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Mass spectrometry data Mass spectrometry data should be provided in the mzML format following the HUPO Protein Standards Initiative guidelines; for peptide mass fingerprinting the total percentage of sequence coverage and number of peptides matching it should be given Mass spectrometric analysis and quantification of proteins and peptides: the authors should provide detailed information on how raw data was converted into a format for database searching (e.g. peak list from raw MS or MS/MS data), the search engine used, the database(s), scoring function(s), false discovery rate (how calculated) and statistical methods employed For posttranslational protein modifications results of fragmentation analysis and spectra should be provided. If no evidence for assigning a modification to a single amino acid is provided it should be reported as ambiguous. a) Proteomics To ensure reproducibility, please provide experimental details for (gel-based) proteomics data such as how the duplicates were performed and how the data was processed with what standard. Data Proteome Protein interaction Recommended databases PeptideAtlas, ProteomeXchange MEx consortium b) Functional genomics data/deep sequencing data (such as microarray, RNA-seq or ChIP-seq data) Functional genomics data (e.g. microarray, RNA-seq or ChIP-seq data) should follow the standards proposed by the Functional Genomics Data Society, and Gene nomenclature should be standardised with human gene names and symbols from a gene nomenclature database. For unpublished genomic data the guidelines of the Fort Lauderdale and Toronto agreements should be followed and the authors should contact the owner of the genomic data before starting their research. Genomic data generated from HeLa cells: We highly recommend authors to comply with the NIH HeLa Genome Data Use Agreement. Data Recommended databases Expression, epigenetics, phenol- or genotypes, genomic variants (GWAS studies), human sequence data Database of Genotypes and Phenotypes (dbGaP) Protein-protein, protein-DNA/RNA and molecular The IntAct molecular interaction database interactions (IntAct) miRNA sequences and annotation miRBase Human genomic data, genetic polymorphisms dbSNP, the Database of Genomic Variants Archive (DGVa), Database of Genomic Structural Variation (dbVAR) c) Sequence variants Nucleic acids sequences and variation Data Nucleic acid sequences Variations Metagenome, sequence alignment, sequence information Recommended databases DNA Data Bank of Japan (DDBJ) European Molecular Biology Laboratory (EMBL/EBI) Nucleotide Sequence Database GenBank (National Center for Biotechnology Information) NCBI Sequence Read Archive (SRA), ENA’s Sequence Read Archive, NCBI Trace Archive dbSNP European Variation Archive (EVA) dbVar Database of Genomic Variants Archive (DGVa) EBI Metagenomics Protein sequences Data Protein sequences Recommended databases Universal Protein Resource (UniProt)