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==Data from publications== | ==Data from publications== | ||
- | The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of | + | The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of February 9, 2020. |
#Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/12177431 498]. | #Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/12177431 498]. | ||
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#Geis-Asteggiante L, Belew AT, Clements VK, Edwards NJ, Ostrand-Rosenberg S, El-Sayed NM, Fenselau C, (2017) "Differential content of proteins, mRNAs, and miRNAs suggests that MDSC and their exosomes may mediate distinct immune suppressive functions." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29139296 29139296]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00646 10.1021/acs.jproteome.7b00646]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29139296 60]. | #Geis-Asteggiante L, Belew AT, Clements VK, Edwards NJ, Ostrand-Rosenberg S, El-Sayed NM, Fenselau C, (2017) "Differential content of proteins, mRNAs, and miRNAs suggests that MDSC and their exosomes may mediate distinct immune suppressive functions." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29139296 29139296]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00646 10.1021/acs.jproteome.7b00646]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29139296 60]. | ||
#Worzfeld T, Finkernagel F, Reinartz S, Konzer A, Adhikary T, Nist A, Stiewe T, Wagner U, Looso M, Graumann J, Müller R, (2017) "Proteotranscriptomics Reveal Signaling Networks in the Ovarian Cancer Microenvironment." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29141914 29141914]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000400 10.1074/mcp.RA117.000400]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29141914 121]. | #Worzfeld T, Finkernagel F, Reinartz S, Konzer A, Adhikary T, Nist A, Stiewe T, Wagner U, Looso M, Graumann J, Müller R, (2017) "Proteotranscriptomics Reveal Signaling Networks in the Ovarian Cancer Microenvironment." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29141914 29141914]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000400 10.1074/mcp.RA117.000400]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29141914 121]. | ||
+ | #Raffel S, Falcone M, Kneisel N, Hansson J, Wang W, Lutz C, Bullinger L, Poschet G, Nonnenmacher Y, Barnert A, Bahr C, Zeisberger P, Przybylla A, Sohn M, Tönjes M, Erez A, Adler L, Jensen P, Scholl C, Fröhling S, Cocciardi S, Wuchter P, Thiede C, Flörcken A, Westermann J, Ehninger G, Lichter P, Hiller K, Hell R, Herrmann C, Ho AD, Krijgsveld J, Radlwimmer B, Trumpp A, (2017) "BCAT1 restricts αKG levels in AML stem cells leading to IDHmut-like DNA hypermethylation." <i>Nature</i> <b>551</b>(7680):384–388; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29144447 29144447]; doi: [https://dx.doi.org/10.1038/nature24294 10.1038/nature24294]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29144447 10]. | ||
#Yilmaz O, Patinote A, Nguyen TV, Com E, Lavigne R, Pineau C, Sullivan CV, Bobe J, (2017) "Scrambled eggs: Proteomic portraits and novel biomarkers of egg quality in zebrafish (Danio rerio)." <i>PLoS One</i> <b>12</b>(11):e0188084; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29145436 29145436]; doi: [https://dx.doi.org/10.1371/journal.pone.0188084 10.1371/journal.pone.0188084]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29145436 57]. | #Yilmaz O, Patinote A, Nguyen TV, Com E, Lavigne R, Pineau C, Sullivan CV, Bobe J, (2017) "Scrambled eggs: Proteomic portraits and novel biomarkers of egg quality in zebrafish (Danio rerio)." <i>PLoS One</i> <b>12</b>(11):e0188084; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29145436 29145436]; doi: [https://dx.doi.org/10.1371/journal.pone.0188084 10.1371/journal.pone.0188084]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29145436 57]. | ||
