Line 825: | Line 825: | ||
#Piersma SR, Knol JC, de Reus I, Labots M, Sampadi BK, Pham TV, Ishihama Y, Verheul HM, Jimenez CR, (2015) "Feasibility of label-free phosphoproteomics and application to base-line signaling of colorectal cancer cell lines." <i>J Proteomics</i> <b>127</b>(Pt B):247–58; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25841592 25841592]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.03.019 10.1016/j.jprot.2015.03.019]; GPMDB: [http://gpmdb.org/data/keyword/25841592 31]. | #Piersma SR, Knol JC, de Reus I, Labots M, Sampadi BK, Pham TV, Ishihama Y, Verheul HM, Jimenez CR, (2015) "Feasibility of label-free phosphoproteomics and application to base-line signaling of colorectal cancer cell lines." <i>J Proteomics</i> <b>127</b>(Pt B):247–58; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25841592 25841592]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.03.019 10.1016/j.jprot.2015.03.019]; GPMDB: [http://gpmdb.org/data/keyword/25841592 31]. | ||
#Krisp C, Yang H, van Soest R, Molloy MP, (2015) "Online Peptide fractionation using a multiphasic microfluidic liquid chromatography chip improves reproducibility and detection limits for quantitation in discovery and targeted proteomics." <i>Mol Cell Proteomics</i> <b>14</b>(6):1708–19; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25850434 25850434]; doi: [https://dx.doi.org/10.1074/mcp.M114.046425 10.1074/mcp.M114.046425]; GPMDB: [http://gpmdb.org/data/keyword/25850434 12]. | #Krisp C, Yang H, van Soest R, Molloy MP, (2015) "Online Peptide fractionation using a multiphasic microfluidic liquid chromatography chip improves reproducibility and detection limits for quantitation in discovery and targeted proteomics." <i>Mol Cell Proteomics</i> <b>14</b>(6):1708–19; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25850434 25850434]; doi: [https://dx.doi.org/10.1074/mcp.M114.046425 10.1074/mcp.M114.046425]; GPMDB: [http://gpmdb.org/data/keyword/25850434 12]. | ||
+ | #Stuart SA, Houel S, Lee T, Wang N, Old WM, Ahn NG, (2015) "A Phosphoproteomic Comparison of B-RAFV600E and MKK1/2 Inhibitors in Melanoma Cells." <i>Mol Cell Proteomics</i> <b>14</b>(6):1599–615; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25850435 25850435]; doi: [https://dx.doi.org/10.1074/mcp.M114.047233 10.1074/mcp.M114.047233]; GPMDB: [http://gpmdb.org/data/keyword/25850435 48]. | ||
#Oberstein A, Perlman DH, Shenk T, Terry LJ, (2015) "Human cytomegalovirus pUL97 kinase induces global changes in the infected cell phosphoproteome." <i>Proteomics</i> <b>15</b>(12):2006–22; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25867546 25867546]; doi: [https://dx.doi.org/10.1002/pmic.201400607 10.1002/pmic.201400607]; GPMDB: [http://gpmdb.org/data/keyword/25867546 8]. | #Oberstein A, Perlman DH, Shenk T, Terry LJ, (2015) "Human cytomegalovirus pUL97 kinase induces global changes in the infected cell phosphoproteome." <i>Proteomics</i> <b>15</b>(12):2006–22; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25867546 25867546]; doi: [https://dx.doi.org/10.1002/pmic.201400607 10.1002/pmic.201400607]; GPMDB: [http://gpmdb.org/data/keyword/25867546 8]. | ||
#Papadopoulos P, Gutiérrez L, Demmers J, Scheer E, Pourfarzad F, Papageorgiou DN, Karkoulia E, Strouboulis J, van de Werken HJ, van der Linden R, Vandenberghe P, Dekkers DH, Philipsen S, Grosveld F, Tora L, (2015) "TAF10 Interacts with the GATA1 Transcription Factor and Controls Mouse Erythropoiesis." <i>Mol Cell Biol</i> <b>35</b>(12):2103–18; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25870109 25870109]; doi: [https://dx.doi.org/10.1128/MCB.01370-14 10.1128/MCB.01370-14]; GPMDB: [http://gpmdb.org/data/keyword/25870109 4]. | #Papadopoulos P, Gutiérrez L, Demmers J, Scheer E, Pourfarzad F, Papageorgiou DN, Karkoulia E, Strouboulis J, van de Werken HJ, van der Linden R, Vandenberghe P, Dekkers DH, Philipsen S, Grosveld F, Tora L, (2015) "TAF10 Interacts with the GATA1 Transcription Factor and Controls Mouse Erythropoiesis." <i>Mol Cell Biol</i> <b>35</b>(12):2103–18; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25870109 25870109]; doi: [https://dx.doi.org/10.1128/MCB.01370-14 10.1128/MCB.01370-14]; GPMDB: [http://gpmdb.org/data/keyword/25870109 4]. | ||
