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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 Apr 10, 2022. |
#Lipton MS, <i>et al.</i> (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: [https://pubmed.ncbi.nlm.nih.gov/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, <i>et al.</i> (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: [https://pubmed.ncbi.nlm.nih.gov/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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#Giovani PA, <i>et al.</i> (2019) "Membrane proteome characterization of periodontal ligament cell sets from deciduous and permanent teeth." <i>J Periodontol</i> <b>90</b>(7):775–787; PMID: [https://pubmed.ncbi.nlm.nih.gov/30499115 30499115]; doi: [https://dx.doi.org/10.1002/JPER.18-0217 10.1002/JPER.18-0217]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30499115 6]. | #Giovani PA, <i>et al.</i> (2019) "Membrane proteome characterization of periodontal ligament cell sets from deciduous and permanent teeth." <i>J Periodontol</i> <b>90</b>(7):775–787; PMID: [https://pubmed.ncbi.nlm.nih.gov/30499115 30499115]; doi: [https://dx.doi.org/10.1002/JPER.18-0217 10.1002/JPER.18-0217]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30499115 6]. | ||
#Gruhlke MCH, <i>et al.</i> (2019) "The human allicin-proteome: S-thioallylation of proteins by the garlic defence substance allicin and its biological effects." <i>Free Radic Biol Med</i> <b>131</b>:144–153; PMID: [https://pubmed.ncbi.nlm.nih.gov/30500420 30500420]; doi: [https://dx.doi.org/10.1016/j.freeradbiomed.2018.11.022 10.1016/j.freeradbiomed.2018.11.022]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30500420 24]. | #Gruhlke MCH, <i>et al.</i> (2019) "The human allicin-proteome: S-thioallylation of proteins by the garlic defence substance allicin and its biological effects." <i>Free Radic Biol Med</i> <b>131</b>:144–153; PMID: [https://pubmed.ncbi.nlm.nih.gov/30500420 30500420]; doi: [https://dx.doi.org/10.1016/j.freeradbiomed.2018.11.022 10.1016/j.freeradbiomed.2018.11.022]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30500420 24]. | ||
+ | #Xiong F, <i>et al.</i> (2019) "Quantitative proteomics reveals distinct composition of amyloid plaques in Alzheimer's disease." <i>Alzheimers Dement</i> <b>15</b>(3):429–440; PMID: [https://pubmed.ncbi.nlm.nih.gov/30502339 30502339]; doi: [https://dx.doi.org/10.1016/j.jalz.2018.10.006 10.1016/j.jalz.2018.10.006]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30502339 1]. | ||
#Wolf A, <i>et al.</i> (2018) "Olfactory cleft proteome does not reflect olfactory performance in patients with idiopathic and postinfectious olfactory disorder: A pilot study." <i>Sci Rep</i> <b>8</b>(1):17554; PMID: [https://pubmed.ncbi.nlm.nih.gov/30510230 30510230]; doi: [https://dx.doi.org/10.1038/s41598-018-35776-8 10.1038/s41598-018-35776-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30510230 21]. | #Wolf A, <i>et al.</i> (2018) "Olfactory cleft proteome does not reflect olfactory performance in patients with idiopathic and postinfectious olfactory disorder: A pilot study." <i>Sci Rep</i> <b>8</b>(1):17554; PMID: [https://pubmed.ncbi.nlm.nih.gov/30510230 30510230]; doi: [https://dx.doi.org/10.1038/s41598-018-35776-8 10.1038/s41598-018-35776-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30510230 21]. | ||
