In this study, we introduce a streamlined pipeline using customized and concatenated GENCODE and neXtProt databases with controlled false discovery rate (FDR) for finding GENCODE ASVs and missing proteins while mapping onto single amino acid variants (SAAVs) from Hippocampal dataset.
[dataset license: CC0 1.0 Universal (CC0 1.0)]
Keywords: C-HPP ; alternative splicing variant ; single amino acid variant
Principal Investigators: (in alphabetical order) |
Jong Shin Yoo, Korea Basic Science Institute, Rep of Korea |
Submitting User: | tilldawn |
Hwang H, Park GW, Park JY, Lee HK, Lee JY, Jeong JE, Park SR, Yates JR, Kwon KH, Park YM, Lee HJ, Paik YK, Kim JY, Yoo JS.
Next Generation Proteomic Pipeline for Chromosome-Based Proteomic Research Using NeXtProt and GENCODE Databases.
J. Proteome Res. Epub 2017 Oct 13.
Kwon KH, Kim JY, Kim SY, Min HK, Lee HJ, Ji IJ, Kang T, Park GW, An HJ, Lee B, Ravid R, Ferrer I, Chung CK, Paik YK, Hancock WS, Park YM, Yoo JS.
Chromosome 11-centric human proteome analysis of human brain hippocampus tissue.
J. Proteome Res. 2013 Jan 4;12(1):97-105.
Hwang H, Park GW, Kim KH, Lee JY, Lee HK, Ji ES, Park SK, Xu T, Yates JR, Kwon KH, Park YM, Lee HJ, Paik YK, Kim JY, Yoo JS.
Chromosome-Based Proteomic Study for Identifying Novel Protein Variants from Human Hippocampal Tissue Using Customized neXtProt and GENCODE Databases.
J. Proteome Res. 2015 Dec 4;14(12):5028-37. Epub 2015 Nov 16.
Park GW, Hwang H, Kim KH, Lee JY, Lee HK, Park JY, Ji ES, Park SR, Yates JR, Kwon KH, Park YM, Lee HJ, Paik YK, Kim JY, Yoo JS.
Integrated Proteomic Pipeline Using Multiple Search Engines for a Proteogenomic Study with a Controlled Protein False Discovery Rate.
J. Proteome Res. 2016 Nov 4;15(11):4082-4090. Epub 2016 Aug 30.
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