ArticleNucleic acids research2009
SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
12 citing papers in PubMed.
- Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation.Annual review of analytical chemistry (Palo Alto, Calif.) · 2016Review
- sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments.Bioinformatics (Oxford, England) · 2014Article
- Integrating genomic, transcriptomic, and interactome data to improve Peptide and protein identification in shotgun proteomics.Journal of proteome research · 2014Review
- Large-scale mass spectrometric detection of variant peptides resulting from nonsynonymous nucleotide differences.Journal of proteome research · 2014Article
- CFGP 2.0: a versatile web-based platform for supporting comparative and evolutionary genomics of fungi and Oomycetes.Nucleic acids research · 2013Article
- An examination of the OMIM database for associating mutation to a consensus reference sequence.Protein & cell · 2012Article
- A bioinformatics workflow for variant peptide detection in shotgun proteomics.Molecular & cellular proteomics : MCP · 2011Article
- Cyber infrastructure for Fusarium: three integrated platforms supporting strain identification, phylogenetics, comparative genomics and knowledge sharing.Nucleic acids research · 2011Article
- CanProVar: a human cancer proteome variation database.Human mutation · 2010Article
- Fungal secretome database: integrated platform for annotation of fungal secretomes.BMC genomics · 2010Article
- IMGD: an integrated platform supporting comparative genomics and phylogenetics of insect mitochondrial genomes.BMC genomics · 2009Article
- SNUGB: a versatile genome browser supporting comparative and functional fungal genomics.BMC genomics · 2008Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Some mutations resulting in protein sequence change might be tightly related to certain human diseases by affecting its roles, such as sickle cell anemia. Until now several databases, such as PMD, OMIM and HGMD, have been developed, providing useful information about human disease-related mutation. Tandem mass spectrometry (MS) has been used for characterizing proteins in various conditions; however, there is no system in place for finding disease-related mutated proteins within the MS results. Here, a Systematical Platform for Identifying Mutated Proteins (SysPIMP; http://pimp.starflr.info/) was developed to efficiently identify human disease-related mutated proteins within MS results. SysPIMP comprises of three layers: (i) a standardized data warehouse, (ii) a pipeline layer for maintaining human disease databases and X!Tandem and BLAST and (iii) a web-based interface. From OMIM AV part, PMD and SwissProt databases, 35,497 non-redundant human disease-related mutated sequences were collected with disease information described by OMIM terms. With the interfaces to browse sequences archived in SysPIMP, X!Tandem, an open source database-search engine used to identify proteins within MS data, was integrated into SysPIMP to help support the detection of potential human disease-related mutants in MS results. In addition, together with non-redundant disease-related mutated sequences, original non-mutated sequences are also provided in SysPIMP for comparative research. Based on this system, SysPIMP will be the platform for efficiently and intensively studying human diseases caused by mutation.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.