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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 July 20, | + | 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 July 20, 2021. |
#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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#Young C, Podtelejnikov AV, Nielsen ML, (2017) "Improved Reversed Phase Chromatography of Hydrophilic Peptides from Spatial and Temporal Changes in Column Temperature." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28387123 28387123]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b01055 10.1021/acs.jproteome.6b01055]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28387123 12]. | #Young C, Podtelejnikov AV, Nielsen ML, (2017) "Improved Reversed Phase Chromatography of Hydrophilic Peptides from Spatial and Temporal Changes in Column Temperature." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28387123 28387123]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b01055 10.1021/acs.jproteome.6b01055]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28387123 12]. | ||
#Beach RR, Ricci-Tam C, Brennan CM, Moomau CA, Hsu PH, Hua B, Silberman RE, Springer M, Amon A, (2017) "Aneuploidy Causes Non-genetic Individuality." <i>Cell</i> <b>169</b>(2):229–242.e21; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28388408 28388408]; doi: [https://dx.doi.org/10.1016/j.cell.2017.03.021 10.1016/j.cell.2017.03.021]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28388408 3]. | #Beach RR, Ricci-Tam C, Brennan CM, Moomau CA, Hsu PH, Hua B, Silberman RE, Springer M, Amon A, (2017) "Aneuploidy Causes Non-genetic Individuality." <i>Cell</i> <b>169</b>(2):229–242.e21; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28388408 28388408]; doi: [https://dx.doi.org/10.1016/j.cell.2017.03.021 10.1016/j.cell.2017.03.021]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28388408 3]. | ||
+ | #Lobingier BT, Hüttenhain R, Eichel K, Miller KB, Ting AY, von Zastrow M, Krogan NJ, (2017) "An Approach to Spatiotemporally Resolve Protein Interaction Networks in Living Cells." <i>Cell</i> <b>169</b>(2):350–360.e12; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28388416 28388416]; doi: [https://dx.doi.org/10.1016/j.cell.2017.03.022 10.1016/j.cell.2017.03.022]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28388416 45]. | ||
#Worst TS, von Hardenberg J, Gross JC, Erben P, Schnoelzer M, Hausser I, Bugert P, Michel MS, Boutros M, (2017) "A database-augmented, exosome-based mass spectrometry approach exemplarily identifies circulating claudin 3 as biomarker in prostate cancer." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28396511 28396511]; doi: [https://dx.doi.org/10.1074/mcp.M117.068577 10.1074/mcp.M117.068577]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28396511 17]. | #Worst TS, von Hardenberg J, Gross JC, Erben P, Schnoelzer M, Hausser I, Bugert P, Michel MS, Boutros M, (2017) "A database-augmented, exosome-based mass spectrometry approach exemplarily identifies circulating claudin 3 as biomarker in prostate cancer." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28396511 28396511]; doi: [https://dx.doi.org/10.1074/mcp.M117.068577 10.1074/mcp.M117.068577]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28396511 17]. | ||
#Mohr S, Doebele C, Comoglio F, Berg T, Beck J, Bohnenberger H, Alexe G, Corso J, Ströbel P, Wachter A, Beissbarth T, Schnütgen F, Cremer A, Haetscher N, Göllner S, Rouhi A, Palmqvist L, Rieger MA, Schroeder T, Bönig H, Müller-Tidow C, Kuchenbauer F, Schütz E, Green AR, Urlaub H, Stegmaier K, Humphries RK, Serve H, Oellerich T, (2017) "Hoxa9 and Meis1 Cooperatively Induce Addiction to Syk Signaling by Suppressing miR-146a in Acute Myeloid Leukemia." <i>Cancer Cell</i> <b>31</b>(4):549–562.e11; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28399410 28399410]; doi: [https://dx.doi.org/10.1016/j.ccell.2017.03.001 