#Tascher G, <i>et al.</i> (2019) "Analysis of femurs from mice embarked on board BION-M1 biosatellite reveals a decrease in immune cell development, including B cells, after 1 wk of recovery on Earth." <i>FASEB J</i> <b>33</b>(3):3772–3783; PMID: [https://pubmed.ncbi.nlm.nih.gov/30521760 30521760]; doi: [https://dx.doi.org/10.1096/fj.201801463R 10.1096/fj.201801463R]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30521760 36]. | #Tascher G, <i>et al.</i> (2019) "Analysis of femurs from mice embarked on board BION-M1 biosatellite reveals a decrease in immune cell development, including B cells, after 1 wk of recovery on Earth." <i>FASEB J</i> <b>33</b>(3):3772–3783; PMID: [https://pubmed.ncbi.nlm.nih.gov/30521760 30521760]; doi: [https://dx.doi.org/10.1096/fj.201801463R 10.1096/fj.201801463R]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30521760 36]. | ||
Line 2,033: | Line 2,034: | ||
#Liu Z, <i>et al.</i> (2019) "Integrative Transcriptome and Proteome Analysis Identifies Major Metabolic Pathways Involved in Pepper Fruit Development." <i>J Proteome Res</i> <b>18</b>(3):982–994; PMID: [https://pubmed.ncbi.nlm.nih.gov/30650966 30650966]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00673 10.1021/acs.jproteome.8b00673]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30650966 24]. | #Liu Z, <i>et al.</i> (2019) "Integrative Transcriptome and Proteome Analysis Identifies Major Metabolic Pathways Involved in Pepper Fruit Development." <i>J Proteome Res</i> <b>18</b>(3):982–994; PMID: [https://pubmed.ncbi.nlm.nih.gov/30650966 30650966]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00673 10.1021/acs.jproteome.8b00673]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30650966 24]. | ||
#van Oorschot R, <i>et al.</i> (2019) "Molecular mechanisms of bleeding disorderassociated GFI1B<sup>Q287*</sup> mutation and its affected pathways in megakaryocytes and platelets." <i>Haematologica</i> <b>104</b>(7):1460–1472; PMID: [https://pubmed.ncbi.nlm.nih.gov/30655368 30655368]; doi: [https://dx.doi.org/10.3324/haematol.2018.194555 10.3324/haematol.2018.194555]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30655368 63]. | #van Oorschot R, <i>et al.</i> (2019) "Molecular mechanisms of bleeding disorderassociated GFI1B<sup>Q287*</sup> mutation and its affected pathways in megakaryocytes and platelets." <i>Haematologica</i> <b>104</b>(7):1460–1472; PMID: [https://pubmed.ncbi.nlm.nih.gov/30655368 30655368]; doi: [https://dx.doi.org/10.3324/haematol.2018.194555 10.3324/haematol.2018.194555]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30655368 63]. | ||
+ | #Kosmacz M, <i>et al.</i> (2019) "Protein and metabolite composition of Arabidopsis stress granules." <i>New Phytol</i> <b>222</b>(3):1420–1433; PMID: [https://pubmed.ncbi.nlm.nih.gov/30664249 30664249]; doi: [https://dx.doi.org/10.1111/nph.15690 10.1111/nph.15690]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30664249 20]. | ||
#Tsukada T, <i>et al.</i> (2019) "Identification of TGFβ-induced proteins in non-endocrine mouse pituitary cell line TtT/GF by SILAC-assisted quantitative mass spectrometry." <i>Cell Tissue Res</i> <b>376</b>(2):281–293; PMID: [https://pubmed.ncbi.nlm.nih.gov/30666536 30666536]; doi: [https://dx.doi.org/10.1007/s00441-018-02989-2 10.1007/s00441-018-02989-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30666536 11]. | #Tsukada T, <i>et al.</i> (2019) "Identification of TGFβ-induced proteins in non-endocrine mouse pituitary cell line TtT/GF by SILAC-assisted quantitative mass spectrometry." <i>Cell Tissue Res</i> <b>376</b>(2):281–293; PMID: [https://pubmed.ncbi.nlm.nih.gov/30666536 30666536]; doi: [https://dx.doi.org/10.1007/s00441-018-02989-2 10.1007/s00441-018-02989-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30666536 11]. | ||