#Cherry JD, Zeineddin A, Dammer EB, Webster JA, Duong D, Seyfried NT, Levey AI, Alvarez VE, Huber BR, Stein TD, Kiernan PT, McKee AC, Lah JJ, Hales CM, (2017) "Characterization of Detergent Insoluble Proteome in Chronic Traumatic Encephalopathy." <i>J Neuropathol Exp Neurol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29145658 29145658]; doi: [https://dx.doi.org/10.1093/jnen/nlx100 10.1093/jnen/nlx100]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29145658 4]. | #Cherry JD, Zeineddin A, Dammer EB, Webster JA, Duong D, Seyfried NT, Levey AI, Alvarez VE, Huber BR, Stein TD, Kiernan PT, McKee AC, Lah JJ, Hales CM, (2017) "Characterization of Detergent Insoluble Proteome in Chronic Traumatic Encephalopathy." <i>J Neuropathol Exp Neurol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29145658 29145658]; doi: [https://dx.doi.org/10.1093/jnen/nlx100 10.1093/jnen/nlx100]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29145658 4]. | ||
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#Dybas JM, O'Leary CE, Ding H, Spruce LA, Seeholzer SH, Oliver PM, (2019) "Integrative proteomics reveals an increase in non-degradative ubiquitylation in activated CD4<sup>+</sup> T cells." <i>Nat Immunol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31061531 31061531]; doi: [https://dx.doi.org/10.1038/s41590-019-0381-6 10.1038/s41590-019-0381-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31061531 118]. | #Dybas JM, O'Leary CE, Ding H, Spruce LA, Seeholzer SH, Oliver PM, (2019) "Integrative proteomics reveals an increase in non-degradative ubiquitylation in activated CD4<sup>+</sup> T cells." <i>Nat Immunol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31061531 31061531]; doi: [https://dx.doi.org/10.1038/s41590-019-0381-6 10.1038/s41590-019-0381-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31061531 118]. | ||
#Papaioannou MD, Djuric U, Kao J, Karimi S, Zadeh G, Aldape K, Diamandis P, (2019) "Proteomic analysis of meningiomas reveals clinically-distinct molecular patterns." <i>Neuro Oncol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31077268 31077268]; doi: [https://dx.doi.org/10.1093/neuonc/noz084 10.1093/neuonc/noz084]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31077268 78]. | #Papaioannou MD, Djuric U, Kao J, Karimi S, Zadeh G, Aldape K, Diamandis P, (2019) "Proteomic analysis of meningiomas reveals clinically-distinct molecular patterns." <i>Neuro Oncol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31077268 31077268]; doi: [https://dx.doi.org/10.1093/neuonc/noz084 10.1093/neuonc/noz084]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31077268 78]. | ||
+ | #Spörrer M, Prochnicki A, Tölle RC, Nyström A, Esser PR, Homberg M, Athanasiou I, Zingkou E, Schilling A, Gerum R, Thievessen I, Winter L, Bruckner-Tuderman L, Fabry B, Magin TM, Dengjel J, Schröder R, Kiritsi D, (2019) "Treatment of keratinocytes with 4-phenylbutyrate in epidermolysis bullosa: Lessons for therapies in keratin disorders." <i>EBioMedicine</i> <b>44</b>:502–515; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31078522 31078522]; doi: [https://dx.doi.org/10.1016/j.ebiom.2019.04.062 10.1016/j.ebiom.2019.04.062]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31078522 41]. | ||
#Wang H, Sheehan RP, Palmer AC, Everley RA, Boswell SA, Ron-Harel N, Ringel AE, Holton KM, Jacobson CA, Erickson AR, Maliszewski L, Haigis MC, Sorger PK, (2019) "Adaptation of Human iPSC-Derived Cardiomyocytes to Tyrosine Kinase Inhibitors Reduces Acute Cardiotoxicity via Metabolic Reprogramming." <i>Cell Syst</i> <b>8</b>(5):412–426.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31078528 31078528]; doi: [https://dx.doi.org/10.1016/j.cels.2019.03.009 10.1016/j.cels.2019.03.009]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31078528 24]. | #Wang H, Sheehan RP, Palmer AC, Everley RA, Boswell SA, Ron-Harel N, Ringel AE, Holton KM, Jacobson CA, Erickson AR, Maliszewski L, Haigis MC, Sorger PK, (2019) "Adaptation of Human iPSC-Derived Cardiomyocytes to Tyrosine Kinase Inhibitors Reduces Acute Cardiotoxicity via Metabolic Reprogramming." <i>Cell Syst</i> <b>8</b>(5):412–426.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31078528 31078528]; doi: [https://dx.doi.org/10.1016/j.cels.2019.03.009 10.1016/j.cels.2019.03.009]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31078528 24]. | ||