10.1016/j.ccell.2017.03.001]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28399410 30]. | #Mohr S, Doebele C, Comoglio F, Berg T, Beck J, Bohnenberger H, Alexe G, Corso J, Ströbel P, Wachter A, Beissbarth T, Schnütgen F, Cremer A, Haetscher N, Göllner S, Rouhi A, Palmqvist L, Rieger MA, Schroeder T, Bönig H, Müller-Tidow C, Kuchenbauer F, Schütz E, Green AR, Urlaub H, Stegmaier K, Humphries RK, Serve H, Oellerich T, (2017) "Hoxa9 and Meis1 Cooperatively Induce Addiction to Syk Signaling by Suppressing miR-146a in Acute Myeloid Leukemia." <i>Cancer Cell</i> <b>31</b>(4):549–562.e11; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28399410 28399410]; doi: [https://dx.doi.org/10.1016/j.ccell.2017.03.001 10.1016/j.ccell.2017.03.001]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28399410 30]. | ||
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#Brumbaugh J, Di Stefano B, Wang X, Borkent M, Forouzmand E, Clowers KJ, Ji F, Schwarz BA, Kalocsay M, Elledge SJ, Chen Y, Sadreyev RI, Gygi SP, Hu G, Shi Y, Hochedlinger K, (2018) "Nudt21 Controls Cell Fate by Connecting Alternative Polyadenylation to Chromatin Signaling." <i>Cell</i> <b>172</b>(1-2):106–120.e21; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29249356 29249356]; doi: [https://dx.doi.org/10.1016/j.cell.2017.11.023 10.1016/j.cell.2017.11.023]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29249356 24]. | #Brumbaugh J, Di Stefano B, Wang X, Borkent M, Forouzmand E, Clowers KJ, Ji F, Schwarz BA, Kalocsay M, Elledge SJ, Chen Y, Sadreyev RI, Gygi SP, Hu G, Shi Y, Hochedlinger K, (2018) "Nudt21 Controls Cell Fate by Connecting Alternative Polyadenylation to Chromatin Signaling." <i>Cell</i> <b>172</b>(1-2):106–120.e21; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29249356 29249356]; doi: [https://dx.doi.org/10.1016/j.cell.2017.11.023 10.1016/j.cell.2017.11.023]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29249356 24]. | ||
#Krogager TP, Ernst RJ, Elliott TS, Calo L, Beránek V, Ciabatti E, Spillantini MG, Tripodi M, Hastings MH, Chin JW, (2017) "Labeling and identifying cell-specific proteomes in the mouse brain." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29251727 29251727]; doi: [https://dx.doi.org/10.1038/nbt.4056 10.1038/nbt.4056]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29251727 33]. | #Krogager TP, Ernst RJ, Elliott TS, Calo L, Beránek V, Ciabatti E, Spillantini MG, Tripodi M, Hastings MH, Chin JW, (2017) "Labeling and identifying cell-specific proteomes in the mouse brain." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29251727 29251727]; doi: [https://dx.doi.org/10.1038/nbt.4056 10.1038/nbt.4056]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29251727 33]. | ||
+ | #Mackmull MT, Klaus B, Heinze I, Chokkalingam M, Beyer A, Russell RB, Ori A, Beck M, (2017) "Landscape of nuclear transport receptor cargo specificity." <i>Mol Syst Biol</i> <b>13</b>(12):962; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29254951 29254951]; doi: [https://dx.doi.org/10.15252/msb.20177608 10.15252/msb.20177608]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29254951 315]. | ||
#Bielecka ZF, Malinowska A, Brodaczewska KK, Klemba A, Kieda C, Krasowski P, Grzesiuk E, Piwowarski J, Czarnecka AM, Szczylik C, (2017) "Hypoxic 3D in vitro culture models reveal distinct resistance processes to TKIs in renal cancer cells." <i>Cell Biosci</i> <b>7</b>:71; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29270287 29270287]; doi: [https://dx.doi.org/10.1186/s13578-017-0197-8 10.1186/s13578-017-0197-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29270287 12]. | #Bielecka ZF, Malinowska A, Brodaczewska KK, Klemba A, Kieda C, Krasowski P, Grzesiuk E, Piwowarski J, Czarnecka AM, Szczylik C, (2017) "Hypoxic 3D in vitro culture models reveal distinct resistance processes to TKIs in renal cancer cells." <i>Cell Biosci</i> <b>7</b>:71; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29270287 29270287]; doi: [https://dx.doi.org/10.1186/s13578-017-0197-8 10.1186/s13578-017-0197-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29270287 12]. | ||