#Gärtner SMK, <i>et al.</i> (2019) "Stage-specific testes proteomics of Drosophila melanogaster identifies essential proteins for male fertility." <i>Eur J Cell Biol</i> <b>98</b>(2-4):103–115; PMID: [https://pubmed.ncbi.nlm.nih.gov/30679029 30679029]; doi: [https://dx.doi.org/10.1016/j.ejcb.2019.01.001 10.1016/j.ejcb.2019.01.001]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30679029 180]. | #Gärtner SMK, <i>et al.</i> (2019) "Stage-specific testes proteomics of Drosophila melanogaster identifies essential proteins for male fertility." <i>Eur J Cell Biol</i> <b>98</b>(2-4):103–115; PMID: [https://pubmed.ncbi.nlm.nih.gov/30679029 30679029]; doi: [https://dx.doi.org/10.1016/j.ejcb.2019.01.001 10.1016/j.ejcb.2019.01.001]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30679029 180]. | ||
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#Voß H, <i>et al.</i> (2020) "Differential regulation of extracellular matrix proteins in three recurrent liver metastases of a single patient with colorectal cancer." <i>Clin Exp Metastasis</i> <b>37</b>(6):649–656; PMID: [https://pubmed.ncbi.nlm.nih.gov/33099724 33099724]; doi: [https://dx.doi.org/10.1007/s10585-020-10058-8 10.1007/s10585-020-10058-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33099724 12]. | #Voß H, <i>et al.</i> (2020) "Differential regulation of extracellular matrix proteins in three recurrent liver metastases of a single patient with colorectal cancer." <i>Clin Exp Metastasis</i> <b>37</b>(6):649–656; PMID: [https://pubmed.ncbi.nlm.nih.gov/33099724 33099724]; doi: [https://dx.doi.org/10.1007/s10585-020-10058-8 10.1007/s10585-020-10058-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33099724 12]. | ||
#Di Meo A, <i>et al.</i> (2021) "Proteomic Profiling of the Human Tissue and Biological Fluid Proteome." <i>J Proteome Res</i> <b>20</b>(1):444–452; PMID: [https://pubmed.ncbi.nlm.nih.gov/33107741 33107741]; doi: [https://dx.doi.org/10.1021/acs.jproteome.0c00502 10.1021/acs.jproteome.0c00502]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33107741 92]. | #Di Meo A, <i>et al.</i> (2021) "Proteomic Profiling of the Human Tissue and Biological Fluid Proteome." <i>J Proteome Res</i> <b>20</b>(1):444–452; PMID: [https://pubmed.ncbi.nlm.nih.gov/33107741 33107741]; doi: [https://dx.doi.org/10.1021/acs.jproteome.0c00502 10.1021/acs.jproteome.0c00502]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33107741 92]. | ||
+ | #Swanson LC, <i>et al.</i> (2020) "Survival Following Traumatic Brain Injury in <i>Drosophila</i> Is Increased by Heterozygosity for a Mutation of the NF-κB Innate Immune Response Transcription Factor Relish." <i>Genetics</i> <b>216</b>(4):1117–1136; PMID: [https://pubmed.ncbi.nlm.nih.gov/33109529 33109529]; doi: [https://dx.doi.org/10.1534/genetics.120.303776 10.1534/genetics.120.303776]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33109529 61]. | ||
#Alayi TD, <i>et al.</i> (2020) "Tandem Mass Tag-Based Serum Proteome Profiling for Biomarker Discovery in Young Duchenne Muscular Dystrophy Boys." <i>ACS Omega</i> <b>5</b>(41):26504–26517; PMID: [https://pubmed.ncbi.nlm.nih.gov/33110978 33110978]; doi: [https://dx.doi.org/10.1021/acsomega.0c03206 10.1021/acsomega.0c03206]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33110978 72]. | #Alayi TD, <i>et al.</i> (2020) "Tandem Mass Tag-Based Serum Proteome Profiling for Biomarker Discovery in Young Duchenne Muscular Dystrophy Boys." <i>ACS Omega</i> <b>5</b>(41):26504–26517; PMID: [https://pubmed.ncbi.nlm.nih.gov/33110978 33110978]; doi: [https://dx.doi.org/10.1021/acsomega.0c03206 10.1021/acsomega.0c03206]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33110978 72]. | ||