Line 992: | Line 993: | ||
#Su S, Zhu X, Lin L, Chen X, Wang Y, Zi J, Dong Y, Xie Y, Zhu Y, Zhang J, Zhu J, Xu D, Xu N, Lou X, Liu S, (2015) "Lowering endogenous cathepsin D abundance results in ROS accumulation and cell senescence." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26657266 26657266]; doi: [https://dx.doi.org/10.1074/mcp.M115.050179 10.1074/mcp.M115.050179]; GPMDB: [http://gpmdb.org/data/keyword/26657266 154]. | #Su S, Zhu X, Lin L, Chen X, Wang Y, Zi J, Dong Y, Xie Y, Zhu Y, Zhang J, Zhu J, Xu D, Xu N, Lou X, Liu S, (2015) "Lowering endogenous cathepsin D abundance results in ROS accumulation and cell senescence." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26657266 26657266]; doi: [https://dx.doi.org/10.1074/mcp.M115.050179 10.1074/mcp.M115.050179]; GPMDB: [http://gpmdb.org/data/keyword/26657266 154]. | ||
#Chen M, Hu Y, Liu J, Wu Q, Zhang C, Yu J, Xiao J, Wei F, Wu J, (2015) "Improvement of genome assembly completeness and identification of novel full-length protein-coding genes by RNA-seq in the giant panda genome." <i>Sci Rep</i> <b>5</b>:18019; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26658305 26658305]; doi: [https://dx.doi.org/10.1038/srep18019 10.1038/srep18019]; GPMDB: [http://gpmdb.org/data/keyword/26658305 36]. | #Chen M, Hu Y, Liu J, Wu Q, Zhang C, Yu J, Xiao J, Wei F, Wu J, (2015) "Improvement of genome assembly completeness and identification of novel full-length protein-coding genes by RNA-seq in the giant panda genome." <i>Sci Rep</i> <b>5</b>:18019; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26658305 26658305]; doi: [https://dx.doi.org/10.1038/srep18019 10.1038/srep18019]; GPMDB: [http://gpmdb.org/data/keyword/26658305 36]. | ||
- | #Mizuno Y, Nagano-Shoji M, Kubo S, Kawamura Y, Yoshida A, Kawasaki H, Nishiyama M, Yoshida M, Kosono S, ( | + | #Mizuno Y, Nagano-Shoji M, Kubo S, Kawamura Y, Yoshida A, Kawasaki H, Nishiyama M, Yoshida M, Kosono S, (2016) "Altered acetylation and succinylation profiles in Corynebacterium glutamicum in response to conditions inducing glutamate overproduction." <i>Microbiologyopen</i> <b>5</b>(1):152–73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26663479 26663479]; doi: [https://dx.doi.org/10.1002/mbo3.320 10.1002/mbo3.320]; GPMDB: [http://gpmdb.org/data/keyword/26663479 10]. |
#Ulaganathan VK, Sperl B, Rapp UR, Ullrich A, (2015) "Germline variant FGFR4  p.G388R exposes a membrane-proximal STAT3 binding site." <i>Nature</i> <b>528</b>(7583):570–4; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26675719 26675719]; doi: [https://dx.doi.org/10.1038/nature16449 10.1038/nature16449]; GPMDB: [http://gpmdb.org/data/keyword/26675719 32]. | #Ulaganathan VK, Sperl B, Rapp UR, Ullrich A, (2015) "Germline variant FGFR4  p.G388R exposes a membrane-proximal STAT3 binding site." <i>Nature</i> <b>528</b>(7583):570–4; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26675719 26675719]; doi: [https://dx.doi.org/10.1038/nature16449 10.1038/nature16449]; GPMDB: [http://gpmdb.org/data/keyword/26675719 32]. | ||
