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ppdb specifications


Unique identifier OMICS_01874
Name ppdb
Restrictions to use None
Maintained Yes

Publication for ppdb

ppdb citations


Cold and Heat Stress Diversely Alter Both Cauliflower Respiration and Distinct Mitochondrial Proteins Including OXPHOS Components and Matrix Enzymes

Int J Mol Sci
PMCID: 5877738
PMID: 29547512
DOI: 10.3390/ijms19030877

[…] (Available online: www.musite.net; []). Methylation sites were predicted by PMes (Available online: http://bioinfo.ncu.edu.cn/inquiries_PMeS.aspx; []). The data were compared with Arabidopsis data at PPDB (Available online: http://ppdb.tc.cornell.edu/dbsearch/searchmod.aspx). PPDB experimental sources concerned Zybailov et al. [] as well as Kim et al. [] data. Additional modified residues were pre […]


A comprehensive proteomic analysis of elaioplasts from citrus fruits reveals insights into elaioplast biogenesis and function

PMCID: 5802726
PMID: 29423236
DOI: 10.1038/s41438-017-0014-x

[…] in two bio-replicates, were identified from purified elaioplasts. The raw data obtained from the elaioplast proteins were refined by searches against five plastid databanks (Plprot, AT-CHLORO, SUBA, PPDB, and Uniprot) and by three targeting predictors (WoLF PSORT, Predotar, and Target P). Based on the chosen criteria for plastid-localized proteins (Materials and Methods), an inventory of 655 puta […]


Mapping of quantitative trait loci for grain yield and its components in a US popular winter wheat TAM 111 using 90K SNPs

PLoS One
PMCID: 5739412
PMID: 29267314
DOI: 10.1371/journal.pone.0189669

[…] and 0.01–0.02 in M3. This 2nd QTL on 2B.1 was also linked to days to heading in M1 with a PVE range of 2.5–30.6%. Based on the database search of the linked SNP markers, this QTL is very close to the PpdB1 gene, 1.9 Mb apart on the Chinese Spring reference genome (www.wheatgenome.org) and is associated with protein coding gene heat shock 70kDa protein TRIAE_CS42_2BS_TGACv1_146035_AA0453700, Traes_ […]


Functional divergence and origin of the DAG like gene family in plants

Sci Rep
PMCID: 5515838
PMID: 28720816
DOI: 10.1038/s41598-017-05961-2

[…] Two in silico programs, Predotar and TargetP, were used to predict the putative organelle localization of ZmDAL proteins. The maize organelle proteomics database (PPDB, http://ppdb.tc.cornell.edu/) was screened to detect the accumulation of ZmDAL proteins. […]


Comprehensive proteomic analysis of developing protein bodies in maize (Zea mays) endosperm provides novel insights into its biogenesis

J Exp Bot
PMCID: 5181578
PMID: 27789589
DOI: 10.1093/jxb/erw396
call_split See protocol

[…] vices/TargetP/) and WoLFPSORT (http://cbrc3.cbrc.jp/cbrc/news/wolf_eng.html), as well as information for best-hit Arabidopsis homologs in published organelle proteomes in the Plant Proteome Database (PPDB) (http://ppdb.tc.cornell.edu/; ). The abundance of the identified proteins was calculated using a normalized spectral abundance factors (NSAFs) method (). […]


Proteomic Insight into the Response of Arabidopsis Chloroplasts to Darkness

PLoS One
PMCID: 4854468
PMID: 27137770
DOI: 10.1371/journal.pone.0154235
call_split See protocol

[…] ethod. The gene numbers were derived from Arabidopsis TAIR database (http://www.arabidopsis.org/). The localizations of the proteins were determined through Swissprot database, AT-CHLORO database and PPDB database. The proteins were classified according to UniProt-GOA database, InterProScan software, and KEGG database.The mass spectrometry proteomics data have been deposited to the ProteomeXchange […]


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ppdb institution(s)
The United Graduate School of Agricultural Science, Gifu University, Gifu City, Gifu, Japan; Faculty of Applied Biological Sciences, Gifu University, Gifu City, Gifu, Japan; Center for Sustainable Resource Science, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan; Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan: Advanced Science Research Center, Kanazawa University, Takaramachi, Ishikawa, Japan: National Institute for Basic Biology, Myodaiji, Okazaki City, Aichi, Japan; Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Okazaki, Japan; Faculty of Biology, University of Freiburg, Freiburg, Germany, Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany; Graduate School of Environmental Life Science, Kyoto Prefectural University, Shimogamo, Sakyo-ku, Kyoto, Japan

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