#Gao Y, Liu X, Tang B, Li C, Kou Z, Li L, Liu W, Wu Y, Kou X, Li J, Zhao Y, Yin J, Wang H, Chen S, Liao L, Gao S, (2017) "Protein Expression Landscape of Mouse Embryos during Pre-implantation Development." <i>Cell Rep</i> <b>21</b>(13):3957–3969; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29281840 29281840]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.11.111 10.1016/j.celrep.2017.11.111]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29281840 2]. | #Gao Y, Liu X, Tang B, Li C, Kou Z, Li L, Liu W, Wu Y, Kou X, Li J, Zhao Y, Yin J, Wang H, Chen S, Liao L, Gao S, (2017) "Protein Expression Landscape of Mouse Embryos during Pre-implantation Development." <i>Cell Rep</i> <b>21</b>(13):3957–3969; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29281840 29281840]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.11.111 10.1016/j.celrep.2017.11.111]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29281840 2]. | ||
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#Nilsen BW, Simon-Santamaria J, Örtengren U, Jensen E, Bruun JA, Michelsen VB, Sørensen KK, (2018) "Dose- and time-dependent effects of triethylene glycol dimethacrylate on the proteome of human THP-1 monocytes." <i>Eur J Oral Sci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30051916 30051916]; doi: [https://dx.doi.org/10.1111/eos.12559 10.1111/eos.12559]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30051916 92]. | #Nilsen BW, Simon-Santamaria J, Örtengren U, Jensen E, Bruun JA, Michelsen VB, Sørensen KK, (2018) "Dose- and time-dependent effects of triethylene glycol dimethacrylate on the proteome of human THP-1 monocytes." <i>Eur J Oral Sci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30051916 30051916]; doi: [https://dx.doi.org/10.1111/eos.12559 10.1111/eos.12559]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30051916 92]. | ||
#Stokman MF, Bijnsdorp IV, Schelfhorst T, Pham TV, Piersma SR, Knol JC, Giles RH, Bongers EMHF, Knoers NVAM, Lilien MR, Jiménez CR, Renkema KY, (2018) "Changes in the urinary extracellular vesicle proteome are associated with nephronophthisis-related ciliopathies." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30071318 30071318]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.07.008 10.1016/j.jprot.2018.07.008]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30071318 120]. | #Stokman MF, Bijnsdorp IV, Schelfhorst T, Pham TV, Piersma SR, Knol JC, Giles RH, Bongers EMHF, Knoers NVAM, Lilien MR, Jiménez CR, Renkema KY, (2018) "Changes in the urinary extracellular vesicle proteome are associated with nephronophthisis-related ciliopathies." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30071318 30071318]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.07.008 10.1016/j.jprot.2018.07.008]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30071318 120]. | ||
- | |||
#Park S, Park JH, Jung HJ, Jang JH, Ahn S, Kim Y, Suh PG, Chae S, Yoon JH, Ryu SH, Hwang D, (2018) "A secretome profile indicative of oleate-induced proliferation of HepG2 hepatocellular carcinoma cells." <i>Exp Mol Med</i> <b>50</b>(8):93; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30076294 30076294]; doi: [https://dx.doi.org/10.1038/s12276-018-0120-3 10.1038/s12276-018-0120-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30076294 24]. | #Park S, Park JH, Jung HJ, Jang JH, Ahn S, Kim Y, Suh PG, Chae S, Yoon JH, Ryu SH, Hwang D, (2018) "A secretome profile indicative of oleate-induced proliferation of HepG2 hepatocellular carcinoma cells." <i>Exp Mol Med</i> <b>50</b>(8):93; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30076294 30076294]; doi: [https://dx.doi.org/10.1038/s12276-018-0120-3 10.1038/s12276-018-0120-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30076294 24]. | ||