#Aronica L, Kasparek T, Ruchman D, Marquez Y, Cipak L, Cipakova I, Anrather D, Mikolaskova B, Radtke M, Sarkar S, Pai CC, Blaikley E, Walker C, Shen KF, Schroeder R, Barta A, Forsburg SL, Humphrey TC, (2015) "The spliceosome-associated protein Nrl1 suppresses homologous recombination-dependent R-loop formation in fission yeast." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26682798 26682798]; doi: [https://dx.doi.org/10.1093/nar/gkv1473 10.1093/nar/gkv1473]; GPMDB: [http://gpmdb.org/data/keyword/26682798 4]. | #Aronica L, Kasparek T, Ruchman D, Marquez Y, Cipak L, Cipakova I, Anrather D, Mikolaskova B, Radtke M, Sarkar S, Pai CC, Blaikley E, Walker C, Shen KF, Schroeder R, Barta A, Forsburg SL, Humphrey TC, (2015) "The spliceosome-associated protein Nrl1 suppresses homologous recombination-dependent R-loop formation in fission yeast." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26682798 26682798]; doi: [https://dx.doi.org/10.1093/nar/gkv1473 10.1093/nar/gkv1473]; GPMDB: [http://gpmdb.org/data/keyword/26682798 4]. | ||
Line 1,036: | Line 1,037: | ||
#Coman C, Solari FA, Hentschel A, Sickmann A, Zahedi RP, Ahrends R, (2016) "SIMPLEX: a combinatorial multimolecular omics approach for systems biology." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26814187 26814187]; doi: [https://dx.doi.org/10.1074/mcp.M115.053702 10.1074/mcp.M115.053702]; GPMDB: [http://gpmdb.org/data/keyword/26814187 68]. | #Coman C, Solari FA, Hentschel A, Sickmann A, Zahedi RP, Ahrends R, (2016) "SIMPLEX: a combinatorial multimolecular omics approach for systems biology." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26814187 26814187]; doi: [https://dx.doi.org/10.1074/mcp.M115.053702 10.1074/mcp.M115.053702]; GPMDB: [http://gpmdb.org/data/keyword/26814187 68]. | ||
#Bigaud E, Corrales FJ, (2016) "Methylthioadenosine regulates liver cells proteome and methylproteome. Implications in liver biology and disease." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26819315 26819315]; doi: [https://dx.doi.org/10.1074/mcp.M115.055772 10.1074/mcp.M115.055772]; GPMDB: [http://gpmdb.org/data/keyword/26819315 3]. | #Bigaud E, Corrales FJ, (2016) "Methylthioadenosine regulates liver cells proteome and methylproteome. Implications in liver biology and disease." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26819315 26819315]; doi: [https://dx.doi.org/10.1074/mcp.M115.055772 10.1074/mcp.M115.055772]; GPMDB: [http://gpmdb.org/data/keyword/26819315 3]. | ||
+ | #Steger M, Tonelli F, Ito G, Davies P, Trost M, Vetter M, Wachter S, Lorentzen E, Duddy G, Wilson S, Baptista MA, Fiske BK, Fell MJ, Morrow JA, Reith AD, Alessi DR, Mann M, (2016) "Phosphoproteomics reveals that Parkinson's disease kinase LRRK2 regulates a subset of Rab GTPases." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26824392 26824392]; doi: [https://dx.doi.org/10.7554/eLife.12813 10.7554/eLife.12813]; GPMDB: [http://gpmdb.org/data/keyword/26824392 216]. | ||
#Chen Z, Tran M, Tang M, Wang W, Gong Z, Chen J, (2016) "Proteomic Analysis Reveals a Novel MutS Partner Involved in Mismatch Repair Pathway." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26828036 26828036]; doi: [https://dx.doi.org/10.1074/mcp.M115.056093 10.1074/mcp.M115.056093]; GPMDB: [http://gpmdb.org/data/keyword/26828036 22]. | #Chen Z, Tran M, Tang M, Wang W, Gong Z, Chen J, (2016) "Proteomic Analysis Reveals a Novel MutS Partner Involved in Mismatch Repair Pathway." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26828036 26828036]; doi: [https://dx.doi.org/10.1074/mcp.M115.056093 10.1074/mcp.M115.056093]; GPMDB: [http://gpmdb.org/data/keyword/26828036 22]. | ||
