius V, Zechner R, Choudhary C, (2015) "Analysis of acetylation stoichiometry suggests that SIRT3 repairs nonenzymatic acetylation lesions." <i>EMBO J</i> <b>34</b>(21):2620–32; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26358839 26358839]; doi: [https://dx.doi.org/10.15252/embj.201591271 10.15252/embj.201591271]; GPMDB: [http://gpmdb.org/data/keyword/26358839 142]. | ||
#Grundner-Culemann K, Dybowski JN, Klammer M, Tebbe A, Schaab C, Daub H, (2016) "Comparative proteome analysis across non-small cell lung cancer cell lines." <i>J Proteomics</i> <b>130</b>:1–10; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26361996 26361996]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.09.003 10.1016/j.jprot.2015.09.003]; GPMDB: [http://gpmdb.org/data/keyword/26361996 23]. | #Grundner-Culemann K, Dybowski JN, Klammer M, Tebbe A, Schaab C, Daub H, (2016) "Comparative proteome analysis across non-small cell lung cancer cell lines." <i>J Proteomics</i> <b>130</b>:1–10; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26361996 26361996]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.09.003 10.1016/j.jprot.2015.09.003]; GPMDB: [http://gpmdb.org/data/keyword/26361996 23]. | ||
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#Clark DJ, Fondrie WE, Liao Z, Hanson PI, Fulton A, Mao L, Yang AJ, (2015) "Redefining the Breast Cancer Exosome Proteome by Tandem Mass Tag Quantitative Proteomics and Multivariate Cluster Analysis." <i>Anal Chem</i> <b>87</b>(20):10462–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26378940 26378940]; doi: [https://dx.doi.org/10.1021/acs.analchem.5b02586 10.1021/acs.analchem.5b02586]; GPMDB: [http://gpmdb.org/data/keyword/26378940 2]. | #Clark DJ, Fondrie WE, Liao Z, Hanson PI, Fulton A, Mao L, Yang AJ, (2015) "Redefining the Breast Cancer Exosome Proteome by Tandem Mass Tag Quantitative Proteomics and Multivariate Cluster Analysis." <i>Anal Chem</i> <b>87</b>(20):10462–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26378940 26378940]; doi: [https://dx.doi.org/10.1021/acs.analchem.5b02586 10.1021/acs.analchem.5b02586]; GPMDB: [http://gpmdb.org/data/keyword/26378940 2]. | ||
#Kieselbach T, Zijnge V, Granström E, Oscarsson J, (2015) "Proteomics of Aggregatibacter actinomycetemcomitans Outer Membrane Vesicles." <i>PLoS One</i> <b>10</b>(9):e0138591; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26381655 26381655]; doi: [https://dx.doi.org/10.1371/journal.pone.0138591 10.1371/journal.pone.0138591]; GPMDB: [http://gpmdb.org/data/keyword/26381655 5]. | #Kieselbach T, Zijnge V, Granström E, Oscarsson J, (2015) "Proteomics of Aggregatibacter actinomycetemcomitans Outer Membrane Vesicles." <i>PLoS One</i> <b>10</b>(9):e0138591; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26381655 26381655]; doi: [https://dx.doi.org/10.1371/journal.pone.0138591 10.1371/journal.pone.0138591]; GPMDB: [http://gpmdb.org/data/keyword/26381655 5]. | ||
+ | #Paulo JA, O'Connell JD, Gaun A, Gygi SP, (2015) "Proteome-wide quantitative multiplexed profiling of protein expression: carbon-source dependency in Saccharomyces cerevisiae." <i>Mol Biol Cell</i> <b>26</b>(22):4063–74; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26399295 26399295]; doi: [https://dx.doi.org/10.1091/mbc.E15-07-0499 10.1091/mbc.E15-07-0499]; GPMDB: [http://gpmdb.org/data/keyword/26399295 1]. | ||
#Liu T, Tian CF, Chen WX, (2015) "Site-Specific Ser/Thr/Tyr Phosphoproteome of Sinorhizobium meliloti at Stationary Phase." <i>PLoS One</i> <b>10</b>(9):e0139143; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26401955 26401955]; doi: [https://dx.doi.org/10.1371/journal.pone.0139143 10.1371/journal.pone.0139143]; GPMDB: [http://gpmdb.org/data/keyword/26401955 2]. | #Liu T, Tian CF, Chen WX, (2015) "Site-Specific Ser/Thr/Tyr Phosphoproteome of Sinorhizobium meliloti at Stationary Phase." <i>PLoS One</i> <b>10</b>(9):e0139143; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26401955 26401955]; doi: [https://dx.doi.org/10.1371/journal.pone.0139143 10.1371/journal.pone.0139143]; GPMDB: [http://gpmdb.org/data/keyword/26401955 2]. | ||
#Li S, Dislich B, Brakebusch CH, Lichtenthaler SF, Brocker T, (2015) "Control of Homeostasis and Dendritic Cell Survival by the GTPase RhoA." <i>J Immunol</i> <b>195</b>(9):4244–56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26408665 26408665]; doi: [https://dx.doi.org/10.4049/jimmunol.1500676 10.4049/jimmunol.1500676]; GPMDB: [http://gpmdb.org/data/keyword/26408665 60]. | #Li S, Dislich B, Brakebusch CH, Lichtenthaler SF, Brocker T, (2015) "Control of Homeostasis and Dendritic Cell Survival by the GTPase RhoA." <i>J Immunol</i> <b>195</b>(9):4244–56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26408665 26408665]; doi: [https://dx.doi.org/10.4049/jimmunol.1500676 10.4049/jimmunol.1500676]; GPMDB: [http://gpmdb.org/data/keyword/26408665 60]. | ||
Line 1,021: | Line 1,023: | ||
