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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 May | + | 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 22, 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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#Schlage P, Egli FE, Nanni P, Wang LW, Kizhakkedathu JN, Apte SS, auf dem Keller U, (2014) "Time-resolved analysis of the matrix metalloproteinase 10 substrate degradome." <i>Mol Cell Proteomics</i> <b>13</b>(2):580–93; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24281761 24281761]; doi: [https://dx.doi.org/10.1074/mcp.M113.035139 10.1074/mcp.M113.035139]; GPMDB: [http://gpmdb.org/data/keyword/24281761 34]. | #Schlage P, Egli FE, Nanni P, Wang LW, Kizhakkedathu JN, Apte SS, auf dem Keller U, (2014) "Time-resolved analysis of the matrix metalloproteinase 10 substrate degradome." <i>Mol Cell Proteomics</i> <b>13</b>(2):580–93; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24281761 24281761]; doi: [https://dx.doi.org/10.1074/mcp.M113.035139 10.1074/mcp.M113.035139]; GPMDB: [http://gpmdb.org/data/keyword/24281761 34]. | ||
#Aquino PF, Lima DB, de Saldanha da Gama Fischer J, Melani RD, Nogueira FC, Chalub SR, Soares ER, Barbosa VC, Domont GB, Carvalho PC, (2014) "Exploring the proteomic landscape of a gastric cancer biopsy with the shotgun imaging analyzer." <i>J Proteome Res</i> <b>13</b>(1):314–20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24283986 24283986]; doi: [https://dx.doi.org/10.1021/pr400919k 10.1021/pr400919k]; GPMDB: [http://gpmdb.org/data/keyword/24283986 152]. | #Aquino PF, Lima DB, de Saldanha da Gama Fischer J, Melani RD, Nogueira FC, Chalub SR, Soares ER, Barbosa VC, Domont GB, Carvalho PC, (2014) "Exploring the proteomic landscape of a gastric cancer biopsy with the shotgun imaging analyzer." <i>J Proteome Res</i> <b>13</b>(1):314–20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24283986 24283986]; doi: [https://dx.doi.org/10.1021/pr400919k 10.1021/pr400919k]; GPMDB: [http://gpmdb.org/data/keyword/24283986 152]. | ||
+ | #Nensa FM, Neumann MH, Schrötter A, Przyborski A, Mastalski T, Susdalzew S, Looβe C, Helling S, El Magraoui F, Erdmann R, Meyer HE, Uszkoreit J, Eisenacher M, Suh J, Guénette SY, Röhner N, Kögel D, Theiss C, Marcus K, Müller T, (2014) "Amyloid beta a4 precursor protein-binding family B member 1 (FE65) interactomics revealed synaptic vesicle glycoprotein 2A (SV2A) and sarcoplasmic/endoplasmic reticulum calcium ATPase 2 (SERCA2) as new binding proteins in the human brain." <i>Mol Cell Proteomics</i> <b>13</b>(2):475–88; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24284412 24284412]; doi: [https://dx.doi.org/10.1074/mcp.M113.029280 10.1074/mcp.M113.029280]; GPMDB: [http://gpmdb.org/data/keyword/24284412 60]. | ||
#Jüschke C, Dohnal I, Pichler P, Harzer H, Swart R, Ammerer G, Mechtler K, Knoblich JA, (2013) "Transcriptome and proteome quantification of a tumor model provides novel insights into post-transcriptional gene regulation." <i>Genome Biol</i> <b>14</b>(11):r133; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24289286 24289286]; doi: [https://dx.doi.org/10.1186/gb-2013-14-11-r133 10.1186/gb-2013-14-11-r133]; GPMDB: [http://gpmdb.org/data/keyword/24289286 203]. | #Jüschke C, Dohnal I, Pichler P, Harzer H, Swart R, Ammerer G, Mechtler K, Knoblich JA, (2013) "Transcriptome and proteome quantification of a tumor model provides novel insights into post-transcriptional gene regulation." <i>Genome Biol</i> <b>14</b>(11):r133; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24289286 24289286]; doi: [https://dx.doi.org/10.1186/gb-2013-14-11-r133 10.1186/gb-2013-14-11-r133]; GPMDB: [http://gpmdb.org/data/keyword/24289286 203]. | ||