#Lichtman JS, Ferreyra JA, Ng KM, Smits SA, Sonnenburg JL, Elias JE, (2016) "Host-Microbiota Interactions in the Pathogenesis of Antibiotic-Associated Diseases." <i>Cell Rep</i> <b>14</b>(5):1049–61; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26832403 26832403]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.01.009 10.1016/j.celrep.2016.01.009]; GPMDB: [http://gpmdb.org/data/keyword/26832403 486]. | #Lichtman JS, Ferreyra JA, Ng KM, Smits SA, Sonnenburg JL, Elias JE, (2016) "Host-Microbiota Interactions in the Pathogenesis of Antibiotic-Associated Diseases." <i>Cell Rep</i> <b>14</b>(5):1049–61; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26832403 26832403]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.01.009 10.1016/j.celrep.2016.01.009]; GPMDB: [http://gpmdb.org/data/keyword/26832403 486]. | ||
Line 1,046: | Line 1,048: | ||
#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]. | ||
#Meierhofer D, Halbach M, Sen NE, Gispert S, Auburger G, (2016) "Atxn2-Knock-Out mice show branched chain amino acids and fatty acids pathway alterations." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26850065 26850065]; doi: [https://dx.doi.org/10.1074/mcp.M115.056770 10.1074/mcp.M115.056770]; GPMDB: [http://gpmdb.org/data/keyword/26850065 48]. | #Meierhofer D, Halbach M, Sen NE, Gispert S, Auburger G, (2016) "Atxn2-Knock-Out mice show branched chain amino acids and fatty acids pathway alterations." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26850065 26850065]; doi: [https://dx.doi.org/10.1074/mcp.M115.056770 10.1074/mcp.M115.056770]; GPMDB: [http://gpmdb.org/data/keyword/26850065 48]. | ||
- | #Gielisch I, Hardt C, Wittig I, Meierhofer D, (2016) "An impaired respiratory electron chain triggers down-regulation of the energy metabolism and de-ubiquitination of solute carrier amino acid transporters." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26852163 26852163]; doi: [https://dx.doi.org/10.1074/mcp.M115.053181 10.1074/mcp.M115.053181]; GPMDB: [http://gpmdb.org/data/keyword/26852163 | + | #Gielisch I, Hardt C, Wittig I, Meierhofer D, (2016) "An impaired respiratory electron chain triggers down-regulation of the energy metabolism and de-ubiquitination of solute carrier amino acid transporters." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26852163 26852163]; doi: [https://dx.doi.org/10.1074/mcp.M115.053181 10.1074/mcp.M115.053181]; GPMDB: [http://gpmdb.org/data/keyword/26852163 60]. |
#Peffers MJ, Collins J, Fang Y, Goljanek-Whysall K, Rushton M, Loughlin J, Proctor C, Clegg PD, (2016) "Age-related changes in mesenchymal stem cells identified using a multi-omics approach." <i>Eur Cell Mater</i> <b>31</b>:136–59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26853623 26853623]; GPMDB: [http://gpmdb.org/data/keyword/26853623 8]. | #Peffers MJ, Collins J, Fang Y, Goljanek-Whysall K, Rushton M, Loughlin J, Proctor C, Clegg PD, (2016) "Age-related changes in mesenchymal stem cells identified using a multi-omics approach." <i>Eur Cell Mater</i> <b>31</b>:136–59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26853623 26853623]; GPMDB: [http://gpmdb.org/data/keyword/26853623 8]. | ||
#Billing AM, Ben Hamidane H, Dib SS, Cotton RJ, Bhagwat AM, Kumar P, Hayat S, Yousri NA, Goswami N, Suhre K, Rafii A, Graumann J, (2016) "Comprehensive transcriptomic and proteomic characterization of human mesenchymal stem cells reveals source specific cellular markers." <i>Sci Rep</i> <b>6</b>:21507; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26857143 26857143]; doi: [https://dx.doi.org/10.1038/srep21507 10.1038/srep21507]; GPMDB: [http://gpmdb.org/data/keyword/26857143 9]. | #Billing AM, Ben Hamidane H, Dib SS, Cotton RJ, Bhagwat AM, Kumar P, Hayat S, Yousri NA, Goswami N, Suhre K, Rafii A, Graumann J, (2016) "Comprehensive transcriptomic and proteomic characterization of human mesenchymal stem cells reveals source specific cellular markers." <i>Sci Rep</i> <b>6</b>:21507; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26857143 26857143]; doi: [https://dx.doi.org/10.1038/srep21507 10.1038/srep21507]; GPMDB: [http://gpmdb.org/data/keyword/26857143 9]. | ||