#Clark DJ, Fondrie WE, Yang A, Mao L, (2016) "Triple SILAC quantitative proteomic analysis reveals differential abundance of cell signaling proteins between normal and lung cancer-derived exosomes." <i>J Proteomics</i> <b>133</b>:161–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26739763 26739763]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.12.023 10.1016/j.jprot.2015.12.023]; GPMDB: [http://gpmdb.org/data/keyword/26739763 3]. | #Clark DJ, Fondrie WE, Yang A, Mao L, (2016) "Triple SILAC quantitative proteomic analysis reveals differential abundance of cell signaling proteins between normal and lung cancer-derived exosomes." <i>J Proteomics</i> <b>133</b>:161–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26739763 26739763]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.12.023 10.1016/j.jprot.2015.12.023]; GPMDB: [http://gpmdb.org/data/keyword/26739763 3]. | ||
#Wandinger SK, Lahortiga I, Jacobs K, Klammer M, Jordan N, Elschenbroich S, Parade M, Jacoby E, Linders JT, Brehmer D, Cools J, Daub H, (2016) "Quantitative Phosphoproteomics Analysis of ERBB3/ERBB4 Signaling." <i>PLoS One</i> <b>11</b>(1):e0146100; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26745281 26745281]; doi: [https://dx.doi.org/10.1371/journal.pone.0146100 10.1371/journal.pone.0146100]; GPMDB: [http://gpmdb.org/data/keyword/26745281 72]. | #Wandinger SK, Lahortiga I, Jacobs K, Klammer M, Jordan N, Elschenbroich S, Parade M, Jacoby E, Linders JT, Brehmer D, Cools J, Daub H, (2016) "Quantitative Phosphoproteomics Analysis of ERBB3/ERBB4 Signaling." <i>PLoS One</i> <b>11</b>(1):e0146100; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26745281 26745281]; doi: [https://dx.doi.org/10.1371/journal.pone.0146100 10.1371/journal.pone.0146100]; GPMDB: [http://gpmdb.org/data/keyword/26745281 72]. | ||
- | #Christoforou A, Mulvey CM, Breckels LM, Geladaki A, Hurrell T, Hayward PC, Naake T, Gatto L, Viner R, Arias | + | #Christoforou A, Mulvey CM, Breckels LM, Geladaki A, Hurrell T, Hayward PC, Naake T, Gatto L, Viner R, Martinez Arias A, Lilley KS, (2016) "A draft map of the mouse pluripotent stem cell spatial proteome." <i>Nat Commun</i> <b>7</b>:8992; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26754106 26754106]; doi: [https://dx.doi.org/10.1038/ncomms9992 10.1038/ncomms9992]; GPMDB: [http://gpmdb.org/data/keyword/26754106 2]. |
#Jin J, Tian R, Pasculescu A, Dai AY, Williton K, Taylor L, Savitski MM, Bantscheff M, Woodgett JR, Pawson T, Colwill K, (2016) "Mutational Analysis of Glycogen Synthase Kinase 3β Protein Kinase Together with Kinome-Wide Binding and Stability Studies Suggests Context-Dependent Recognition of Kinases by the Chaperone Heat Shock Protein 90." <i>Mol Cell Biol</i> <b>36</b>(6):1007–18; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26755559 26755559]; doi: [https://dx.doi.org/10.1128/MCB.01045-15 10.1128/MCB.01045-15]; GPMDB: [http://gpmdb.org/data/keyword/26755559 17]. | #Jin J, Tian R, Pasculescu A, Dai AY, Williton K, Taylor L, Savitski MM, Bantscheff M, Woodgett JR, Pawson T, Colwill K, (2016) "Mutational Analysis of Glycogen Synthase Kinase 3β Protein Kinase Together with Kinome-Wide Binding and Stability Studies Suggests Context-Dependent Recognition of Kinases by the Chaperone Heat Shock Protein 90." <i>Mol Cell Biol</i> <b>36</b>(6):1007–18; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26755559 26755559]; doi: [https://dx.doi.org/10.1128/MCB.01045-15 10.1128/MCB.01045-15]; GPMDB: [http://gpmdb.org/data/keyword/26755559 17]. | ||
#So EC, Schroeder GN, Carson D, Mattheis C, Mousnier A, Broncel M, Tate EW, Frankel G, (2016) "The Rab-binding Profiles of Bacterial Virulence Factors during Infection." <i>J Biol Chem</i> <b>291</b>(11):5832–43; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26755725 26755725]; doi: [https://dx.doi.org/10.1074/jbc.M115.700930 10.1074/jbc.M115.700930]; GPMDB: [http://gpmdb.org/data/keyword/26755725 60]. | #So EC, Schroeder GN, Carson D, Mattheis C, Mousnier A, Broncel M, Tate EW, Frankel G, (2016) "The Rab-binding Profiles of Bacterial Virulence Factors during Infection." <i>J Biol Chem</i> <b>291</b>(11):5832–43; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26755725 26755725]; doi: [https://dx.doi.org/10.1074/jbc.M115.700930 10.1074/jbc.M115.700930]; GPMDB: [http://gpmdb.org/data/keyword/26755725 60]. | ||
- | #Geddes JM, Caza M, Croll D, Stoynov N, Foster LJ, Kronstad JW, (2016) "Analysis of the Protein Kinase A-Regulated Proteome of Cryptococcus neoformans Identifies a Role for the Ubiquitin-Proteasome Pathway in Capsule Formation." <i>MBio</i> <b>7</b>(1):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26758180 26758180]; doi: [https://dx.doi.org/10.1128/mBio.01862-15 10.1128/mBio.01862-15]; GPMDB: [http://gpmdb.org/data/keyword/26758180 133]. | + | #Geddes JM, Caza M, Croll D, Stoynov N, Foster LJ, Kronstad JW, (2016) "Analysis of the Protein Kinase A-Regulated Proteome of Cryptococcus neoformans Identifies a Role for the Ubiquitin-Proteasome Pathway in Capsule Formation." <i>MBio</i> <b>7</b>(1):e01862–15; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26758180 26758180]; doi: [https://dx.doi.org/10.1128/mBio.01862-15 10.1128/mBio.01862-15]; GPMDB: [http://gpmdb.org/data/keyword/26758180 133]. |