#Murphy JP, Kim Y, Clements DR, Konda P, Schuster H, Kowalewski DJ, Paulo JA, Cohen AM, Stevanovic S, Gygi SP, Gujar S, (2019) "Therapy-Induced MHC I Ligands Shape Neo-Antitumor CD8 T Cell Responses during Oncolytic Virus-Based Cancer Immunotherapy." <i>J Proteome Res</i> <b>18</b>(6):2666–2675; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31095916 31095916]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00173 10.1021/acs.jproteome.9b00173]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31095916 11]. | #Murphy JP, Kim Y, Clements DR, Konda P, Schuster H, Kowalewski DJ, Paulo JA, Cohen AM, Stevanovic S, Gygi SP, Gujar S, (2019) "Therapy-Induced MHC I Ligands Shape Neo-Antitumor CD8 T Cell Responses during Oncolytic Virus-Based Cancer Immunotherapy." <i>J Proteome Res</i> <b>18</b>(6):2666–2675; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31095916 31095916]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00173 10.1021/acs.jproteome.9b00173]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31095916 11]. | ||
#Ott E, Kawaguchi Y, Özgen N, Yamagishi A, Rabbow E, Rettberg P, Weckwerth W, Milojevic T, (2019) "Proteomic and Metabolomic Profiling of <i>Deinococcus radiodurans</i> Recovering After Exposure to Simulated Low Earth Orbit Vacuum Conditions." <i>Front Microbiol</i> <b>10</b>:909; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31110498 31110498]; doi: [https://dx.doi.org/10.3389/fmicb.2019.00909 10.3389/fmicb.2019.00909]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31110498 17]. | #Ott E, Kawaguchi Y, Özgen N, Yamagishi A, Rabbow E, Rettberg P, Weckwerth W, Milojevic T, (2019) "Proteomic and Metabolomic Profiling of <i>Deinococcus radiodurans</i> Recovering After Exposure to Simulated Low Earth Orbit Vacuum Conditions." <i>Front Microbiol</i> <b>10</b>:909; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31110498 31110498]; doi: [https://dx.doi.org/10.3389/fmicb.2019.00909 10.3389/fmicb.2019.00909]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31110498 17]. | ||
#Chu F, Mason KE, Anex DS, Jones AD, Hart BR, (2019) "Hair Proteome Variation at Different Body Locations on Genetically Variant Peptide Detection for Protein-Based Human Identification." <i>Sci Rep</i> <b>9</b>(1):7641; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31113963 31113963]; doi: [https://dx.doi.org/10.1038/s41598-019-44007-7 10.1038/s41598-019-44007-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31113963 36]. | #Chu F, Mason KE, Anex DS, Jones AD, Hart BR, (2019) "Hair Proteome Variation at Different Body Locations on Genetically Variant Peptide Detection for Protein-Based Human Identification." <i>Sci Rep</i> <b>9</b>(1):7641; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31113963 31113963]; doi: [https://dx.doi.org/10.1038/s41598-019-44007-7 10.1038/s41598-019-44007-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31113963 36]. | ||
- | #Charitou T, Srihari S, Lynn MA, Jarboui MA, Fasterius E, Moldovan M, Shirasawa S, Tsunoda T, Ueffing M, Xie J, Xin J, Wang X, Proud CG, Boldt K, Al-Khalili Szigyarto C, Kolch W, Lynn DJ, (2019) "Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRAS<sup>G13D</sup> mutation." <i>Br J Cancer</i> <b>121</b>(1):37–50; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31133691 31133691]; doi: [https://dx.doi.org/10.1038/s41416-019-0477-7 10.1038/s41416-019-0477-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31133691 | + | #Charitou T, Srihari S, Lynn MA, Jarboui MA, Fasterius E, Moldovan M, Shirasawa S, Tsunoda T, Ueffing M, Xie J, Xin J, Wang X, Proud CG, Boldt K, Al-Khalili Szigyarto C, Kolch W, Lynn DJ, (2019) "Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRAS<sup>G13D</sup> mutation." <i>Br J Cancer</i> <b>121</b>(1):37–50; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31133691 31133691]; doi: [https://dx.doi.org/10.1038/s41416-019-0477-7 10.1038/s41416-019-0477-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31133691 523]. |
#Sap KA, Guler AT, Bezstarosti K, Bury AE, Juenemann K, Demmers J, Reits E, (2019) "Global Proteome and Ubiquitinome Changes in the Soluble and Insoluble Fractions of Q175 Huntington Mice Brains." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31138642 31138642]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001486 10.1074/mcp.RA119.001486]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31138642 64]. | #Sap KA, Guler AT, Bezstarosti K, Bury AE, Juenemann K, Demmers J, Reits E, (2019) "Global Proteome and Ubiquitinome Changes in the Soluble and Insoluble Fractions of Q175 Huntington Mice Brains." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31138642 31138642]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001486 10.1074/mcp.RA119.001486]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31138642 64]. | ||