#Wang C, Weerapana E, Blewett MM, Cravatt BF, (2014) "A chemoproteomic platform to quantitatively map targets of lipid-derived electrophiles." <i>Nat Methods</i> <b>11</b>(1):79–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24292485 24292485]; doi: [https://dx.doi.org/10.1038/nmeth.2759 10.1038/nmeth.2759]; GPMDB: [http://gpmdb.org/data/keyword/24292485 180]. | #Wang C, Weerapana E, Blewett MM, Cravatt BF, (2014) "A chemoproteomic platform to quantitatively map targets of lipid-derived electrophiles." <i>Nat Methods</i> <b>11</b>(1):79–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24292485 24292485]; doi: [https://dx.doi.org/10.1038/nmeth.2759 10.1038/nmeth.2759]; GPMDB: [http://gpmdb.org/data/keyword/24292485 180]. | ||
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#Nyström A, Thriene K, Mittapalli V, Kern JS, Kiritsi D, Dengjel J, Bruckner-Tuderman L, (2015) "Losartan ameliorates dystrophic epidermolysis bullosa and uncovers new disease mechanisms." <i>EMBO Mol Med</i> <b>7</b>(9):1211–28; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26194911 26194911]; doi: [https://dx.doi.org/10.15252/emmm.201505061 10.15252/emmm.201505061]; GPMDB: [http://gpmdb.org/data/keyword/26194911 110]. | #Nyström A, Thriene K, Mittapalli V, Kern JS, Kiritsi D, Dengjel J, Bruckner-Tuderman L, (2015) "Losartan ameliorates dystrophic epidermolysis bullosa and uncovers new disease mechanisms." <i>EMBO Mol Med</i> <b>7</b>(9):1211–28; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26194911 26194911]; doi: [https://dx.doi.org/10.15252/emmm.201505061 10.15252/emmm.201505061]; GPMDB: [http://gpmdb.org/data/keyword/26194911 110]. | ||
#Zheng B, Zhao D, Zhang P, Shen C, Guo Y, Zhou T, Guo X, Zhou Z, Sha J, (2015) "Quantitative Proteomics Reveals the Essential Roles of Stromal Interaction Molecule 1 (STIM1) in the Testicular Cord Formation in Mouse Testis." <i>Mol Cell Proteomics</i> <b>14</b>(10):2682–91; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26199344 26199344]; doi: [https://dx.doi.org/10.1074/mcp.M115.049569 10.1074/mcp.M115.049569]; GPMDB: [http://gpmdb.org/data/keyword/26199344 2]. | #Zheng B, Zhao D, Zhang P, Shen C, Guo Y, Zhou T, Guo X, Zhou Z, Sha J, (2015) "Quantitative Proteomics Reveals the Essential Roles of Stromal Interaction Molecule 1 (STIM1) in the Testicular Cord Formation in Mouse Testis." <i>Mol Cell Proteomics</i> <b>14</b>(10):2682–91; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26199344 26199344]; doi: [https://dx.doi.org/10.1074/mcp.M115.049569 10.1074/mcp.M115.049569]; GPMDB: [http://gpmdb.org/data/keyword/26199344 2]. | ||
+ | #Wang IX, Ramrattan G, Cheung VG, (2015) "Genetic variation in insulin-induced kinase signaling." <i>Mol Syst Biol</i> <b>11</b>(7):820; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26202599 26202599]; GPMDB: [http://gpmdb.org/data/keyword/26202599 46]. | ||
#Courtney DG, Poulsen ET, Kennedy S, Moore JE, Atkinson SD, Maurizi E, Nesbit MA, Moore CB, Enghild JJ, (2015) "Protein Composition of TGFBI-R124C- and TGFBI-R555W-Associated Aggregates Suggests Multiple Mechanisms Leading to Lattice and Granular Corneal Dystrophy." <i>Invest Ophthalmol Vis Sci</i> <b>56</b>(8):4653–61; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26207300 26207300]; doi: [https://dx.doi.org/10.1167/iovs.15-16922 10.1167/iovs.15-16922]; GPMDB: [http://gpmdb.org/data/keyword/26207300 39]. | #Courtney DG, Poulsen ET, Kennedy S, Moore JE, Atkinson SD, Maurizi E, Nesbit MA, Moore CB, Enghild JJ, (2015) "Protein Composition of TGFBI-R124C- and TGFBI-R555W-Associated Aggregates Suggests Multiple Mechanisms Leading to Lattice and Granular Corneal Dystrophy." <i>Invest Ophthalmol Vis Sci</i> <b>56</b>(8):4653–61; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26207300 26207300]; doi: [https://dx.doi.org/10.1167/iovs.15-16922 10.1167/iovs.15-16922]; GPMDB: [http://gpmdb.org/data/keyword/26207300 39]. | ||