#de la Parra C, Ernlund A, Alard A, Ruggles K, Ueberheide B, Schneider RJ, (2018) "A widespread alternate form of cap-dependent mRNA translation initiation." <i>Nat Commun</i> <b>9</b>(1):3068; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30076308 30076308]; doi: [https://dx.doi.org/10.1038/s41467-018-05539-0 10.1038/s41467-018-05539-0]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30076308 21]. | #de la Parra C, Ernlund A, Alard A, Ruggles K, Ueberheide B, Schneider RJ, (2018) "A widespread alternate form of cap-dependent mRNA translation initiation." <i>Nat Commun</i> <b>9</b>(1):3068; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30076308 30076308]; doi: [https://dx.doi.org/10.1038/s41467-018-05539-0 10.1038/s41467-018-05539-0]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30076308 21]. | ||
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#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]. | #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]. | ||
+ | #Shraibman B, Barnea E, Kadosh DM, Haimovich Y, Slobodin G, Rosner I, López-Larrea C, Hilf N, Kuttruff S, Song C, Britten C, Castle J, Kreiter S, Frenzel K, Tatagiba M, Tabatabai G, Dietrich PY, Dutoit V, Wick W, Platten M, Winkler F, von Deimling A, Kroep J, Sahuquillo J, Martinez-Ricarte F, Rodon J, Lassen U, Ottensmeier C, van der Burg SH, Thor Straten P, Poulsen HS, Ponsati B, Okada H, Rammensee HG, Sahin U, Singh H, Admon A, (2019) "Identification of Tumor Antigens Among the HLA Peptidomes of Glioblastoma Tumors and Plasma." <i>Mol Cell Proteomics</i> <b>18</b>(6):1255–1268; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31154438 31154438]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001524 10.1074/mcp.RA119.001524]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31154438 75]. | ||
#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]. | ||
#Wang Y, Tatham MH, Schmidt-Heck W, Swann C, Singh-Dolt K, Meseguer-Ripolles J, Lucendo-Villarin B, Kunath T, Rudd TR, Smith AJH, Hengstler JG, Godoy P, Hay RT, Hay DC, (2019) "Multiomics Analyses of HNF4α Protein Domain Function during Human Pluripotent Stem Cell Differentiation." <i>iScience</i> <b>16</b>:206–217; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31185456 31185456]; doi: [https://dx.doi.org/10.1016/j.isci.2019.05.028 10.1016/j.isci.2019.05.028]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31185456 96]. | #Wang Y, Tatham MH, Schmidt-Heck W, Swann C, Singh-Dolt K, Meseguer-Ripolles J, Lucendo-Villarin B, Kunath T, Rudd TR, Smith AJH, Hengstler JG, Godoy P, Hay RT, Hay DC, (2019) "Multiomics Analyses of HNF4α Protein Domain Function during Human Pluripotent Stem Cell Differentiation." <i>iScience</i> <b>16</b>:206–217; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31185456 31185456]; doi: [https://dx.doi.org/10.1016/j.isci.2019.05.028 10.1016/j.isci.2019.05.028]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31185456 96]. | ||
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#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]. | #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]. | ||
+ | #Deshmukh AS, Peijs L, Beaudry JL, Jespersen NZ, Nielsen CH, Ma T, Brunner AD, Larsen TJ, Bayarri-Olmos R, Prabhakar BS, Helgstrand C, Severinsen MCK, Holst B, Kjaer A, Tang-Christensen M, Sanfridson A, Garred P, Privé GG, Pedersen BK, Gerhart-Hines Z, Nielsen S, Drucker DJ, Mann M, Scheele C, (2019) "Proteomics-Based Comparative Mapping of the Secretomes of Human Brown and White Adipocytes Reveals EPDR1 as a Novel Batokine." <i>Cell Metab</i> <b>30</b>(5):963–975.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31668873 31668873]; doi: [https://dx.doi.org/10.1016/j.cmet.2019.10.001 10.1016/j.cmet.2019.10.001]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31668873 28]. | ||