#Pladevall-Morera D, Munk S, Ingham A, Garribba L, Albers E, Liu Y, Olsen JV, Lopez-Contreras AJ, (2019) "Proteomic characterization of chromosomal common fragile site (CFS)-associated proteins uncovers ATRX as a regulator of CFS stability." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31180492 31180492]; doi: [https://dx.doi.org/10.1093/nar/gkz510 10.1093/nar/gkz510]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31180492 32]. | #Pladevall-Morera D, Munk S, Ingham A, Garribba L, Albers E, Liu Y, Olsen JV, Lopez-Contreras AJ, (2019) "Proteomic characterization of chromosomal common fragile site (CFS)-associated proteins uncovers ATRX as a regulator of CFS stability." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31180492 31180492]; doi: [https://dx.doi.org/10.1093/nar/gkz510 10.1093/nar/gkz510]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31180492 32]. | ||
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#Sjödin S, Brinkmalm G, Öhrfelt A, Parnetti L, Paciotti S, Hansson O, Hardy J, Blennow K, Zetterberg H, Brinkmalm A, (2019) "Endo-lysosomal proteins and ubiquitin CSF concentrations in Alzheimer's and Parkinson's disease." <i>Alzheimers Res Ther</i> <b>11</b>(1):82; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31521194 31521194]; doi: [https://dx.doi.org/10.1186/s13195-019-0533-9 10.1186/s13195-019-0533-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31521194 27]. | #Sjödin S, Brinkmalm G, Öhrfelt A, Parnetti L, Paciotti S, Hansson O, Hardy J, Blennow K, Zetterberg H, Brinkmalm A, (2019) "Endo-lysosomal proteins and ubiquitin CSF concentrations in Alzheimer's and Parkinson's disease." <i>Alzheimers Res Ther</i> <b>11</b>(1):82; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31521194 31521194]; doi: [https://dx.doi.org/10.1186/s13195-019-0533-9 10.1186/s13195-019-0533-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31521194 27]. | ||
#Israel S, Ernst M, Psathaki OE, Drexler HCA, Casser E, Suzuki Y, Makalowski W, Boiani M, Fuellen G, Taher L, (2019) "An integrated genome-wide multi-omics analysis of gene expression dynamics in the preimplantation mouse embryo." <i>Sci Rep</i> <b>9</b>(1):13356; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31527703 31527703]; doi: [https://dx.doi.org/10.1038/s41598-019-49817-3 10.1038/s41598-019-49817-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31527703 21]. | #Israel S, Ernst M, Psathaki OE, Drexler HCA, Casser E, Suzuki Y, Makalowski W, Boiani M, Fuellen G, Taher L, (2019) "An integrated genome-wide multi-omics analysis of gene expression dynamics in the preimplantation mouse embryo." <i>Sci Rep</i> <b>9</b>(1):13356; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31527703 31527703]; doi: [https://dx.doi.org/10.1038/s41598-019-49817-3 10.1038/s41598-019-49817-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31527703 21]. | ||
+ | #Moutaoufik MT, Malty R, Amin S, Zhang Q, Phanse S, Gagarinova A, Zilocchi M, Hoell L, Minic Z, Gagarinova M, Aoki H, Stockwell J, Jessulat M, Goebels F, Broderick K, Scott NE, Vlasblom J, Musso G, Prasad B, Lamantea E, Garavaglia B, Rajput A, Murayama K, Okazaki Y, Foster LJ, Bader GD, Cayabyab FS, Babu M, (2019) "Rewiring of the Human Mitochondrial Interactome during Neuronal Reprogramming Reveals Regulators of the Respirasome and Neurogenesis." <i>iScience</i> <b>19</b>:1114–1132; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31536960 31536960]; doi: [https://dx.doi.org/10.1016/j.isci.2019.08.057 10.1016/j.isci.2019.08.057]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31536960 708]. | ||
#Uckeley ZM, Moeller R, Kühn LI, Nilsson E, Robens C, Lasswitz L, Lindqvist R, Lenman A, Passos V, Voss Y, Sommerauer C, Kampmann M, Goffinet C, Meissner F, Överby AK, Lozach PY, Gerold G, (2019) "Quantitative proteomics of Uukuniemi virus - host cell interactions reveals GBF1 as proviral host factor for phleboviruses." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31570497 31570497]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001631 10.1074/mcp.RA119.001631]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31570497 20]. | #Uckeley ZM, Moeller R, Kühn LI, Nilsson E, Robens C, Lasswitz L, Lindqvist R, Lenman A, Passos V, Voss Y, Sommerauer C, Kampmann M, Goffinet C, Meissner F, Överby AK, Lozach PY, Gerold G, (2019) "Quantitative proteomics of Uukuniemi virus - host cell interactions reveals GBF1 as proviral host factor for phleboviruses." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31570497 31570497]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001631 10.1074/mcp.RA119.001631]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31570497 20]. | ||