#Uren PJ, Bahrami-Samani E, de Araujo PR, Vogel C, Qiao M, Burns SC, Smith AD, Penalva LO, (2016) "High-throughput analyses of hnRNP H1 dissects its multi-functional aspect." <i>RNA Biol</i> <b>13</b>(4):400–11; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26760575 26760575]; doi: [https://dx.doi.org/10.1080/15476286.2015.1138030 10.1080/15476286.2015.1138030]; GPMDB: [http://gpmdb.org/data/keyword/26760575 32]. | #Uren PJ, Bahrami-Samani E, de Araujo PR, Vogel C, Qiao M, Burns SC, Smith AD, Penalva LO, (2016) "High-throughput analyses of hnRNP H1 dissects its multi-functional aspect." <i>RNA Biol</i> <b>13</b>(4):400–11; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26760575 26760575]; doi: [https://dx.doi.org/10.1080/15476286.2015.1138030 10.1080/15476286.2015.1138030]; GPMDB: [http://gpmdb.org/data/keyword/26760575 32]. | ||
#Neubert P, Halim A, Zauser M, Essig A, Joshi HJ, Zatorska E, Larsen IS, Loibl M, Castells-Ballester J, Aebi M, Clausen H, Strahl S, (2016) "Mapping the O-Mannose Glycoproteome in Saccharomyces cerevisiae." <i>Mol Cell Proteomics</i> <b>15</b>(4):1323–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26764011 26764011]; doi: [https://dx.doi.org/10.1074/mcp.M115.057505 10.1074/mcp.M115.057505]; GPMDB: [http://gpmdb.org/data/keyword/26764011 6]. | #Neubert P, Halim A, Zauser M, Essig A, Joshi HJ, Zatorska E, Larsen IS, Loibl M, Castells-Ballester J, Aebi M, Clausen H, Strahl S, (2016) "Mapping the O-Mannose Glycoproteome in Saccharomyces cerevisiae." <i>Mol Cell Proteomics</i> <b>15</b>(4):1323–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26764011 26764011]; doi: [https://dx.doi.org/10.1074/mcp.M115.057505 10.1074/mcp.M115.057505]; GPMDB: [http://gpmdb.org/data/keyword/26764011 6]. | ||
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#Long B, Muhamad R, Yan G, Yu J, Fan Q, Wang Z, Li X, Purnomoadi A, Achmadi J, Yan X, (2016) "Quantitative proteomics analysis reveals glutamine deprivation activates fatty acid β-oxidation pathway in HepG2 cells." <i>Amino Acids</i> <b>48</b>(5):1297–307; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26837383 26837383]; doi: [https://dx.doi.org/10.1007/s00726-016-2182-7 10.1007/s00726-016-2182-7]; GPMDB: [http://gpmdb.org/data/keyword/26837383 1]. | #Long B, Muhamad R, Yan G, Yu J, Fan Q, Wang Z, Li X, Purnomoadi A, Achmadi J, Yan X, (2016) "Quantitative proteomics analysis reveals glutamine deprivation activates fatty acid β-oxidation pathway in HepG2 cells." <i>Amino Acids</i> <b>48</b>(5):1297–307; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26837383 26837383]; doi: [https://dx.doi.org/10.1007/s00726-016-2182-7 10.1007/s00726-016-2182-7]; GPMDB: [http://gpmdb.org/data/keyword/26837383 1]. | ||
#Iwamoto N, D'Alessandro LA, Depner S, Hahn B, Kramer BA, Lucarelli P, Vlasov A, Stepath M, Böhm ME, Deharde D, Damm G, Seehofer D, Lehmann WD, Klingmüller U, Schilling M, (2016) "Context-specific flow through the MEK/ERK module produces cell- and ligand-specific patterns of ERK single and double phosphorylation." <i>Sci Signal</i> <b>9</b>(413):ra13; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26838549 26838549]; doi: [https://dx.doi.org/10.1126/scisignal.aab1967 10.1126/scisignal.aab1967]; GPMDB: [http://gpmdb.org/data/keyword/26838549 66]. | #Iwamoto N, D'Alessandro LA, Depner S, Hahn B, Kramer BA, Lucarelli P, Vlasov A, Stepath M, Böhm ME, Deharde D, Damm G, Seehofer D, Lehmann WD, Klingmüller U, Schilling M, (2016) "Context-specific flow through the MEK/ERK module produces cell- and ligand-specific patterns of ERK single and double phosphorylation." <i>Sci Signal</i> <b>9</b>(413):ra13; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26838549 26838549]; doi: [https://dx.doi.org/10.1126/scisignal.aab1967 10.1126/scisignal.aab1967]; GPMDB: [http://gpmdb.org/data/keyword/26838549 66]. | ||
- | #Huang H, Yoo CY, Bindbeutel R, Goldsworthy J, Tielking A, Alvarez S, Naldrett MJ, Evans BS, Chen M, Nusinow DA, (2016) "PCH1 integrates circadian and light-signaling pathways to control photoperiod-responsive growth in Arabidopsis." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26839287 26839287]; doi: [https://dx.doi.org/10.7554/eLife.13292 10.7554/eLife.13292]; GPMDB: [http://gpmdb.org/data/keyword/26839287 9]. | + | #Huang H, Yoo CY, Bindbeutel R, Goldsworthy J, Tielking A, Alvarez S, Naldrett MJ, Evans BS, Chen M, Nusinow DA, (2016) "PCH1 integrates circadian and light-signaling pathways to control photoperiod-responsive growth in Arabidopsis." <i>Elife</i> <b>5</b>:e13292; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26839287 26839287]; doi: [https://dx.doi.org/10.7554/eLife.13292 10.7554/eLife.13292]; GPMDB: [http://gpmdb.org/data/keyword/26839287 9]. |