#Alvarez Hayes J, Surmann K, Lamberti Y, Depke M, Dhople V, Blancá B, Ruiz E, Vecerek B, Schmidt F, Völker U, Rodriguez ME, (2020) "Hfq modulates global protein pattern and stress response in Bordetella pertussis." <i>J Proteomics</i> <b>211</b>:103559; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31669358 31669358]; doi: [https://dx.doi.org/10.1016/j.jprot.2019.103559 10.1016/j.jprot.2019.103559]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31669358 16]. | #Alvarez Hayes J, Surmann K, Lamberti Y, Depke M, Dhople V, Blancá B, Ruiz E, Vecerek B, Schmidt F, Völker U, Rodriguez ME, (2020) "Hfq modulates global protein pattern and stress response in Bordetella pertussis." <i>J Proteomics</i> <b>211</b>:103559; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31669358 31669358]; doi: [https://dx.doi.org/10.1016/j.jprot.2019.103559 10.1016/j.jprot.2019.103559]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31669358 16]. | ||
#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 61]. | #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 61]. | ||
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#Ojalill M, Virtanen N, Rappu P, Siljamäki E, Taimen P, Heino J, (2020) "Interaction between prostate cancer cells and prostate fibroblasts promotes accumulation and proteolytic processing of basement membrane proteins." <i>Prostate</i> <b>80</b>(9):715–726; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32364250 32364250]; doi: [https://dx.doi.org/10.1002/pros.23985 10.1002/pros.23985]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32364250 18]. | #Ojalill M, Virtanen N, Rappu P, Siljamäki E, Taimen P, Heino J, (2020) "Interaction between prostate cancer cells and prostate fibroblasts promotes accumulation and proteolytic processing of basement membrane proteins." <i>Prostate</i> <b>80</b>(9):715–726; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32364250 32364250]; doi: [https://dx.doi.org/10.1002/pros.23985 10.1002/pros.23985]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32364250 18]. | ||
#Bekes K, Mitulović G, Meißner N, Resch U, Gruber R, (2020) "Saliva proteomic patterns in patients with molar incisor hypomineralization." <i>Sci Rep</i> <b>10</b>(1):7560; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32371984 32371984]; doi: [https://dx.doi.org/10.1038/s41598-020-64614-z 10.1038/s41598-020-64614-z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32371984 10]. | #Bekes K, Mitulović G, Meißner N, Resch U, Gruber R, (2020) "Saliva proteomic patterns in patients with molar incisor hypomineralization." <i>Sci Rep</i> <b>10</b>(1):7560; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32371984 32371984]; doi: [https://dx.doi.org/10.1038/s41598-020-64614-z 10.1038/s41598-020-64614-z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32371984 10]. | ||
+ | #Bansal P, Madlung J, Schaaf K, Macek B, Bono F, (2020) "An interaction network of RNA-binding proteins involved in Drosophila oogenesis." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32554711 32554711]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001912 10.1074/mcp.RA119.001912]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32554711 24]. | ||
#Zecha J, Lee CY, Bayer FP, Meng C, Grass V, Zerweck J, Schnatbaum K, Michler T, Pichlmair A, Ludwig C, Kuster B, (2020) "Data, reagents, assays and merits of proteomics for SARS-CoV-2 research and testing." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32591346 32591346]; doi: [https://dx.doi.org/10.1074/mcp.RA120.002164 10.1074/mcp.RA120.002164]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32591346 96]. | #Zecha J, Lee CY, Bayer FP, Meng C, Grass V, Zerweck J, Schnatbaum K, Michler T, Pichlmair A, Ludwig C, Kuster B, (2020) "Data, reagents, assays and merits of proteomics for SARS-CoV-2 research and testing." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32591346 32591346]; doi: [https://dx.doi.org/10.1074/mcp.RA120.002164 10.1074/mcp.RA120.002164]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32591346 96]. | ||