#Kawahara R, Recuero S, Nogueira FCS, Domont GB, Leite KRM, Srougi M, Thaysen-Andersen M, Palmisano G, (2019) "Tissue Proteome Signatures Associated with Five Grades of Prostate Cancer and Benign Prostatic Hyperplasia." <i>Proteomics</i> <b></b>:e1900174; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31576646 31576646]; doi: [https://dx.doi.org/10.1002/pmic.201900174 10.1002/pmic.201900174]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31576646 5]. | #Kawahara R, Recuero S, Nogueira FCS, Domont GB, Leite KRM, Srougi M, Thaysen-Andersen M, Palmisano G, (2019) "Tissue Proteome Signatures Associated with Five Grades of Prostate Cancer and Benign Prostatic Hyperplasia." <i>Proteomics</i> <b></b>:e1900174; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31576646 31576646]; doi: [https://dx.doi.org/10.1002/pmic.201900174 10.1002/pmic.201900174]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31576646 5]. | ||
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#McRae EKS, Dupas SJ, Booy EP, Piragasam RS, Fahlman RP, McKenna SA, (2019) "An RNA guanine quadruplex regulated pathway to TRAIL-sensitization by DDX21." <i>RNA</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31653714 31653714]; doi: [https://dx.doi.org/10.1261/rna.072199.119 10.1261/rna.072199.119]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31653714 108]. | #McRae EKS, Dupas SJ, Booy EP, Piragasam RS, Fahlman RP, McKenna SA, (2019) "An RNA guanine quadruplex regulated pathway to TRAIL-sensitization by DDX21." <i>RNA</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31653714 31653714]; doi: [https://dx.doi.org/10.1261/rna.072199.119 10.1261/rna.072199.119]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31653714 108]. | ||
#Kenny A, Jiménez-Mateos EM, Zea-Sevilla MA, Rábano A, Gili-Manzanaro P, Prehn JHM, Henshall DC, Ávila J, Engel T, Hernández F, (2019) "Proteins and microRNAs are differentially expressed in tear fluid from patients with Alzheimer's disease." <i>Sci Rep</i> <b>9</b>(1):15437; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31659197 31659197]; doi: [https://dx.doi.org/10.1038/s41598-019-51837-y 10.1038/s41598-019-51837-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31659197 32]. | #Kenny A, Jiménez-Mateos EM, Zea-Sevilla MA, Rábano A, Gili-Manzanaro P, Prehn JHM, Henshall DC, Ávila J, Engel T, Hernández F, (2019) "Proteins and microRNAs are differentially expressed in tear fluid from patients with Alzheimer's disease." <i>Sci Rep</i> <b>9</b>(1):15437; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31659197 31659197]; doi: [https://dx.doi.org/10.1038/s41598-019-51837-y 10.1038/s41598-019-51837-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31659197 32]. | ||
+ | #Arima N, Sasaki Y, Lee LH, Zhang H, Figueiredo JL, Mlynarchik AK, Qiao J, Yamada I, Higashi H, Ha AH, Halu A, Mizuno K, Singh SA, Yamazaki Y, Aikawa M, (2020) "Multiorgan Systems Study Reveals Igfbp7 as a Suppressor of Gluconeogenesis after Gastric Bypass Surgery." <i>J Proteome Res</i> <b>19</b>(1):129–143; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31661273 31661273]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00441 10.1021/acs.jproteome.9b00441]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31661273 4]. | ||
#Mallam AL, Sae-Lee W, Schaub JM, Tu F, Battenhouse A, Jang YJ, Kim J, Wallingford JB, Finkelstein IJ, Marcotte EM, Drew K, (2019) "Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes." <i>Cell Rep</i> <b>29</b>(5):1351–1368.e5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31665645 31665645]; doi: [https://dx.doi.org/10.1016/j.celrep.2019.09.060 10.1016/j.celrep.2019.09.060]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31665645 122]. | #Mallam AL, Sae-Lee W, Schaub JM, Tu F, Battenhouse A, Jang YJ, Kim J, Wallingford JB, Finkelstein IJ, Marcotte EM, Drew K, (2019) "Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes." <i>Cell Rep</i> <b>29</b>(5):1351–1368.e5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31665645 31665645]; doi: [https://dx.doi.org/10.1016/j.celrep.2019.09.060 10.1016/j.celrep.2019.09.060]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31665645 122]. | ||