- | #Kowal J, Arras G, Colombo M, Jouve M, Morath JP, Primdal-Bengtson B, Dingli F, Loew D, Tkach M, Théry C, (2016) "Proteomic comparison defines novel markers to characterize heterogeneous populations of extracellular vesicle subtypes." <i>Proc Natl Acad Sci U S A</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26858453 26858453]; doi: [https://dx.doi.org/10.1073/pnas.1521230113 10.1073/pnas.1521230113]; GPMDB: [http://gpmdb.org/data/keyword/26858453 56]. | + | #Kowal J, Arras G, Colombo M, Jouve M, Morath JP, Primdal-Bengtson B, Dingli F, Loew D, Tkach M, Théry C, (2016) "Proteomic comparison defines novel markers to characterize heterogeneous populations of extracellular vesicle subtypes." <i>Proc Natl Acad Sci U S A</i> <b>113</b>(8):E968–77; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26858453 26858453]; doi: [https://dx.doi.org/10.1073/pnas.1521230113 10.1073/pnas.1521230113]; GPMDB: [http://gpmdb.org/data/keyword/26858453 56]. |
#Locard-Paulet M, Lim L, Veluscek G, McMahon K, Sinclair J, van Weverwijk A, Worboys JD, Yuan Y, Isacke CM, Jørgensen C, (2016) "Phosphoproteomic analysis of interacting tumor and endothelial cells identifies regulatory mechanisms of transendothelial migration." <i>Sci Signal</i> <b>9</b>(414):ra15; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26861043 26861043]; doi: [https://dx.doi.org/10.1126/scisignal.aac5820 10.1126/scisignal.aac5820]; GPMDB: [http://gpmdb.org/data/keyword/26861043 76]. | #Locard-Paulet M, Lim L, Veluscek G, McMahon K, Sinclair J, van Weverwijk A, Worboys JD, Yuan Y, Isacke CM, Jørgensen C, (2016) "Phosphoproteomic analysis of interacting tumor and endothelial cells identifies regulatory mechanisms of transendothelial migration." <i>Sci Signal</i> <b>9</b>(414):ra15; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26861043 26861043]; doi: [https://dx.doi.org/10.1126/scisignal.aac5820 10.1126/scisignal.aac5820]; GPMDB: [http://gpmdb.org/data/keyword/26861043 76]. | ||
#Prior KK, Wittig I, Leisegang MS, Groenendyk J, Weissmann N, Michalak M, Jansen-Dürr P, Shah AM, Brandes RP, (2016) "The endoplasmic reticulum chaperone calnexin is a NADPH oxidase Nox4 interacting protein." <i>J Biol Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26861875 26861875]; doi: [https://dx.doi.org/10.1074/jbc.M115.710772 10.1074/jbc.M115.710772]; GPMDB: [http://gpmdb.org/data/keyword/26861875 80]. | #Prior KK, Wittig I, Leisegang MS, Groenendyk J, Weissmann N, Michalak M, Jansen-Dürr P, Shah AM, Brandes RP, (2016) "The endoplasmic reticulum chaperone calnexin is a NADPH oxidase Nox4 interacting protein." <i>J Biol Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26861875 26861875]; doi: [https://dx.doi.org/10.1074/jbc.M115.710772 10.1074/jbc.M115.710772]; GPMDB: [http://gpmdb.org/data/keyword/26861875 80]. | ||
+ | #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>; 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>; 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]. | ||
+ | #Lee HL, Chiang IC, Liang SY, Lee DY, Chang GD, Wang KY, Lin SY, Shih YL, (2016) "Quantitative proteomics analysis reveals the Min system of Escherichia coli modulates reversible protein association with the inner membrane." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26889046 26889046]; doi: [https://dx.doi.org/10.1074/mcp.M115.053603 10.1074/mcp.M115.053603]; GPMDB: [http://gpmdb.org/data/keyword/26889046 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>; 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]. | ||
+ | #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 13]. |
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 February 7, 2016.