#Díez P, Droste C, Dégano RM, González-Muñoz M, Ibarrola N, Pérez-Andrés M, Garin-Muga A, Segura V, Marko-Varga G, LaBaer J, Orfao A, Corrales FJ, De Las Rivas J, Fuentes M, (2015) "Integration of Proteomics and Transcriptomics Data Sets for the Analysis of a Lymphoma B-Cell Line in the Context of the Chromosome-Centric Human Proteome Project." <i>J Proteome Res</i> <b>14</b>(9):3530–40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26216070 26216070]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00474 10.1021/acs.jproteome.5b00474]; GPMDB: [http://gpmdb.org/data/keyword/26216070 60]. | #Díez P, Droste C, Dégano RM, González-Muñoz M, Ibarrola N, Pérez-Andrés M, Garin-Muga A, Segura V, Marko-Varga G, LaBaer J, Orfao A, Corrales FJ, De Las Rivas J, Fuentes M, (2015) "Integration of Proteomics and Transcriptomics Data Sets for the Analysis of a Lymphoma B-Cell Line in the Context of the Chromosome-Centric Human Proteome Project." <i>J Proteome Res</i> <b>14</b>(9):3530–40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26216070 26216070]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00474 10.1021/acs.jproteome.5b00474]; GPMDB: [http://gpmdb.org/data/keyword/26216070 60]. | ||
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#Vincent D, Ezernieks V, Elkins A, Nguyen N, Moate PJ, Cocks BG, Rochfort S, (2015) "Milk Bottom-Up Proteomics: Method Optimization." <i>Front Genet</i> <b>6</b>:360; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26793233 26793233]; doi: [https://dx.doi.org/10.3389/fgene.2015.00360 10.3389/fgene.2015.00360]; GPMDB: [http://gpmdb.org/data/keyword/26793233 262]. | #Vincent D, Ezernieks V, Elkins A, Nguyen N, Moate PJ, Cocks BG, Rochfort S, (2015) "Milk Bottom-Up Proteomics: Method Optimization." <i>Front Genet</i> <b>6</b>:360; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26793233 26793233]; doi: [https://dx.doi.org/10.3389/fgene.2015.00360 10.3389/fgene.2015.00360]; GPMDB: [http://gpmdb.org/data/keyword/26793233 262]. | ||
#Li Q, Lex RK, Chung H, Giovanetti SM, Ji Z, Ji H, Person MD, Kim J, Vokes SA, (2016) "The Pluripotency Factor NANOG Binds to GLI Proteins and Represses Hedgehog-mediated Transcription." <i>J Biol Chem</i> <b>291</b>(13):7171–82; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26797124 26797124]; doi: [https://dx.doi.org/10.1074/jbc.M116.714857 10.1074/jbc.M116.714857]; GPMDB: [http://gpmdb.org/data/keyword/26797124 10]. | #Li Q, Lex RK, Chung H, Giovanetti SM, Ji Z, Ji H, Person MD, Kim J, Vokes SA, (2016) "The Pluripotency Factor NANOG Binds to GLI Proteins and Represses Hedgehog-mediated Transcription." <i>J Biol Chem</i> <b>291</b>(13):7171–82; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26797124 26797124]; doi: [https://dx.doi.org/10.1074/jbc.M116.714857 10.1074/jbc.M116.714857]; GPMDB: [http://gpmdb.org/data/keyword/26797124 10]. | ||
- | #Schüller R, Forné I, Straub T, Schreieck A, Texier Y, Shah N, Decker TM, Cramer P, Imhof A, Eick D, (2016) "Heptad-Specific Phosphorylation of RNA Polymerase | + | #Schüller R, Forné I, Straub T, Schreieck A, Texier Y, Shah N, Decker TM, Cramer P, Imhof A, Eick D, (2016) "Heptad-Specific Phosphorylation of RNA Polymerase II CTD." <i>Mol Cell</i> <b>61</b>(2):305–14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26799765 26799765]; doi: [https://dx.doi.org/10.1016/j.molcel.2015.12.003 10.1016/j.molcel.2015.12.003]; GPMDB: [http://gpmdb.org/data/keyword/26799765 209]. |