#Gibbard E, <i>et al.</i> (2021) "Whole-proteome analysis of mesonephric-derived cancers describes new potential biomarkers." <i>Hum Pathol</i> <b>108</b>:1–11; PMID: [https://pubmed.ncbi.nlm.nih.gov/33121982 33121982]; doi: [https://dx.doi.org/10.1016/j.humpath.2020.10.005 10.1016/j.humpath.2020.10.005]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33121982 8]. | #Gibbard E, <i>et al.</i> (2021) "Whole-proteome analysis of mesonephric-derived cancers describes new potential biomarkers." <i>Hum Pathol</i> <b>108</b>:1–11; PMID: [https://pubmed.ncbi.nlm.nih.gov/33121982 33121982]; doi: [https://dx.doi.org/10.1016/j.humpath.2020.10.005 10.1016/j.humpath.2020.10.005]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33121982 8]. | ||
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#Ouni E, <i>et al.</i> (2020) "Divide-and-Conquer Matrisome Protein (DC-MaP) Strategy: An MS-Friendly Approach to Proteomic Matrisome Characterization." <i>Int J Mol Sci</i> <b>21</b>(23):; PMID: [https://pubmed.ncbi.nlm.nih.gov/33266304 33266304]; doi: [https://dx.doi.org/10.3390/ijms21239141 10.3390/ijms21239141]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33266304 90]. | #Ouni E, <i>et al.</i> (2020) "Divide-and-Conquer Matrisome Protein (DC-MaP) Strategy: An MS-Friendly Approach to Proteomic Matrisome Characterization." <i>Int J Mol Sci</i> <b>21</b>(23):; PMID: [https://pubmed.ncbi.nlm.nih.gov/33266304 33266304]; doi: [https://dx.doi.org/10.3390/ijms21239141 10.3390/ijms21239141]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33266304 90]. | ||
#Braun F, <i>et al.</i> (2020) "The proteomic landscape of small urinary extracellular vesicles during kidney transplantation." <i>J Extracell Vesicles</i> <b>10</b>(1):e12026; PMID: [https://pubmed.ncbi.nlm.nih.gov/33304478 33304478]; doi: [https://dx.doi.org/10.1002/jev2.12026 10.1002/jev2.12026]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33304478 89]. | #Braun F, <i>et al.</i> (2020) "The proteomic landscape of small urinary extracellular vesicles during kidney transplantation." <i>J Extracell Vesicles</i> <b>10</b>(1):e12026; PMID: [https://pubmed.ncbi.nlm.nih.gov/33304478 33304478]; doi: [https://dx.doi.org/10.1002/jev2.12026 10.1002/jev2.12026]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33304478 89]. | ||
+ | #Jacomin AC, <i>et al.</i> (2021) "Degradation of arouser by endosomal microautophagy is essential for adaptation to starvation in <i>Drosophila</i>." <i>Life Sci Alliance</i> <b>4</b>(2):; PMID: [https://pubmed.ncbi.nlm.nih.gov/33318080 33318080]; doi: [https://dx.doi.org/10.26508/lsa.202000965 10.26508/lsa.202000965]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33318080 8]. | ||
#Bailey A, <i>et al.</i> (2021) "Characterization of the Class I MHC Peptidome Resulting From DNCB Exposure of HaCaT Cells." <i>Toxicol Sci</i> <b>180</b>(1):136–147; PMID: [https://pubmed.ncbi.nlm.nih.gov/33372950 33372950]; doi: [https://dx.doi.org/10.1093/toxsci/kfaa184 10.1093/toxsci/kfaa184]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33372950 35]. | #Bailey A, <i>et al.</i> (2021) "Characterization of the Class I MHC Peptidome Resulting From DNCB Exposure of HaCaT Cells." <i>Toxicol Sci</i> <b>180</b>(1):136–147; PMID: [https://pubmed.ncbi.nlm.nih.gov/33372950 33372950]; doi: [https://dx.doi.org/10.1093/toxsci/kfaa184 10.1093/toxsci/kfaa184]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33372950 35]. | ||