#Thorpe CT, Peffers MJ, Simpson D, Halliwell E, Screen HR, Clegg PD, (2016) "Anatomical heterogeneity of tendon: Fascicular and interfascicular tendon compartments have distinct proteomic composition." <i>Sci Rep</i> <b>6</b>:20455; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26842662 26842662]; doi: [https://dx.doi.org/10.1038/srep20455 10.1038/srep20455]; GPMDB: [http://gpmdb.org/data/keyword/26842662 20]. | #Thorpe CT, Peffers MJ, Simpson D, Halliwell E, Screen HR, Clegg PD, (2016) "Anatomical heterogeneity of tendon: Fascicular and interfascicular tendon compartments have distinct proteomic composition." <i>Sci Rep</i> <b>6</b>:20455; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26842662 26842662]; doi: [https://dx.doi.org/10.1038/srep20455 10.1038/srep20455]; GPMDB: [http://gpmdb.org/data/keyword/26842662 20]. | ||
#Chidiac R, Zhang Y, Tessier S, Faubert D, Delisle C, Gratton JP, (2016) "Comparative phosphoproteomics analysis of VEGF and Angiopoietin-1 signaling reveals ZO-1 as a critical regulator of endothelial cell proliferation." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26846344 26846344]; doi: [https://dx.doi.org/10.1074/mcp.M115.053298 10.1074/mcp.M115.053298]; GPMDB: [http://gpmdb.org/data/keyword/26846344 13]. | #Chidiac R, Zhang Y, Tessier S, Faubert D, Delisle C, Gratton JP, (2016) "Comparative phosphoproteomics analysis of VEGF and Angiopoietin-1 signaling reveals ZO-1 as a critical regulator of endothelial cell proliferation." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26846344 26846344]; doi: [https://dx.doi.org/10.1074/mcp.M115.053298 10.1074/mcp.M115.053298]; GPMDB: [http://gpmdb.org/data/keyword/26846344 13]. | ||
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#Lamberti Y, Cafiero JH, Surmann K, Valdez H, Holubova J, Večerek B, Sebo P, Schmidt F, Völker U, Rodriguez ME, (2016) "Proteome analysis of Bordetella pertussis isolated from human macrophages." <i>J Proteomics</i> <b>136</b>:55–67; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26873878 26873878]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.02.002 10.1016/j.jprot.2016.02.002]; GPMDB: [http://gpmdb.org/data/keyword/26873878 9]. | #Lamberti Y, Cafiero JH, Surmann K, Valdez H, Holubova J, Večerek B, Sebo P, Schmidt F, Völker U, Rodriguez ME, (2016) "Proteome analysis of Bordetella pertussis isolated from human macrophages." <i>J Proteomics</i> <b>136</b>:55–67; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26873878 26873878]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.02.002 10.1016/j.jprot.2016.02.002]; GPMDB: [http://gpmdb.org/data/keyword/26873878 9]. | ||
#Knöppel A, Näsvall J, Andersson DI, (2016) "Compensating the Fitness Costs of Synonymous Mutations." <i>Mol Biol Evol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26882986 26882986]; doi: [https://dx.doi.org/10.1093/molbev/msw028 10.1093/molbev/msw028]; GPMDB: [http://gpmdb.org/data/keyword/26882986 72]. | #Knöppel A, Näsvall J, Andersson DI, (2016) "Compensating the Fitness Costs of Synonymous Mutations." <i>Mol Biol Evol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26882986 26882986]; doi: [https://dx.doi.org/10.1093/molbev/msw028 10.1093/molbev/msw028]; GPMDB: [http://gpmdb.org/data/keyword/26882986 72]. | ||
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#Zufferey A, Ibberson M, Reny JL, Nolli S, Schvartz D, Docquier M, Xenarios I, Sanchez JC, Fontana P, (2016) "New molecular insights into modulation of platelet reactivity in aspirin-treated patients using a network-based approach." <i>Hum Genet</i> <b>135</b>(4):403–14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26883867 26883867]; doi: [https://dx.doi.org/10.1007/s00439-016-1642-1 10.1007/s00439-016-1642-1]; GPMDB: [http://gpmdb.org/data/keyword/26883867 13]. | #Zufferey A, Ibberson M, Reny JL, Nolli S, Schvartz D, Docquier M, Xenarios I, Sanchez JC, Fontana P, (2016) "New molecular insights into modulation of platelet reactivity in aspirin-treated patients using a network-based approach." <i>Hum Genet</i> <b>135</b>(4):403–14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26883867 26883867]; doi: [https://dx.doi.org/10.1007/s00439-016-1642-1 10.1007/s00439-016-1642-1]; GPMDB: [http://gpmdb.org/data/keyword/26883867 13]. | ||
#Huebner AR, Cheng L, Somparn P, Knepper MA, Fenton RA, Pisitkun T, (2016) "Deubiquitylation of protein cargo is not an essential step in exosome formation." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26884507 26884507]; doi: [https://dx.doi.org/10.1074/mcp.M115.054965 10.1074/mcp.M115.054965]; GPMDB: [http://gpmdb.org/data/keyword/26884507 64]. | #Huebner AR, Cheng L, Somparn P, Knepper MA, Fenton RA, Pisitkun T, (2016) "Deubiquitylation of protein cargo is not an essential step in exosome formation." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26884507 26884507]; doi: [https://dx.doi.org/10.1074/mcp.M115.054965 10.1074/mcp.M115.054965]; GPMDB: [http://gpmdb.org/data/keyword/26884507 64]. | ||