#Wojtuszkiewicz A, Schuurhuis GJ, Kessler FL, Piersma SR, Knol JC, Pham TV, Jansen G, Musters RJ, van Meerloo J, Assaraf YG, Kaspers GJ, Zweegman S, Cloos J, Jimenez CR, (2016) "Exosomes Secreted by Apoptosis-Resistant Acute Myeloid Leukemia (AML) Blasts Harbor Regulatory Network Proteins Potentially Involved in Antagonism of Apoptosis." <i>Mol Cell Proteomics</i> <b>15</b>(4):1281–98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26801919 26801919]; doi: [https://dx.doi.org/10.1074/mcp.M115.052944 10.1074/mcp.M115.052944]; GPMDB: [http://gpmdb.org/data/keyword/26801919 271]. | #Wojtuszkiewicz A, Schuurhuis GJ, Kessler FL, Piersma SR, Knol JC, Pham TV, Jansen G, Musters RJ, van Meerloo J, Assaraf YG, Kaspers GJ, Zweegman S, Cloos J, Jimenez CR, (2016) "Exosomes Secreted by Apoptosis-Resistant Acute Myeloid Leukemia (AML) Blasts Harbor Regulatory Network Proteins Potentially Involved in Antagonism of Apoptosis." <i>Mol Cell Proteomics</i> <b>15</b>(4):1281–98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26801919 26801919]; doi: [https://dx.doi.org/10.1074/mcp.M115.052944 10.1074/mcp.M115.052944]; GPMDB: [http://gpmdb.org/data/keyword/26801919 271]. | ||
#Serra A, Zhu H, Gallart-Palau X, Park JE, Ho HH, Tam JP, Sze SK, (2016) "Plasma proteome coverage is increased by unique peptide recovery from sodium deoxycholate precipitate." <i>Anal Bioanal Chem</i> <b>408</b>(7):1963–73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26804737 26804737]; doi: [https://dx.doi.org/10.1007/s00216-016-9312-7 10.1007/s00216-016-9312-7]; GPMDB: [http://gpmdb.org/data/keyword/26804737 40]. | #Serra A, Zhu H, Gallart-Palau X, Park JE, Ho HH, Tam JP, Sze SK, (2016) "Plasma proteome coverage is increased by unique peptide recovery from sodium deoxycholate precipitate." <i>Anal Bioanal Chem</i> <b>408</b>(7):1963–73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26804737 26804737]; doi: [https://dx.doi.org/10.1007/s00216-016-9312-7 10.1007/s00216-016-9312-7]; GPMDB: [http://gpmdb.org/data/keyword/26804737 40]. | ||
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#Sahebekhtiari N, Thomsen MM, Sloth JJ, Stenbroen V, Zeviani M, Gregersen N, Viscomi C, Palmfeldt J, (2016) "Quantitative proteomics suggests metabolic reprogramming during ETHE1 deficiency." <i>Proteomics</i> <b>16</b>(7):1166–76; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26867521 26867521]; doi: [https://dx.doi.org/10.1002/pmic.201500336 10.1002/pmic.201500336]; GPMDB: [http://gpmdb.org/data/keyword/26867521 50]. | #Sahebekhtiari N, Thomsen MM, Sloth JJ, Stenbroen V, Zeviani M, Gregersen N, Viscomi C, Palmfeldt J, (2016) "Quantitative proteomics suggests metabolic reprogramming during ETHE1 deficiency." <i>Proteomics</i> <b>16</b>(7):1166–76; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26867521 26867521]; doi: [https://dx.doi.org/10.1002/pmic.201500336 10.1002/pmic.201500336]; GPMDB: [http://gpmdb.org/data/keyword/26867521 50]. | ||
#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> <b>33</b>(6):1461–77; 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]. |
#Creedon H, Gómez-Cuadrado L, Tarnauskaitė Ž, Balla J, Canel M, MacLeod KG, Serrels B, Fraser C, Unciti-Broceta A, Tracey N, Le Bihan T, Klinowska T, Sims AH, Byron A, Brunton VG, (2016) "Identification of novel pathways linking epithelial-to-mesenchymal transition with resistance to HER2-targeted therapy." <i>Oncotarget</i> <b>7</b>(10):11539–52; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26883193 26883193]; doi: [https://dx.doi.org/10.18632/oncotarget.7317 10.18632/oncotarget.7317]; GPMDB: [http://gpmdb.org/data/keyword/26883193 6]. | #Creedon H, Gómez-Cuadrado L, Tarnauskaitė Ž, Balla J, Canel M, MacLeod KG, Serrels B, Fraser C, Unciti-Broceta A, Tracey N, Le Bihan T, Klinowska T, Sims AH, Byron A, Brunton VG, (2016) "Identification of novel pathways linking epithelial-to-mesenchymal transition with resistance to HER2-targeted therapy." <i>Oncotarget</i> <b>7</b>(10):11539–52; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26883193 26883193]; doi: [https://dx.doi.org/10.18632/oncotarget.7317 10.18632/oncotarget.7317]; GPMDB: [http://gpmdb.org/data/keyword/26883193 6]. | ||