#Lepa C, <i>et al.</i> (2021) "TrkC Is Essential for Nephron Function and Trans-Activates Igf1R Signaling." <i>J Am Soc Nephrol</i> <b>32</b>(2):357–374; PMID: [https://pubmed.ncbi.nlm.nih.gov/33380522 33380522]; doi: [https://dx.doi.org/10.1681/ASN.2020040424 10.1681/ASN.2020040424]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33380522 143]. | #Lepa C, <i>et al.</i> (2021) "TrkC Is Essential for Nephron Function and Trans-Activates Igf1R Signaling." <i>J Am Soc Nephrol</i> <b>32</b>(2):357–374; PMID: [https://pubmed.ncbi.nlm.nih.gov/33380522 33380522]; doi: [https://dx.doi.org/10.1681/ASN.2020040424 10.1681/ASN.2020040424]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33380522 143]. | ||
#Tam V, <i>et al.</i> (2020) "DIPPER, a spatiotemporal proteomics atlas of human intervertebral discs for exploring ageing and degeneration dynamics." <i>Elife</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/33382035 33382035]; doi: [https://dx.doi.org/10.7554/eLife.64940 10.7554/eLife.64940]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33382035 263]. | #Tam V, <i>et al.</i> (2020) "DIPPER, a spatiotemporal proteomics atlas of human intervertebral discs for exploring ageing and degeneration dynamics." <i>Elife</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/33382035 33382035]; doi: [https://dx.doi.org/10.7554/eLife.64940 10.7554/eLife.64940]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33382035 263]. | ||
+ | #Barbosa P, <i>et al.</i> (2021) "SCF-Fbxo42 promotes synaptonemal complex assembly by downregulating PP2A-B56." <i>J Cell Biol</i> <b>220</b>(2):; PMID: [https://pubmed.ncbi.nlm.nih.gov/33382409 33382409]; doi: [https://dx.doi.org/10.1083/jcb.202009167 10.1083/jcb.202009167]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33382409 14]. | ||
#Subbannayya Y, <i>et al.</i> (2020) "The Proteomic Landscape of Resting and Activated CD4+ T Cells Reveal Insights into Cell Differentiation and Function." <i>Int J Mol Sci</i> <b>22</b>(1):; PMID: [https://pubmed.ncbi.nlm.nih.gov/33383959 33383959]; doi: [https://dx.doi.org/10.3390/ijms22010275 10.3390/ijms22010275]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33383959 3]. | #Subbannayya Y, <i>et al.</i> (2020) "The Proteomic Landscape of Resting and Activated CD4+ T Cells Reveal Insights into Cell Differentiation and Function." <i>Int J Mol Sci</i> <b>22</b>(1):; PMID: [https://pubmed.ncbi.nlm.nih.gov/33383959 33383959]; doi: [https://dx.doi.org/10.3390/ijms22010275 10.3390/ijms22010275]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33383959 3]. | ||
#Dietze R, <i>et al.</i> (2021) "Phosphoproteomics identify arachidonic-acid-regulated signal transduction pathways modulating macrophage functions with implications for ovarian cancer." <i>Theranostics</i> <b>11</b>(3):1377–1395; PMID: [https://pubmed.ncbi.nlm.nih.gov/33391540 33391540]; doi: [https://dx.doi.org/10.7150/thno.52442 10.7150/thno.52442]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33391540 63]. | #Dietze R, <i>et al.</i> (2021) "Phosphoproteomics identify arachidonic-acid-regulated signal transduction pathways modulating macrophage functions with implications for ovarian cancer." <i>Theranostics</i> <b>11</b>(3):1377–1395; PMID: [https://pubmed.ncbi.nlm.nih.gov/33391540 33391540]; doi: [https://dx.doi.org/10.7150/thno.52442 10.7150/thno.52442]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33391540 63]. | ||
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#Huang KK, <i>et al.</i> (2021) "Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer." <i>Genome Biol</i> <b>22</b>(1):44; PMID: [https://pubmed.ncbi.nlm.nih.gov/33482911 33482911]; doi: [https://dx.doi.org/10.1186/s13059-021-02261-x 10.1186/s13059-021-02261-x]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33482911 80]. | #Huang KK, <i>et al.</i> (2021) "Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer." <i>Genome Biol</i> <b>22</b>(1):44; PMID: [https://pubmed.ncbi.nlm.nih.gov/33482911 33482911]; doi: [https://dx.doi.org/10.1186/s13059-021-02261-x 10.1186/s13059-021-02261-x]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33482911 80]. | ||