- | #Newey A, Griffiths B, Michaux J, Pak HS, Stevenson BJ, Woolston A, Semiannikova M, Spain G, Barber LJ, Matthews N, Rao S, Watkins D, Chau I, Coukos G, Racle J, Gfeller D, Starling N, Cunningham D, Bassani-Sternberg M, Gerlinger M, (2019) "Immunopeptidomics of colorectal cancer organoids reveals a sparse HLA class I neoantigen landscape and no increase in neoantigens with interferon or MEK-inhibitor treatment." <i>J Immunother Cancer</i> <b>7</b>(1):309; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31735170 31735170]; doi: [https://dx.doi.org/10.1186/s40425-019-0769-8 10.1186/s40425-019-0769-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31735170 | + | #Sohier P, Sanson R, Leduc M, Audebourg A, Broussard C, Salnot V, Just PA, Pasmant E, Mayeux P, Guillonneau F, Romagnolo B, Perret C, Terris B, (2019) "Proteome analysis of formalin-fixed paraffin-embedded colorectal adenomas reveals the heterogeneous nature of traditional serrated adenomas compared to other colorectal adenomas." <i>J Pathol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31729028 31729028]; doi: [https://dx.doi.org/10.1002/path.5366 10.1002/path.5366]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31729028 55]. |
+ | #Newey A, Griffiths B, Michaux J, Pak HS, Stevenson BJ, Woolston A, Semiannikova M, Spain G, Barber LJ, Matthews N, Rao S, Watkins D, Chau I, Coukos G, Racle J, Gfeller D, Starling N, Cunningham D, Bassani-Sternberg M, Gerlinger M, (2019) "Immunopeptidomics of colorectal cancer organoids reveals a sparse HLA class I neoantigen landscape and no increase in neoantigens with interferon or MEK-inhibitor treatment." <i>J Immunother Cancer</i> <b>7</b>(1):309; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31735170 31735170]; doi: [https://dx.doi.org/10.1186/s40425-019-0769-8 10.1186/s40425-019-0769-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31735170 193]. | ||
+ | #Thompson A, Wölmer N, Koncarevic S, Selzer S, Böhm G, Legner H, Schmid P, Kienle S, Penning P, Höhle C, Berfelde A, Martinez-Pinna R, Farztdinov V, Jung S, Kuhn K, Pike I, (2019) "TMTpro: Design, Synthesis, and Initial Evaluation of a Proline-Based Isobaric 16-Plex Tandem Mass Tag Reagent Set." <i>Anal Chem</i> <b>91</b>(24):15941–15950; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31738517 31738517]; doi: [https://dx.doi.org/10.1021/acs.analchem.9b04474 10.1021/acs.analchem.9b04474]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31738517 20]. | ||
+ | #Kim JJ, Lee SY, Gong F, Battenhouse AM, Boutz DR, Bashyal A, Refvik ST, Chiang CM, Xhemalce B, Paull TT, Brodbelt JS, Marcotte EM, Miller KM, (2019) "Systematic bromodomain protein screens identify homologous recombination and R-loop suppression pathways involved in genome integrity." <i>Genes Dev</i> <b>33</b>(23-24):1751–1774; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31753913 31753913]; doi: [https://dx.doi.org/10.1101/gad.331231.119 10.1101/gad.331231.119]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31753913 66]. | ||
+ | #Fang EF, Hou Y, Lautrup S, Jensen MB, Yang B, SenGupta T, Caponio D, Khezri R, Demarest TG, Aman Y, Figueroa D, Morevati M, Lee HJ, Kato H, Kassahun H, Lee JH, Filippelli D, Okur MN, Mangerich A, Croteau DL, Maezawa Y, Lyssiotis CA, Tao J, Yokote K, Rusten TE, Mattson MP, Jasper H, Nilsen H, Bohr VA, (2019) "NAD<sup>+</sup> augmentation restores mitophagy and limits accelerated aging in Werner syndrome." <i>Nat Commun</i> <b>10</b>(1):5284; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31754102 31754102]; doi: [https://dx.doi.org/10.1038/s41467-019-13172-8 10.1038/s41467-019-13172-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31754102 32]. | ||
+ | #Zhang Y, Lin Z, Tan Y, Bu F, Hao P, Zhang K, Yang H, Liu S, Ren Y, (2019) "Exploration of Missing Proteins by a Combination Approach to Enrich the Low-Abundance Hydrophobic Proteins from Four Cancer Cell Lines." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31773964 31773964]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00590 10.1021/acs.jproteome.9b00590]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31773964 16]. | ||