#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]. | ||
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#Sieber J, Hauer C, Bhuvanagiri M, Leicht S, Krijgsveld J, Neu-Yilik G, Hentze MW, Kulozik AE, (2016) "Proteomic Analysis Reveals Branch-specific Regulation of the Unfolded Protein Response by Nonsense-mediated mRNA Decay." <i>Mol Cell Proteomics</i> <b>15</b>(5):1584–97; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26896796 26896796]; doi: [https://dx.doi.org/10.1074/mcp.M115.054056 10.1074/mcp.M115.054056]; GPMDB: [http://gpmdb.org/data/keyword/26896796 4]. | #Sieber J, Hauer C, Bhuvanagiri M, Leicht S, Krijgsveld J, Neu-Yilik G, Hentze MW, Kulozik AE, (2016) "Proteomic Analysis Reveals Branch-specific Regulation of the Unfolded Protein Response by Nonsense-mediated mRNA Decay." <i>Mol Cell Proteomics</i> <b>15</b>(5):1584–97; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26896796 26896796]; doi: [https://dx.doi.org/10.1074/mcp.M115.054056 10.1074/mcp.M115.054056]; GPMDB: [http://gpmdb.org/data/keyword/26896796 4]. | ||
#Zilkenat S, Franz-Wachtel M, Stierhof YD, Galán JE, Macek B, Wagner S, (2016) "Determination of the Stoichiometry of the Complete Bacterial Type III Secretion Needle Complex Using a Combined Quantitative Proteomic Approach." <i>Mol Cell Proteomics</i> <b>15</b>(5):1598–609; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26900162 26900162]; doi: [https://dx.doi.org/10.1074/mcp.M115.056598 10.1074/mcp.M115.056598]; GPMDB: [http://gpmdb.org/data/keyword/26900162 18]. | #Zilkenat S, Franz-Wachtel M, Stierhof YD, Galán JE, Macek B, Wagner S, (2016) "Determination of the Stoichiometry of the Complete Bacterial Type III Secretion Needle Complex Using a Combined Quantitative Proteomic Approach." <i>Mol Cell Proteomics</i> <b>15</b>(5):1598–609; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26900162 26900162]; doi: [https://dx.doi.org/10.1074/mcp.M115.056598 10.1074/mcp.M115.056598]; GPMDB: [http://gpmdb.org/data/keyword/26900162 18]. | ||
- | #Zhao L, Chen Y, Bajaj AO, Eblimit A, Xu M, Soens ZT, Wang F, Ge Z, Jung SY, He F, Li Y, Wensel TG, Qin J, Chen R, (2016) "Integrative subcellular proteomic analysis allows accurate prediction of human disease-causing genes." <i>Genome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26912414 26912414]; doi: [https://dx.doi.org/10.1101/gr.198911.115 10.1101/gr.198911.115]; GPMDB: [http://gpmdb.org/data/keyword/26912414 26]. | + | #Zhao L, Chen Y, Bajaj AO, Eblimit A, Xu M, Soens ZT, Wang F, Ge Z, Jung SY, He F, Li Y, Wensel TG, Qin J, Chen R, (2016) "Integrative subcellular proteomic analysis allows accurate prediction of human disease-causing genes." <i>Genome Res</i> <b>26</b>(5):660–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26912414 26912414]; doi: [https://dx.doi.org/10.1101/gr.198911.115 10.1101/gr.198911.115]; GPMDB: [http://gpmdb.org/data/keyword/26912414 26]. |