#Osório H, <i>et al.</i> (2021) "Proteomics Analysis of Gastric Cancer Patients with Diabetes Mellitus." <i>J Clin Med</i> <b>10</b>(3):; PMID: [https://pubmed.ncbi.nlm.nih.gov/33494396 33494396]; doi: [https://dx.doi.org/10.3390/jcm10030407 10.3390/jcm10030407]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33494396 40]. | #Osório H, <i>et al.</i> (2021) "Proteomics Analysis of Gastric Cancer Patients with Diabetes Mellitus." <i>J Clin Med</i> <b>10</b>(3):; PMID: [https://pubmed.ncbi.nlm.nih.gov/33494396 33494396]; doi: [https://dx.doi.org/10.3390/jcm10030407 10.3390/jcm10030407]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33494396 40]. | ||
+ | #Recasens-Alvarez C, <i>et al.</i> (2021) "Ribosomopathy-associated mutations cause proteotoxic stress that is alleviated by TOR inhibition." <i>Nat Cell Biol</i> <b>23</b>(2):127–135; PMID: [https://pubmed.ncbi.nlm.nih.gov/33495632 33495632]; doi: [https://dx.doi.org/10.1038/s41556-020-00626-1 10.1038/s41556-020-00626-1]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33495632 8]. | ||
#Amer N, <i>et al.</i> (2021) "Aggresomes predict poor outcomes and implicate proteostasis in the pathogenesis of pediatric choroid plexus tumors." <i>J Neurooncol</i> <b>152</b>(1):67–78; PMID: [https://pubmed.ncbi.nlm.nih.gov/33501605 33501605]; doi: [https://dx.doi.org/10.1007/s11060-020-03694-3 10.1007/s11060-020-03694-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33501605 84]. | #Amer N, <i>et al.</i> (2021) "Aggresomes predict poor outcomes and implicate proteostasis in the pathogenesis of pediatric choroid plexus tumors." <i>J Neurooncol</i> <b>152</b>(1):67–78; PMID: [https://pubmed.ncbi.nlm.nih.gov/33501605 33501605]; doi: [https://dx.doi.org/10.1007/s11060-020-03694-3 10.1007/s11060-020-03694-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33501605 84]. | ||
#González-Prieto R, <i>et al.</i> (2021) "Global non-covalent SUMO interaction networks reveal SUMO-dependent stabilization of the non-homologous end joining complex." <i>Cell Rep</i> <b>34</b>(4):108691; PMID: [https://pubmed.ncbi.nlm.nih.gov/33503430 33503430]; doi: [https://dx.doi.org/10.1016/j.celrep.2021.108691 10.1016/j.celrep.2021.108691]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33503430 12]. | #González-Prieto R, <i>et al.</i> (2021) "Global non-covalent SUMO interaction networks reveal SUMO-dependent stabilization of the non-homologous end joining complex." <i>Cell Rep</i> <b>34</b>(4):108691; PMID: [https://pubmed.ncbi.nlm.nih.gov/33503430 33503430]; doi: [https://dx.doi.org/10.1016/j.celrep.2021.108691 10.1016/j.celrep.2021.108691]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33503430 12]. | ||
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#Krishnan RK, <i>et al.</i> (2021) "Revisiting the Role of <i>ß</i>-Tubulin in <i>Drosophila</i> Development: <i>β-tubulin60D</i> is not an Essential Gene, and its Novel <i>Pin</i> <sup><i>1</i></sup> Allele has a Tissue-Specific Dominant-Negative Impact." <i>Front Cell Dev Biol</i> <b>9</b>:787976; PMID: [https://pubmed.ncbi.nlm.nih.gov/35111755 35111755]; doi: [https://dx.doi.org/10.3389/fcell.2021.787976 10.3389/fcell.2021.787976]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35111755 6]. | #Krishnan RK, <i>et al.</i> (2021) "Revisiting the Role of <i>ß</i>-Tubulin in <i>Drosophila</i> Development: <i>β-tubulin60D</i> is not an Essential Gene, and its Novel <i>Pin</i> <sup><i>1</i></sup> Allele has a Tissue-Specific Dominant-Negative Impact." <i>Front Cell Dev Biol</i> <b>9</b>:787976; PMID: [https://pubmed.ncbi.nlm.nih.gov/35111755 35111755]; doi: [https://dx.doi.org/10.3389/fcell.2021.787976 10.3389/fcell.2021.787976]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35111755 6]. | ||