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#De Marchi T, Kuhn E, Dekker LJ, Stingl C, Braakman RB, Opdam M, Linn SC, Sweep FC, Span PN, Luider TM, Foekens JA, Martens JW, Carr SA, Umar A, (2016) "Targeted MS Assay Predicting Tamoxifen Resistance in Estrogen-Receptor-Positive Breast Cancer Tissues and Sera." <i>J Proteome Res</i> <b>15</b>(4):1230–42; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26958999 26958999]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b01119 10.1021/acs.jproteome.5b01119]; GPMDB: [http://gpmdb.org/data/keyword/26958999 78]. | #De Marchi T, Kuhn E, Dekker LJ, Stingl C, Braakman RB, Opdam M, Linn SC, Sweep FC, Span PN, Luider TM, Foekens JA, Martens JW, Carr SA, Umar A, (2016) "Targeted MS Assay Predicting Tamoxifen Resistance in Estrogen-Receptor-Positive Breast Cancer Tissues and Sera." <i>J Proteome Res</i> <b>15</b>(4):1230–42; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26958999 26958999]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b01119 10.1021/acs.jproteome.5b01119]; GPMDB: [http://gpmdb.org/data/keyword/26958999 78]. | ||
#Jo DH, Bae J, Chae S, Kim JH, Han JH, Hwang D, Lee SW, Kim JH, (2016) "Quantitative proteomics reveals β2 integrin-mediated cytoskeletal rearrangement in VEGF-induced retinal vascular hyperpermeability." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26969716 26969716]; doi: [https://dx.doi.org/10.1074/mcp.M115.053249 10.1074/mcp.M115.053249]; GPMDB: [http://gpmdb.org/data/keyword/26969716 72]. | #Jo DH, Bae J, Chae S, Kim JH, Han JH, Hwang D, Lee SW, Kim JH, (2016) "Quantitative proteomics reveals β2 integrin-mediated cytoskeletal rearrangement in VEGF-induced retinal vascular hyperpermeability." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26969716 26969716]; doi: [https://dx.doi.org/10.1074/mcp.M115.053249 10.1074/mcp.M115.053249]; GPMDB: [http://gpmdb.org/data/keyword/26969716 72]. | ||
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#Bonn F, Pané-Farré J, Schlüter R, Schaffer M, Fuchs S, Bernhardt J, Riedel K, Otto A, Völker U, van Dijl JM, Hecker M, Mäder U, Becher D, (2016) "Global analysis of the impact of linezolid onto virulence factor production in S. aureus USA300." <i>Int J Med Microbiol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26996810 26996810]; doi: [https://dx.doi.org/10.1016/j.ijmm.2016.02.004 10.1016/j.ijmm.2016.02.004]; GPMDB: [http://gpmdb.org/data/keyword/26996810 300]. | #Bonn F, Pané-Farré J, Schlüter R, Schaffer M, Fuchs S, Bernhardt J, Riedel K, Otto A, Völker U, van Dijl JM, Hecker M, Mäder U, Becher D, (2016) "Global analysis of the impact of linezolid onto virulence factor production in S. aureus USA300." <i>Int J Med Microbiol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26996810 26996810]; doi: [https://dx.doi.org/10.1016/j.ijmm.2016.02.004 10.1016/j.ijmm.2016.02.004]; GPMDB: [http://gpmdb.org/data/keyword/26996810 300]. | ||
#He JJ, Ma J, Elsheikha HM, Song HQ, Zhou DH, Zhu XQ, (2016) "Proteomic Profiling of Mouse Liver following Acute Toxoplasma gondii Infection." <i>PLoS One</i> <b>11</b>(3):e0152022; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27003162 27003162]; doi: [https://dx.doi.org/10.1371/journal.pone.0152022 10.1371/journal.pone.0152022]; GPMDB: [http://gpmdb.org/data/keyword/27003162 1]. | #He JJ, Ma J, Elsheikha HM, Song HQ, Zhou DH, Zhu XQ, (2016) "Proteomic Profiling of Mouse Liver following Acute Toxoplasma gondii Infection." <i>PLoS One</i> <b>11</b>(3):e0152022; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27003162 27003162]; doi: [https://dx.doi.org/10.1371/journal.pone.0152022 10.1371/journal.pone.0152022]; GPMDB: [http://gpmdb.org/data/keyword/27003162 1]. | ||
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#Sunitha B, Gayathri N, Kumar M, Keshava Prasad TS, Nalini A, Padmanabhan B, Srinivas Bharath MM, (2016) "Muscle biopsies from human muscle diseases with myopathic pathology reveal common alterations in mitochondrial function." <i>J Neurochem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27015874 27015874]; doi: [https://dx.doi.org/10.1111/jnc.13626 10.1111/jnc.13626]; GPMDB: [http://gpmdb.org/data/keyword/27015874 1]. | #Sunitha B, Gayathri N, Kumar M, Keshava Prasad TS, Nalini A, Padmanabhan B, Srinivas Bharath MM, (2016) "Muscle biopsies from human muscle diseases with myopathic pathology reveal common alterations in mitochondrial function." <i>J Neurochem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27015874 27015874]; doi: [https://dx.doi.org/10.1111/jnc.13626 10.1111/jnc.13626]; GPMDB: [http://gpmdb.org/data/keyword/27015874 1]. | ||
#Huang D, Piening BD, Kennedy JJ, Lin C, Jones-Weinert CW, Yan P, Paulovich AG, (2016) "DNA Replication Stress Phosphoproteome Profiles Reveal Novel Functional Phosphorylation Sites on Xrs2 in Saccharomyces cerevisiae." <i>Genetics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27017623 27017623]; doi: [https://dx.doi.org/10.1534/genetics.115.185231 10.1534/genetics.115.185231]; GPMDB: [http://gpmdb.org/data/keyword/27017623 4]. | #Huang D, Piening BD, Kennedy JJ, Lin C, Jones-Weinert CW, Yan P, Paulovich AG, (2016) "DNA Replication Stress Phosphoproteome Profiles Reveal Novel Functional Phosphorylation Sites on Xrs2 in Saccharomyces cerevisiae." <i>Genetics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27017623 27017623]; doi: [https://dx.doi.org/10.1534/genetics.115.185231 10.1534/genetics.115.185231]; GPMDB: [http://gpmdb.org/data/keyword/27017623 4]. | ||