#Abelin JG, Patel J, Lu X, Feeney CM, Fagbami L, Creech AL, Hu R, Lam D, Davison D, Pino L, Qiao JW, Kuhn E, Officer A, Li J, Abbatiello S, Subramanian A, Sidman R, Snyder E, Carr SA, Jaffe JD, (2016) "Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes." <i>Mol Cell Proteomics</i> <b>15</b>(5):1622–41; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26912667 26912667]; doi: [https://dx.doi.org/10.1074/mcp.M116.058354 10.1074/mcp.M116.058354]; GPMDB: [http://gpmdb.org/data/keyword/26912667 4]. | #Abelin JG, Patel J, Lu X, Feeney CM, Fagbami L, Creech AL, Hu R, Lam D, Davison D, Pino L, Qiao JW, Kuhn E, Officer A, Li J, Abbatiello S, Subramanian A, Sidman R, Snyder E, Carr SA, Jaffe JD, (2016) "Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes." <i>Mol Cell Proteomics</i> <b>15</b>(5):1622–41; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26912667 26912667]; doi: [https://dx.doi.org/10.1074/mcp.M116.058354 10.1074/mcp.M116.058354]; GPMDB: [http://gpmdb.org/data/keyword/26912667 4]. | ||
#Chen JX, Cipriani PG, Mecenas D, Polanowska J, Piano F, Gunsalus KC, Selbach M, (2016) "In Vivo Interaction Proteomics in Caenorhabditis elegans Embryos Provides New Insights into P Granule Dynamics." <i>Mol Cell Proteomics</i> <b>15</b>(5):1642–57; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26912668 26912668]; doi: [https://dx.doi.org/10.1074/mcp.M115.053975 10.1074/mcp.M115.053975]; GPMDB: [http://gpmdb.org/data/keyword/26912668 66]. | #Chen JX, Cipriani PG, Mecenas D, Polanowska J, Piano F, Gunsalus KC, Selbach M, (2016) "In Vivo Interaction Proteomics in Caenorhabditis elegans Embryos Provides New Insights into P Granule Dynamics." <i>Mol Cell Proteomics</i> <b>15</b>(5):1642–57; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26912668 26912668]; doi: [https://dx.doi.org/10.1074/mcp.M115.053975 10.1074/mcp.M115.053975]; GPMDB: [http://gpmdb.org/data/keyword/26912668 66]. | ||
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#Wilson MC, Trakarnsanga K, Heesom KJ, Cogan N, Green C, Toye AM, Parsons SF, Ansteee DJ, Frayne J, (2016) "Comparison of the proteome of adult and cord erythroid cells, and changes in the proteome following reticulocyte maturation." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27006477 27006477]; doi: [https://dx.doi.org/10.1074/mcp.M115.057315 10.1074/mcp.M115.057315]; GPMDB: [http://gpmdb.org/data/keyword/27006477 2]. | #Wilson MC, Trakarnsanga K, Heesom KJ, Cogan N, Green C, Toye AM, Parsons SF, Ansteee DJ, Frayne J, (2016) "Comparison of the proteome of adult and cord erythroid cells, and changes in the proteome following reticulocyte maturation." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27006477 27006477]; doi: [https://dx.doi.org/10.1074/mcp.M115.057315 10.1074/mcp.M115.057315]; GPMDB: [http://gpmdb.org/data/keyword/27006477 2]. | ||
#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> <b>203</b>(1):353–68; 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]. |
#Lawrence RT, Searle BC, Llovet A, Villén J, (2016) "Plug-and-play analysis of the human phosphoproteome by targeted high-resolution mass spectrometry." <i>Nat Methods</i> <b>13</b>(5):431–4; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27018578 27018578]; doi: [https://dx.doi.org/10.1038/nmeth.3811 10.1038/nmeth.3811]; GPMDB: [http://gpmdb.org/data/keyword/27018578 6]. | #Lawrence RT, Searle BC, Llovet A, Villén J, (2016) "Plug-and-play analysis of the human phosphoproteome by targeted high-resolution mass spectrometry." <i>Nat Methods</i> <b>13</b>(5):431–4; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27018578 27018578]; doi: [https://dx.doi.org/10.1038/nmeth.3811 10.1038/nmeth.3811]; GPMDB: [http://gpmdb.org/data/keyword/27018578 6]. | ||
#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]. | ||
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#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]. | ||