+ | #Szibor M, Gainutdinov T, Fernandez-Vizarra E, Dufour E, Gizatullina Z, Debska-Vielhaber G, Heidler J, Wittig I, Viscomi C, Gellerich F, Moore AL, (2020) "Bioenergetic consequences from xenotopic expression of a tunicate AOX in mouse mitochondria: Switch from RET and ROS to FET." <i>Biochim Biophys Acta Bioenerg</i> <b>1861</b>(2):148137; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31825809 31825809]; doi: [https://dx.doi.org/10.1016/j.bbabio.2019.148137 10.1016/j.bbabio.2019.148137]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31825809 96]. | ||
+ | #Solleder M, Guillaume P, Racle J, Michaux J, Pak HS, Müller M, Coukos G, Bassani-Sternberg M, Gfeller D, (2019) "Mass spectrometry based immunopeptidomics leads to robust predictions of phosphorylated HLA class I ligands." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31848261 31848261]; doi: [https://dx.doi.org/10.1074/mcp.TIR119.001641 10.1074/mcp.TIR119.001641]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31848261 208]. | ||
+ | #Nobre LV, Nightingale K, Ravenhill BJ, Antrobus R, Soday L, Nichols J, Davies JA, Seirafian S, Wang EC, Davison AJ, Wilkinson GW, Stanton RJ, Huttlin EL, Weekes MP, (2019) "Human cytomegalovirus interactome analysis identifies degradation hubs, domain associations and viral protein functions." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31873071 31873071]; doi: [https://dx.doi.org/10.7554/eLife.49894 10.7554/eLife.49894]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31873071 354]. | ||
+ | #Mühlhofer M, Berchtold E, Stratil CG, Csaba G, Kunold E, Bach NC, Sieber SA, Haslbeck M, Zimmer R, Buchner J, (2019) "The Heat Shock Response in Yeast Maintains Protein Homeostasis by Chaperoning and Replenishing Proteins." <i>Cell Rep</i> <b>29</b>(13):4593–4607.e8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31875563 31875563]; doi: [https://dx.doi.org/10.1016/j.celrep.2019.11.109 10.1016/j.celrep.2019.11.109]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31875563 15]. | ||
+ | #Van JAD, Clotet-Freixas S, Zhou J, Batruch I, Sun C, Glogauer M, Rampoldi L, Elia Y, Mahmud F, Sochett E, Diamandis EP, Scholey J, Konvalinka A, (2019) "Peptidomic analysis of urine from youths with early type 1 diabetes reveals novel bioactivity of uromodulin peptides <i>in vitro</i>." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31879271 31879271]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001858 10.1074/mcp.RA119.001858]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31879271 90]. | ||
+ | #Nguyen AM, Zhou J, Sicairos B, Sonney S, Du Y, (2019) "Upregulation of CD73 Confers Acquired Radioresistance and is Required for Maintaining Irradiation-Selected Pancreatic Cancer Cells in a Mesenchymal State." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31879272 31879272]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001779 10.1074/mcp.RA119.001779]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31879272 20]. | ||
+ | #Mugahid DA, Sengul TG, You X, Wang Y, Steil L, Bergmann N, Radke MH, Ofenbauer A, Gesell-Salazar M, Balogh A, Kempa S, Tursun B, Robbins CT, Völker U, Chen W, Nelson L, Gotthardt M, (2019) "Proteomic and Transcriptomic Changes in Hibernating Grizzly Bears Reveal Metabolic and Signaling Pathways that Protect against Muscle Atrophy." <i>Sci Rep</i> <b>9</b>(1):19976; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31882638 31882638]; doi: [https://dx.doi.org/10.1038/s41598-019-56007-8 10.1038/s41598-019-56007-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31882638 16]. | ||
+ | #Rispoli LA, Edwards JL, Pohler KG, Russell S, Somiari RI, Payton RR, Schrick FN, (2019) "Heat-induced hyperthermia impacts the follicular fluid proteome of the periovulatory follicle in lactating dairy cows." <i>PLoS One</i> <b>14</b>(12):e0227095; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31887207 31887207]; doi: [https://dx.doi.org/10.1371/journal.pone.0227095 10.1371/journal.pone.0227095]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31887207 5]. | ||