#Correll VL, <i>et al.</i> (2022) "Optimization of small extracellular vesicle isolation from expressed prostatic secretions in urine for in-depth proteomic analysis." <i>J Extracell Vesicles</i> <b>11</b>(2):e12184; PMID: [https://pubmed.ncbi.nlm.nih.gov/35119778 35119778]; doi: [https://dx.doi.org/10.1002/jev2.12184 10.1002/jev2.12184]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35119778 9]. | #Correll VL, <i>et al.</i> (2022) "Optimization of small extracellular vesicle isolation from expressed prostatic secretions in urine for in-depth proteomic analysis." <i>J Extracell Vesicles</i> <b>11</b>(2):e12184; PMID: [https://pubmed.ncbi.nlm.nih.gov/35119778 35119778]; doi: [https://dx.doi.org/10.1002/jev2.12184 10.1002/jev2.12184]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35119778 9]. | ||
- | #Wang C, <i>et al.</i> (2022) "Stat4 rs7574865 polymorphism promotes the occurrence and progression of hepatocellular carcinoma via the Stat4/CYP2E1/FGL2 pathway." <i>Cell Death Dis</i> <b>13</b>(2):130; PMID: [https://pubmed.ncbi.nlm.nih.gov/35136014 35136014]; doi: [https://dx.doi.org/10.1038/s41419-022-04584-4 10.1038/s41419-022-04584-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35136014 | + | #Wang C, <i>et al.</i> (2022) "Stat4 rs7574865 polymorphism promotes the occurrence and progression of hepatocellular carcinoma via the Stat4/CYP2E1/FGL2 pathway." <i>Cell Death Dis</i> <b>13</b>(2):130; PMID: [https://pubmed.ncbi.nlm.nih.gov/35136014 35136014]; doi: [https://dx.doi.org/10.1038/s41419-022-04584-4 10.1038/s41419-022-04584-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35136014 93]. |
#Rezaei-Gazik M, <i>et al.</i> (2022) "Direct visualization of pre-protamine 2 detects protamine assembly failures and predicts ICSI success." <i>Mol Hum Reprod</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/35150275 35150275]; doi: [https://dx.doi.org/10.1093/molehr/gaac004 10.1093/molehr/gaac004]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35150275 24]. | #Rezaei-Gazik M, <i>et al.</i> (2022) "Direct visualization of pre-protamine 2 detects protamine assembly failures and predicts ICSI success." <i>Mol Hum Reprod</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/35150275 35150275]; doi: [https://dx.doi.org/10.1093/molehr/gaac004 10.1093/molehr/gaac004]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35150275 24]. | ||
+ | #Aiello G, <i>et al.</i> (2022) "Oxidative Stress Modulation by Carnosine in Scaffold Free Human Dermis Spheroids Model: A Proteomic Study." <i>Int J Mol Sci</i> <b>23</b>(3):; PMID: [https://pubmed.ncbi.nlm.nih.gov/35163388 35163388]; doi: [https://dx.doi.org/10.3390/ijms23031468 10.3390/ijms23031468]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35163388 26]. | ||
#Thim-Uam A, <i>et al.</i> (2022) "Enhanced Bacteremia in Dextran Sulfate-Induced Colitis in Splenectomy Mice Correlates with Gut Dysbiosis and LPS Tolerance." <i>Int J Mol Sci</i> <b>23</b>(3):; PMID: [https://pubmed.ncbi.nlm.nih.gov/35163596 35163596]; doi: [https://dx.doi.org/10.3390/ijms23031676 10.3390/ijms23031676]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35163596 3]. | #Thim-Uam A, <i>et al.</i> (2022) "Enhanced Bacteremia in Dextran Sulfate-Induced Colitis in Splenectomy Mice Correlates with Gut Dysbiosis and LPS Tolerance." <i>Int J Mol Sci</i> <b>23</b>(3):; PMID: [https://pubmed.ncbi.nlm.nih.gov/35163596 35163596]; doi: [https://dx.doi.org/10.3390/ijms23031676 10.3390/ijms23031676]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35163596 3]. | ||