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#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]. | #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> <b>165</b>(4):910–20; 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]. | #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> <b>165</b>(4):910–20; 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]. | ||
- | #Stoehr A, Yang Y, Patel S, Evangelista AM, Aponte A, Wang G, Liu P, Boylston J, Kloner PH, Lin Y, Gucek M, Zhu J, Murphy E, (2016) "Prolyl hydroxylation regulates protein degradation, synthesis and splicing in human induced pluripotent stem cell-derived cardiomyocytes." <i>Cardiovasc Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27095734 27095734]; doi: [https://dx.doi.org/10.1093/cvr/cvw081 10.1093/cvr/cvw081]; GPMDB: [http://gpmdb.org/data/keyword/27095734 12]. | + | #Stoehr A, Yang Y, Patel S, Evangelista AM, Aponte A, Wang G, Liu P, Boylston J, Kloner PH, Lin Y, Gucek M, Zhu J, Murphy E, (2016) "Prolyl hydroxylation regulates protein degradation, synthesis, and splicing in human induced pluripotent stem cell-derived cardiomyocytes." <i>Cardiovasc Res</i> <b>110</b>(3):346–58; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27095734 27095734]; doi: [https://dx.doi.org/10.1093/cvr/cvw081 10.1093/cvr/cvw081]; GPMDB: [http://gpmdb.org/data/keyword/27095734 12]. |
#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]. | #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 396]. | #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 396]. | ||
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#Ulrich V, Rotllan N, Araldi E, Luciano A, Skroblin P, Abonnenc M, Perrotta P, Yin X, Bauer A, Leslie KL, Zhang P, Aryal B, Montgomery RL, Thum T, Martin K, Suarez Y, Mayr M, Fernandez-Hernando C, Sessa WC, (2016) "Chronic miR-29 antagonism promotes favorable plaque remodeling in atherosclerotic mice." <i>EMBO Mol Med</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27137489 27137489]; doi: [https://dx.doi.org/10.15252/emmm.201506031 10.15252/emmm.201506031]; GPMDB: [http://gpmdb.org/data/keyword/27137489 120]. | #Ulrich V, Rotllan N, Araldi E, Luciano A, Skroblin P, Abonnenc M, Perrotta P, Yin X, Bauer A, Leslie KL, Zhang P, Aryal B, Montgomery RL, Thum T, Martin K, Suarez Y, Mayr M, Fernandez-Hernando C, Sessa WC, (2016) "Chronic miR-29 antagonism promotes favorable plaque remodeling in atherosclerotic mice." <i>EMBO Mol Med</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27137489 27137489]; doi: [https://dx.doi.org/10.15252/emmm.201506031 10.15252/emmm.201506031]; GPMDB: [http://gpmdb.org/data/keyword/27137489 120]. | ||
#Zielke RA, Wierzbicki IH, Baarda BI, Gafken PR, Soge OO, Holmes KK, Jerse AE, Unemo M, Sikora AE, (2016) "Proteomics-driven antigen discovery for development of vaccines against gonorrhea." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27141096 27141096]; doi: [https://dx.doi.org/10.1074/mcp.M116.058800 10.1074/mcp.M116.058800]; GPMDB: [http://gpmdb.org/data/keyword/27141096 3]. | #Zielke RA, Wierzbicki IH, Baarda BI, Gafken PR, Soge OO, Holmes KK, Jerse AE, Unemo M, Sikora AE, (2016) "Proteomics-driven antigen discovery for development of vaccines against gonorrhea." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27141096 27141096]; doi: [https://dx.doi.org/10.1074/mcp.M116.058800 10.1074/mcp.M116.058800]; GPMDB: [http://gpmdb.org/data/keyword/27141096 3]. | ||
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+ | #Kempf SJ, Metaxas A, Ibáñez-Vea M, Darvesh S, Finsen B, Larsen MR, (2016) "An integrated proteomics approach shows synaptic plasticity changes in an APP/PS1 Alzheimer's mouse model." <i>Oncotarget</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27144524 27144524]; doi: [https://dx.doi.org/10.18632/oncotarget.9092 10.18632/oncotarget.9092]; GPMDB: [http://gpmdb.org/data/keyword/27144524 104]. | ||