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#Slany A, Bileck A, Kreutz D, Mayer RL, Muqaku B, Gerner C, (2016) "Contribution of human fibroblasts and endothelial cells to the Hallmarks of Inflammation as determined by proteome profiling." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27025457 27025457]; doi: [https://dx.doi.org/10.1074/mcp.M116.058099 10.1074/mcp.M116.058099]; GPMDB: [http://gpmdb.org/data/keyword/27025457 104]. | #Slany A, Bileck A, Kreutz D, Mayer RL, Muqaku B, Gerner C, (2016) "Contribution of human fibroblasts and endothelial cells to the Hallmarks of Inflammation as determined by proteome profiling." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27025457 27025457]; doi: [https://dx.doi.org/10.1074/mcp.M116.058099 10.1074/mcp.M116.058099]; GPMDB: [http://gpmdb.org/data/keyword/27025457 104]. | ||
#Osinalde N, Sánchez-Quiles V, Blagoev B, Kratchmarova I, (2016) "Changes in Gab2 phosphorylation and interaction partners in response to interleukin (IL)-2 stimulation in T-lymphocytes." <i>Sci Rep</i> <b>6</b>:23530; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27025927 27025927]; doi: [https://dx.doi.org/10.1038/srep23530 10.1038/srep23530]; GPMDB: [http://gpmdb.org/data/keyword/27025927 22]. | #Osinalde N, Sánchez-Quiles V, Blagoev B, Kratchmarova I, (2016) "Changes in Gab2 phosphorylation and interaction partners in response to interleukin (IL)-2 stimulation in T-lymphocytes." <i>Sci Rep</i> <b>6</b>:23530; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27025927 27025927]; doi: [https://dx.doi.org/10.1038/srep23530 10.1038/srep23530]; GPMDB: [http://gpmdb.org/data/keyword/27025927 22]. | ||
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#Goldman-Pinkovich A, Balno C, Strasser R, Zeituni-Molad M, Bendelak K, Rentsch D, Ephros M, Wiese M, Jardim A, Myler PJ, Zilberstein D, (2016) "An Arginine Deprivation Response Pathway Is Induced in Leishmania during Macrophage Invasion." <i>PLoS Pathog</i> <b>12</b>(4):e1005494; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27043018 27043018]; doi: [https://dx.doi.org/10.1371/journal.ppat.1005494 10.1371/journal.ppat.1005494]; GPMDB: [http://gpmdb.org/data/keyword/27043018 8]. | #Goldman-Pinkovich A, Balno C, Strasser R, Zeituni-Molad M, Bendelak K, Rentsch D, Ephros M, Wiese M, Jardim A, Myler PJ, Zilberstein D, (2016) "An Arginine Deprivation Response Pathway Is Induced in Leishmania during Macrophage Invasion." <i>PLoS Pathog</i> <b>12</b>(4):e1005494; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27043018 27043018]; doi: [https://dx.doi.org/10.1371/journal.ppat.1005494 10.1371/journal.ppat.1005494]; GPMDB: [http://gpmdb.org/data/keyword/27043018 8]. | ||
#Salvetti A, Couté Y, Epstein A, Arata L, Kraut A, Navratil V, Bouvet P, Greco A, (2016) "Nuclear Functions of Nucleolin through Global Proteomics and Interactomic Approaches." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27049334 27049334]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00126 10.1021/acs.jproteome.6b00126]; GPMDB: [http://gpmdb.org/data/keyword/27049334 7]. | #Salvetti A, Couté Y, Epstein A, Arata L, Kraut A, Navratil V, Bouvet P, Greco A, (2016) "Nuclear Functions of Nucleolin through Global Proteomics and Interactomic Approaches." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27049334 27049334]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00126 10.1021/acs.jproteome.6b00126]; GPMDB: [http://gpmdb.org/data/keyword/27049334 7]. | ||
+ | #Zhou S, Okekeogbu I, Sangireddy S, Ye Z, Li H, Bhatti S, Hui D, McDonald DW, Yang Y, Giri S, Howe KJ, Fish T, Thannhauser TW, (2016) "Proteome Modification in Tomato Plants upon Long-Term Aluminum Treatment." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27052409 27052409]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00128 10.1021/acs.jproteome.6b00128]; GPMDB: [http://gpmdb.org/data/keyword/27052409 68]. | ||
#Slomnicki L, Malinowska A, Kistowski M, Palusinski A, Zheng JJ, Sepp M, Timmusk T, Dadlez M, Hetman M, (2016) "Nucleolar enrichment of brain proteins with critical roles in human neurodevelopment." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27053602 27053602]; doi: [https://dx.doi.org/10.1074/mcp.M115.051920 10.1074/mcp.M115.051920]; GPMDB: [http://gpmdb.org/data/keyword/27053602 18]. | #Slomnicki L, Malinowska A, Kistowski M, Palusinski A, Zheng JJ, Sepp M, Timmusk T, Dadlez M, Hetman M, (2016) "Nucleolar enrichment of brain proteins with critical roles in human neurodevelopment." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27053602 27053602]; doi: [https://dx.doi.org/10.1074/mcp.M115.051920 10.1074/mcp.M115.051920]; GPMDB: [http://gpmdb.org/data/keyword/27053602 18]. | ||