+ | #Murugesan G, <i>et al.</i> (2022) "Quantitative Proteomics of Polarised Macrophages Derived from Induced Pluripotent Stem Cells." <i>Biomedicines</i> <b>10</b>(2):; PMID: [https://pubmed.ncbi.nlm.nih.gov/35203449 35203449]; doi: [https://dx.doi.org/10.3390/biomedicines10020239 10.3390/biomedicines10020239]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35203449 19]. | ||
+ | #Pazzaglia S, <i>et al.</i> (2022) "Micro-RNA and Proteomic Profiles of Plasma-Derived Exosomes from Irradiated Mice Reveal Molecular Changes Preventing Apoptosis in Neonatal Cerebellum." <i>Int J Mol Sci</i> <b>23</b>(4):; PMID: [https://pubmed.ncbi.nlm.nih.gov/35216284 35216284]; doi: [https://dx.doi.org/10.3390/ijms23042169 10.3390/ijms23042169]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35216284 9]. | ||
#COvid-19 Multi-omics Blood ATlas (COMBAT) Consortium. Electronic address: julian.knight@well.ox.ac.uk., <i>et al.</i> (2022) "A blood atlas of COVID-19 defines hallmarks of disease severity and specificity." <i>Cell</i> <b>185</b>(5):916–938.e58; PMID: [https://pubmed.ncbi.nlm.nih.gov/35216673 35216673]; doi: [https://dx.doi.org/10.1016/j.cell.2022.01.012 10.1016/j.cell.2022.01.012]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35216673 559]. | #COvid-19 Multi-omics Blood ATlas (COMBAT) Consortium. Electronic address: julian.knight@well.ox.ac.uk., <i>et al.</i> (2022) "A blood atlas of COVID-19 defines hallmarks of disease severity and specificity." <i>Cell</i> <b>185</b>(5):916–938.e58; PMID: [https://pubmed.ncbi.nlm.nih.gov/35216673 35216673]; doi: [https://dx.doi.org/10.1016/j.cell.2022.01.012 10.1016/j.cell.2022.01.012]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35216673 559]. | ||
+ | #McCullough EL, <i>et al.</i> (2022) "The life history of <i>Drosophila</i> sperm involves molecular continuity between male and female reproductive tracts." <i>Proc Natl Acad Sci U S A</i> <b>119</b>(11):e2119899119; PMID: [https://pubmed.ncbi.nlm.nih.gov/35254899 35254899]; doi: [https://dx.doi.org/10.1073/pnas.2119899119 10.1073/pnas.2119899119]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35254899 95]. | ||
+ | #Krumm J, <i>et al.</i> (2022) "High temporal resolution proteome and phosphoproteome profiling of stem cell-derived hepatocyte development." <i>Cell Rep</i> <b>38</b>(13):110604; PMID: [https://pubmed.ncbi.nlm.nih.gov/35354033 35354033]; doi: [https://dx.doi.org/10.1016/j.celrep.2022.110604 10.1016/j.celrep.2022.110604]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/35354033 490]. |
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 datasets/papers contain serious errors in their metadata/methods sections. When using data from repositories, it is important to be skeptical of any experimental parameter (cell line, tissue type, modification reagents, quantitation methods, etc.) that may impact on your use of the data. We have corrected for as many of these errors as we could detect, but there is no way to be sure that we found them all. When attempting to analyze or reproduce results, keep in mind the likelihood that key parts of the experimental methods may have been recorded incorrectly in the associated metadata or manuscript.
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 Apr 10, 2022.