+ | #Róka B, Tod P, Kaucsár T, Vizovišek M, Vidmar R, Turk B, Fonović M, Szénási G, Hamar P, (2019) "The Acute Phase Response Is a Prominent Renal Proteome Change in Sepsis in Mice." <i>Int J Mol Sci</i> <b>21</b>(1):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31892161 31892161]; doi: [https://dx.doi.org/10.3390/ijms21010200 10.3390/ijms21010200]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31892161 120]. | ||
+ | #Hose J, Escalante LE, Clowers KJ, Dutcher HA, Robinson D, Bouriakov V, Coon JJ, Shishkova E, Gasch AP, (2020) "The genetic basis of aneuploidy tolerance in wild yeast." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31909711 31909711]; doi: [https://dx.doi.org/10.7554/eLife.52063 10.7554/eLife.52063]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31909711 24]. | ||
+ | #Bian Y, Zheng R, Bayer FP, Wong C, Chang YC, Meng C, Zolg DP, Reinecke M, Zecha J, Wiechmann S, Heinzlmeir S, Scherr J, Hemmer B, Baynham M, Gingras AC, Boychenko O, Kuster B, (2020) "Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC-MS/MS." <i>Nat Commun</i> <b>11</b>(1):157; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31919466 31919466]; doi: [https://dx.doi.org/10.1038/s41467-019-13973-x 10.1038/s41467-019-13973-x]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31919466 2175]. | ||
+ | #Meng K, Lu S, Yan X, Sun Y, Gao J, Wang Y, Yin X, Sun Z, He QY, (2020) "Quantitative Mitochondrial Proteomics Reveals ANXA7 as a Crucial Factor in Mitophagy." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31975592 31975592]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00800 10.1021/acs.jproteome.9b00800]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31975592 3]. | ||
+ | #Gonnet J, Poncelet L, Meriaux C, Gonçalves E, Weiss L, Tchitchek N, Pedruzzi E, Soria A, Boccara D, Vogt A, Bonduelle O, Hamm G, Ait-Belkacem R, Stauber J, Fournier I, Wisztorski M, Combadiere B, (2020) "Mechanisms of innate events during skin reaction following intradermal injection of seasonal influenza vaccine." <i>J Proteomics</i> <b>216</b>:103670; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31991189 31991189]; doi: [https://dx.doi.org/10.1016/j.jprot.2020.103670 10.1016/j.jprot.2020.103670]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31991189 48]. |
GPMDB was originally constructed to serve as a reference work for all publicly available proteomics generated using tandem mass spectrometry. Public data is downloaded and reanalyzed using the current version of X! Tandem. The result files generated by the reanalysis and the relevant metadata are imported into the database and made available through the associated web site, ftp site and REST interfaces.
Contents |
The following public data repositories are checked daily for new suitable raw data for reanalysis:
Data made available from specific large projects, such as CPTAC or the Human Proteome Atlas, are also included when they are made available. Every effort is made so that reanalyzed results from all data sources are made available within 48 hours of their being released. In addition, data from lab web sites, ftp sites and direct contributions through the GPM sites made available to researchers are imported into GPMDB as part of a daily incremental update process.
GPMDB has been in operation since Jan. 1, 2004. Several large data source repositories have come into existence and ceased activity in the period since that time. All of the data from those repositories (e.g., TRANCHE, Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.
Simply because data is made available does not mean that it will be included in GPMDB. The data must be approved our quality control AI for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
CAUTION: Many papers contain serious errors in their Methods sections. When using data from the literature, it is important to be skeptical of any experimental parameter (cell line, tissue type, modification reagents, quantitation methoods, etc.) that may impact on your use of the data. We have tried to correct any obvious errors, but there is no way to guarantee that we found them all. When attempting to analyze or reproduce results, keep in mind the likelyhood that even key parts of the experiment methods may have been recorded incorrectly in the associated manuscript, as methods are rarely reviewed properly in the current journal publication process.
The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of February 9, 2020.