#Liberton M, Saha R, Jacobs JM, Nguyen AY, Gritsenko MA, Smith RD, Koppenaal DW, Pakrasi HB, (2016) "Global Proteomic Analysis Reveals an Exclusive Role of Thylakoid Membranes in Bioenergetics of a Model Cyanobacterium." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27056914 27056914]; doi: [https://dx.doi.org/10.1074/mcp.M115.057240 10.1074/mcp.M115.057240]; GPMDB: [http://gpmdb.org/data/keyword/27056914 2]. | #Liberton M, Saha R, Jacobs JM, Nguyen AY, Gritsenko MA, Smith RD, Koppenaal DW, Pakrasi HB, (2016) "Global Proteomic Analysis Reveals an Exclusive Role of Thylakoid Membranes in Bioenergetics of a Model Cyanobacterium." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27056914 27056914]; doi: [https://dx.doi.org/10.1074/mcp.M115.057240 10.1074/mcp.M115.057240]; GPMDB: [http://gpmdb.org/data/keyword/27056914 2]. | ||
#Kähne T, Richter S, Kolodziej A, Smalla KH, Pielot R, Engler A, Ohl FW, Dieterich DC, Seidenbecher C, Tischmeyer W, Naumann M, Gundelfinger ED, (2016) "Proteome rearrangements after auditory learning: high-resolution profiling of synapse-enriched protein fractions from mouse brain." <i>J Neurochem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27062398 27062398]; doi: [https://dx.doi.org/10.1111/jnc.13636 10.1111/jnc.13636]; GPMDB: [http://gpmdb.org/data/keyword/27062398 15]. | #Kähne T, Richter S, Kolodziej A, Smalla KH, Pielot R, Engler A, Ohl FW, Dieterich DC, Seidenbecher C, Tischmeyer W, Naumann M, Gundelfinger ED, (2016) "Proteome rearrangements after auditory learning: high-resolution profiling of synapse-enriched protein fractions from mouse brain." <i>J Neurochem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27062398 27062398]; doi: [https://dx.doi.org/10.1111/jnc.13636 10.1111/jnc.13636]; GPMDB: [http://gpmdb.org/data/keyword/27062398 15]. | ||
- | #Hoernstein SN, Mueller SJ, Fiedler K, Schuelke M, Vanselow JT, Schuessele C, Lang D, Nitschke R, Igloi GL, Schlosser A, Reski R, (2016) "Identification of targets and interaction partners of arginyl-tRNA protein transferase in the moss Physcomitrella patens." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27067052 27067052]; doi: [https://dx.doi.org/10.1074/mcp.M115.057190 10.1074/mcp.M115.057190]; GPMDB: [http://gpmdb.org/data/keyword/27067052 | + | #Hoernstein SN, Mueller SJ, Fiedler K, Schuelke M, Vanselow JT, Schuessele C, Lang D, Nitschke R, Igloi GL, Schlosser A, Reski R, (2016) "Identification of targets and interaction partners of arginyl-tRNA protein transferase in the moss Physcomitrella patens." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27067052 27067052]; doi: [https://dx.doi.org/10.1074/mcp.M115.057190 10.1074/mcp.M115.057190]; GPMDB: [http://gpmdb.org/data/keyword/27067052 134]. |
#Drabovich AP, Pavlou MP, Schiza C, Diamandis EP, (2016) "Dynamics of protein expression reveals primary targets and secondary messengers of estrogen receptor alpha signaling in MCF-7 breast cancer cells." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27067054 27067054]; doi: [https://dx.doi.org/10.1074/mcp.M115.057257 10.1074/mcp.M115.057257]; GPMDB: [http://gpmdb.org/data/keyword/27067054 12]. | #Drabovich AP, Pavlou MP, Schiza C, Diamandis EP, (2016) "Dynamics of protein expression reveals primary targets and secondary messengers of estrogen receptor alpha signaling in MCF-7 breast cancer cells." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27067054 27067054]; doi: [https://dx.doi.org/10.1074/mcp.M115.057257 10.1074/mcp.M115.057257]; GPMDB: [http://gpmdb.org/data/keyword/27067054 12]. | ||
- | #Osinalde N, Mitxelena J, Sanchez-Quiles V, Akimov V, Aloria K, Arizmendi JM, Zubiaga AM, Blagoev B, Kratchmarova I, (2016) "Nuclear phosphoproteomic screen uncovers ACLY as mediator of IL-2-induced proliferation of CD4+ T-lymphocytes." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27067055 27067055]; doi: [https://dx.doi.org/10.1074/mcp.M115.057158 10.1074/mcp.M115.057158]; GPMDB: [http://gpmdb.org/data/keyword/27067055 | + | #Osinalde N, Mitxelena J, Sanchez-Quiles V, Akimov V, Aloria K, Arizmendi JM, Zubiaga AM, Blagoev B, Kratchmarova I, (2016) "Nuclear phosphoproteomic screen uncovers ACLY as mediator of IL-2-induced proliferation of CD4+ T-lymphocytes." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27067055 27067055]; doi: [https://dx.doi.org/10.1074/mcp.M115.057158 10.1074/mcp.M115.057158]; GPMDB: [http://gpmdb.org/data/keyword/27067055 19]. |
#Xu B, Tian R, Wang X, Zhan S, Wang R, Guo Y, Ge W, (2016) "Protein profile changes in the frontotemporal lobes in human severe traumatic brain injury." <i>Brain Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27067185 27067185]; doi: [https://dx.doi.org/10.1016/j.brainres.2016.04.008 10.1016/j.brainres.2016.04.008]; GPMDB: [http://gpmdb.org/data/keyword/27067185 20]. | #Xu B, Tian R, Wang X, Zhan S, Wang R, Guo Y, Ge W, (2016) "Protein profile changes in the frontotemporal lobes in human severe traumatic brain injury." <i>Brain Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27067185 27067185]; doi: [https://dx.doi.org/10.1016/j.brainres.2016.04.008 10.1016/j.brainres.2016.04.008]; GPMDB: [http://gpmdb.org/data/keyword/27067185 20]. | ||
