Protein identification using customized protein sequence databases derived from RNA-Seq data.
暂无分享,去创建一个
Bing Zhang | D. Tabb | R. Slebos | D. Liebler | Xiaojing Wang | Dong Wang | P. Halvey
[1] D. Tabb,et al. MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. , 2007, Journal of proteome research.
[2] D. N. Perkins,et al. Probability‐based protein identification by searching sequence databases using mass spectrometry data , 1999, Electrophoresis.
[3] Eric T. Wang,et al. An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data , 2009, PLoS Comput. Biol..
[4] M. Stephens,et al. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. , 2008, Genome research.
[5] Robertson Craig,et al. TANDEM: matching proteins with tandem mass spectra. , 2004, Bioinformatics.
[6] C. Sander,et al. Predicting the functional impact of protein mutations: application to cancer genomics , 2011, Nucleic acids research.
[7] L. Hood,et al. Complementary Profiling of Gene Expression at the Transcriptome and Proteome Levels in Saccharomyces cerevisiae*S , 2002, Molecular & Cellular Proteomics.
[8] Dustin E. Schones,et al. Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis , 2010, Genome Biology.
[9] E. Wagner,et al. Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail , 2008, Nature Reviews Genetics.
[10] L. Pearl,et al. Structure and mechanism of the Hsp90 molecular chaperone machinery. , 2006, Annual review of biochemistry.
[11] M. Gerstein,et al. Comparing protein abundance and mRNA expression levels on a genomic scale , 2003, Genome Biology.
[12] J. Yates,et al. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. , 2004, Analytical chemistry.
[13] S. Le,et al. Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line , 2010, Molecular systems biology.
[14] A. Nesvizhskii. A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. , 2010, Journal of proteomics.
[15] D. Schriemer,et al. Integration of deep transcriptome and proteome analyses reveals the components of alkaloid metabolism in opium poppy cell cultures , 2010, BMC Plant Biology.
[16] Yi-Kuo Yu,et al. RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration , 2008, BMC Genomics.
[17] D. Tabb,et al. Proteomic parsimony through bipartite graph analysis improves accuracy and transparency. , 2007, Journal of proteome research.
[18] Kang Ning,et al. The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment , 2010, BMC Bioinformatics.
[19] W. Pao,et al. A Bioinformatics Workflow for Variant Peptide Detection in Shotgun Proteomics* , 2011, Molecular & Cellular Proteomics.
[20] V. Thorsson,et al. Integrated Genomic and Proteomic Analyses of Gene Expression in Mammalian Cells*S , 2004, Molecular & Cellular Proteomics.
[21] M. Mann,et al. Defining the transcriptome and proteome in three functionally different human cell lines , 2010, Molecular systems biology.
[22] Damian Fermin,et al. Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics , 2006, Genome Biology.
[23] Christoph Dieterich,et al. De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics. , 2011, Genome research.
[24] Lior Pachter,et al. Sequence Analysis , 2020, Definitions.
[25] E. Winzeler,et al. Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[26] Rong Wang,et al. Integrating shotgun proteomics and mRNA expression data to improve protein identification , 2009, Bioinform..
[27] N. Samatova,et al. Detecting differential and correlated protein expression in label-free shotgun proteomics. , 2006, Journal of proteome research.
[28] M. Gerstein,et al. RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.
[29] M. Mihailović,et al. Molecular characterization of hsp90 isoforms in colorectal cancer cells and its association with tumour progression. , 1992, International journal of oncology.
[30] Michael D. Litton,et al. IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering. , 2009, Journal of proteome research.
[31] Minho Won,et al. Sustained activation of protein kinase C downregulates nuclear factor-κB signaling by dissociation of IKK-γ and Hsp90 complex in human colonic epithelial cells , 2007 .
[32] R. Hendrickson,et al. Detection and validation of non-synonymous coding SNPs from orthogonal analysis of shotgun proteomics data. , 2007, Journal of proteome research.
[33] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[34] Steffen Heber,et al. Detection of alternative splice variants at the proteome level in Aspergillus flavus. , 2010, Journal of proteome research.
[35] R. Durbin,et al. Mapping Quality Scores Mapping Short Dna Sequencing Reads and Calling Variants Using P
[36] Gang Liu,et al. Suppression of inhibitor of differentiation 2, a target of mutant p53, is required for gain-of-function mutations. , 2008, Cancer research.
[37] Blagoy Blagoev,et al. A mass spectrometry–friendly database for cSNP identification , 2007, Nature Methods.
[38] Robert Burke,et al. ProteoWizard: open source software for rapid proteomics tools development , 2008, Bioinform..
[39] E. Birney,et al. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt , 2009, Nature Protocols.
[40] R. Aebersold,et al. Applying mass spectrometry-based proteomics to genetics, genomics and network biology , 2009, Nature Reviews Genetics.
[41] P. Workman,et al. HSP90 as a new therapeutic target for cancer therapy: the story unfolds , 2002, Expert opinion on biological therapy.
[42] N. Edwards,et al. Novel peptide identification from tandem mass spectra using ESTs and sequence database compression , 2007, Molecular systems biology.
[43] B. Williams,et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.
[44] J. Yates,et al. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database , 1994, Journal of the American Society for Mass Spectrometry.
[45] Li Yang,et al. Genomewide characterization of non-polyadenylated RNAs , 2011, Genome Biology.
[46] G. Blandino,et al. Mutant p53 gain of function: reduction of tumor malignancy of human cancer cell lines through abrogation of mutant p53 expression , 2006, Oncogene.
[47] P. Khaitovich,et al. BMC Genomics BioMed Central Methodology article Estimating accuracy of RNA-Seq and microarrays with proteomics , 2022 .