#Dørum S, Steinsbø Ø, Bergseng E, Arntzen MØ, de Souza GA, Sollid LM, (2016) "Gluten-specific antibodies of celiac disease gut plasma cells recognize long proteolytic fragments that typically harbor T-cell epitopes." <i>Sci Rep</i> <b>6</b>:25565; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27146306 27146306]; doi: [https://dx.doi.org/10.1038/srep25565 10.1038/srep25565]; GPMDB: [http://gpmdb.org/data/keyword/27146306 27]. | #Dørum S, Steinsbø Ø, Bergseng E, Arntzen MØ, de Souza GA, Sollid LM, (2016) "Gluten-specific antibodies of celiac disease gut plasma cells recognize long proteolytic fragments that typically harbor T-cell epitopes." <i>Sci Rep</i> <b>6</b>:25565; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27146306 27146306]; doi: [https://dx.doi.org/10.1038/srep25565 10.1038/srep25565]; GPMDB: [http://gpmdb.org/data/keyword/27146306 27]. | ||
#Jhingan GD, Kumari S, Jamwal SV, Kalam H, Arora D, Jain N, KrishnaKumaar L, Samal A, Rao KV, Kumar D, Nandicoori VK, (2016) "Comparative proteomic analyses of avirulent, virulent and clinical strains of Mycobacterium tuberculosis identifies strain-specific patterns." <i>J Biol Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27151218 27151218]; doi: [https://dx.doi.org/10.1074/jbc.M115.666123 10.1074/jbc.M115.666123]; GPMDB: [http://gpmdb.org/data/keyword/27151218 16]. | #Jhingan GD, Kumari S, Jamwal SV, Kalam H, Arora D, Jain N, KrishnaKumaar L, Samal A, Rao KV, Kumar D, Nandicoori VK, (2016) "Comparative proteomic analyses of avirulent, virulent and clinical strains of Mycobacterium tuberculosis identifies strain-specific patterns." <i>J Biol Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27151218 27151218]; doi: [https://dx.doi.org/10.1074/jbc.M115.666123 10.1074/jbc.M115.666123]; GPMDB: [http://gpmdb.org/data/keyword/27151218 16]. | ||
+ | #Hsu CH, Hsu CW, Hsueh C, Wang CL, Wu YC, Wu CC, Liu CC, Yu JS, Chang YS, Yu CJ, (2016) "Identification and characterization of potential biomarkers by quantitative tissue proteomics of primary lung adenocarcinoma." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27161446 27161446]; doi: [https://dx.doi.org/10.1074/mcp.M115.057026 10.1074/mcp.M115.057026]; GPMDB: [http://gpmdb.org/data/keyword/27161446 60]. | ||
+ | #Taha MK, Claus H, Lappann M, Veyrier FJ, Otto A, Becher D, Deghmane AE, Frosch M, Hellenbrand W, Hong E, Parent du Châtelet I, Prior K, Harmsen D, Vogel U, (2016) "Evolutionary Events Associated with an Outbreak of Meningococcal Disease in Men Who Have Sex with Men." <i>PLoS One</i> <b>11</b>(5):e0154047; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27167067 27167067]; doi: [https://dx.doi.org/10.1371/journal.pone.0154047 10.1371/journal.pone.0154047]; GPMDB: [http://gpmdb.org/data/keyword/27167067 12]. | ||
+ | #Tuveng TR, Arntzen MØ, Bengtsson O, Gardner JG, Vaaje-Kolstad G, Eijsink VG, (2016) "Proteomic investigation of the secretome of cellvibrio japonicus during growth on chitin." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27169553 27169553]; doi: [https://dx.doi.org/10.1002/pmic.201500419 10.1002/pmic.201500419]; GPMDB: [http://gpmdb.org/data/keyword/27169553 18]. | ||
+ | #Rao SR, Flores-Rodriguez N, Page SL, Wong C, Robinson PJ, Chircop M, (2016) "The clathrin-dependent spindle proteome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27174698 27174698]; doi: [https://dx.doi.org/10.1074/mcp.M115.054809 10.1074/mcp.M115.054809]; GPMDB: [http://gpmdb.org/data/keyword/27174698 130]. |
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 22, 2016.