+ | #Chen Q, Samidurai A, Thompson J, Hu Y, Das A, Willard B, Lesnefsky EJ, (2020) "Endoplasmic reticulum stress-mediated mitochondrial dysfunction in aged hearts." <i>Biochim Biophys Acta Mol Basis Dis</i> <b>1866</b>(11):165899; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32698045 32698045]; doi: [https://dx.doi.org/10.1016/j.bbadis.2020.165899 10.1016/j.bbadis.2020.165899]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32698045 18]. | ||
+ | #Steiner G, Marban-Doran C, Langer J, Pimenova T, Duran-Pacheco G, Sauter D, Langenkamp A, Solier C, Singer T, Bray-French K, Ducret A, (2020) "Enabling Routine MHC-II-Associated Peptide Proteomics for Risk Assessment of Drug-Induced Immunogenicity." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32786679 32786679]; doi: [https://dx.doi.org/10.1021/acs.jproteome.0c00309 10.1021/acs.jproteome.0c00309]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32786679 162]. | ||
+ | #Kirak O, Ke E, Yang KY, Schwarz A, Plate L, Nham A, Abadejos JR, Valencia A, Wiseman RL, Lui KO, Ku M, (2020) "Premature Activation of Immune Transcription Programs in Autoimmune-Predisposed Mouse Embryonic Stem Cells and Blastocysts." <i>Int J Mol Sci</i> <b>21</b>(16):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32796510 32796510]; doi: [https://dx.doi.org/10.3390/ijms21165743 10.3390/ijms21165743]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32796510 1]. | ||
+ | #Leng L, Cao R, Ma J, Mou D, Zhu Y, Li W, Lv L, Gao D, Zhang S, Gong F, Zhao L, Qiu B, Xiang H, Hu Z, Feng Y, Dai Y, Zhao J, Wu Z, Li H, Zhong W, (2020) "Pathological features of COVID-19-associated lung injury: a preliminary proteomics report based on clinical samples." <i>Signal Transduct Target Ther</i> <b>5</b>(1):240; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/33060566 33060566]; doi: [https://dx.doi.org/10.1038/s41392-020-00355-9 10.1038/s41392-020-00355-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33060566 13]. | ||
+ | #Tijms BM, Gobom J, Reus L, Jansen I, Hong S, Dobricic V, Kilpert F, Ten Kate M, Barkhof F, Tsolaki M, Verhey FRJ, Popp J, Martinez-Lage P, Vandenberghe R, Lleó A, Molinuevo JL, Engelborghs S, Bertram L, Lovestone S, Streffer J, Vos S, Bos I, Alzheimer’s Disease Neuroimaging Initiative (ADNI)., Blennow K, Scheltens P, Teunissen CE, Zetterberg H, Visser PJ, (2020) "Pathophysiological subtypes of Alzheimer's disease based on cerebrospinal fluid proteomics." <i>Brain</i> <b>143</b>(12):3776–3792; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/33439986 33439986]; doi: [https://dx.doi.org/10.1093/brain/awaa325 10.1093/brain/awaa325]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33439986 36]. | ||
+ | #Lobato-Gil S, Heidelberger JB, Maghames C, Bailly A, Brunello L, Rodriguez MS, Beli P, Xirodimas DP, (2021) "Proteome-wide identification of NEDD8 modification sites reveals distinct proteomes for canonical and atypical NEDDylation." <i>Cell Rep</i> <b>34</b>(3):108635; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/33472076 33472076]; doi: [https://dx.doi.org/10.1016/j.celrep.2020.108635 10.1016/j.celrep.2020.108635]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33472076 24]. | ||
+ | #Del Favero G, Janker L, Neuditschko B, Hohenbichler J, Kiss E, Woelflingseder L, Gerner C, Marko D, (2021) "Exploring the dermotoxicity of the mycotoxin deoxynivalenol: combined morphologic and proteomic profiling of human epidermal cells reveals alteration of lipid biosynthesis machinery and membrane structural integrity relevant for skin barrier function." <i>Arch Toxicol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/33890134 33890134]; doi: [https://dx.doi.org/10.1007/s00204-021-03042-y 10.1007/s00204-021-03042-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33890134 58]. |
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 July 20, 2021.