#Rider MA, Hurwitz SN, Meckes DG Jr, (2016) "ExtraPEG: A Polyethylene Glycol-Based Method for Enrichment of Extracellular Vesicles." <i>Sci Rep</i> <b>6</b>:23978; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27068479 27068479]; doi: [https://dx.doi.org/10.1038/srep23978 10.1038/srep23978]; GPMDB: [http://gpmdb.org/data/keyword/27068479 3]. | #Rider MA, Hurwitz SN, Meckes DG Jr, (2016) "ExtraPEG: A Polyethylene Glycol-Based Method for Enrichment of Extracellular Vesicles." <i>Sci Rep</i> <b>6</b>:23978; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27068479 27068479]; doi: [https://dx.doi.org/10.1038/srep23978 10.1038/srep23978]; GPMDB: [http://gpmdb.org/data/keyword/27068479 3]. | ||
#Sarhan AR, Patel TR, Creese AJ, Tomlinson MG, Hellberg C, Heath JK, Hotchin NA, Cunningham DL, (2016) "Regulation of platelet derived growth factor signalling by LAR protein tyrosine phosphatase: a quantitative phosphoproteomics study." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27074791 27074791]; doi: [https://dx.doi.org/10.1074/mcp.M115.053652 10.1074/mcp.M115.053652]; GPMDB: [http://gpmdb.org/data/keyword/27074791 17]. | #Sarhan AR, Patel TR, Creese AJ, Tomlinson MG, Hellberg C, Heath JK, Hotchin NA, Cunningham DL, (2016) "Regulation of platelet derived growth factor signalling by LAR protein tyrosine phosphatase: a quantitative phosphoproteomics study." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27074791 27074791]; doi: [https://dx.doi.org/10.1074/mcp.M115.053652 10.1074/mcp.M115.053652]; GPMDB: [http://gpmdb.org/data/keyword/27074791 17]. | ||
+ | #Lochmatter C, Fischer R, Charles PD, Yu Z, Powrie F, Kessler BM, (2016) "Integrative Phosphoproteomics Links IL-23R Signaling with Metabolic Adaptation in Lymphocytes." <i>Sci Rep</i> <b>6</b>:24491; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27080861 27080861]; doi: [https://dx.doi.org/10.1038/srep24491 10.1038/srep24491]; GPMDB: [http://gpmdb.org/data/keyword/27080861 7]. | ||
#Arts IS, Vertommen D, Baldin F, Laloux G, Collet JF, (2016) "Comprehensively characterizing the thioredoxin interactome in vivo highlights the central role played by this ubiquitous oxidoreductase in redox control." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27081212 27081212]; doi: [https://dx.doi.org/10.1074/mcp.M115.056440 10.1074/mcp.M115.056440]; GPMDB: [http://gpmdb.org/data/keyword/27081212 103]. | #Arts IS, Vertommen D, Baldin F, Laloux G, Collet JF, (2016) "Comprehensively characterizing the thioredoxin interactome in vivo highlights the central role played by this ubiquitous oxidoreductase in redox control." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27081212 27081212]; doi: [https://dx.doi.org/10.1074/mcp.M115.056440 10.1074/mcp.M115.056440]; GPMDB: [http://gpmdb.org/data/keyword/27081212 103]. | ||
- | #Tape CJ, Ling S, Dimitriadi M, McMahon KM, Worboys JD, Leong HS, Norrie IC, Miller CJ, Poulogiannis G, Lauffenburger DA, Jørgensen C, (2016) "Oncogenic KRAS Regulates Tumor Cell Signaling via Stromal Reciprocation." <i>Cell</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27087446 27087446]; doi: [https://dx.doi.org/10.1016/j.cell.2016.03.029 10.1016/j.cell.2016.03.029]; GPMDB: [http://gpmdb.org/data/keyword/27087446 | + | #Tape CJ, Ling S, Dimitriadi M, McMahon KM, Worboys JD, Leong HS, Norrie IC, Miller CJ, Poulogiannis G, Lauffenburger DA, Jørgensen C, (2016) "Oncogenic KRAS Regulates Tumor Cell Signaling via Stromal Reciprocation." <i>Cell</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27087446 27087446]; doi: [https://dx.doi.org/10.1016/j.cell.2016.03.029 10.1016/j.cell.2016.03.029]; GPMDB: [http://gpmdb.org/data/keyword/27087446 374]. |
+ | #Aasebø E, Mjaavatten O, Vaudel M, Farag Y, Selheim F, Berven F, Bruserud Ø, Hernandez-Valladares M, (2016) "Freezing effects on the acute myeloid leukemia cell proteome and phosphoproteome revealed using optimal quantitative workflows." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27107777 27107777]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.03.049 10.1016/j.jprot.2016.03.049]; GPMDB: [http://gpmdb.org/data/keyword/27107777 163]. | ||
+ | #Larance M, Kirkwood KJ, Tinti M, Murillo AB, Ferguson MA, Lamond AI, (2016) "Global Membrane Protein Interactome Analysis using In vivo Crosslinking and MS-based Protein Correlation Profiling." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27114452 27114452]; doi: [https://dx.doi.org/10.1074/mcp.O115.055467 10.1074/mcp.O115.055467]; GPMDB: [http://gpmdb.org/data/keyword/27114452 4]. |
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 pass our internal automated quality control tests for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
The following is a 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 May 1, 2016.