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ProteomicsBuilding comprehensive MS-friendly databases for proteomic analysis of bacterial species of unknown genetic background
Computational approach to build non-redundant protein databases for strains with unknown genomic background
ORGANISM(S): Mycobacterium tuberculosis 
2019-11-12 | PXD011080 | Pride
Bacterial strains Pangenomics Proteogenomics Databases 
TranscriptomicsRNA-Seq and microarray analysis of the Xenopus inner ear transcriptome discloses orthologous OMIM® genes for hereditary disorders of hearing and balance
Purpose: To identify orthologous genes in Xenopus that are implicated in deafness and vestibular disorders in humans and to compare RNA-Seq and microarray to determine the advantages of each technology for Xenopus transcriptomic analysis. Methods: Inner ear RNA from X. laevis stages 56-58 was isolat...
ORGANISM(S): Xenopus laevis 
2016-02-28 | E-GEOD-69701 | biostudies-arrayexpress
GenomicsRat deconvolution as knowledge miner for immune cell trafficking from toxicogenomics databases
Rat deconvolution as knowledge miner for immune cell trafficking from toxicogenomics databases
PRJNA1001893 | ENA
MetabolomicsA Prototypic Small Molecule Database for Bronchoalveolar Lavage-Based Metabolomics
The analysis of bronchoalveolar lavage fluid (BALF) using mass spectrometry-based metabolomics can provide insight into lung diseases, such as asthma. However, the important step of compound identification is hindered by the lack of a small molecule database that is specific for BALF. Here we descri...
2018-02-09 | MTBLS591 | MetaboLights
TranscriptomicsRat deconvolution as knowledge miner for immune cell trafficking from toxicogenomics databases
Toxicogenomics databases are useful for understanding biological responses in individuals because they are derived from well-controlled experiments and include a diverse spectrum of biological responses. Although these databases contain no information regarding immune cells in the liver, which are i...
ORGANISM(S): Rattus norvegicus 
2023-08-15 | GSE239996 | GEO
ProteomicsDeep profiling and custom databases improve detection of proteoforms generated by alternative splicing
Alternative pre-mRNA splicing has long been proposed to greatly contribute to proteome complexity. However, the extent to which mature mRNA isoforms are successfully translated into protein remains controversial. Here, we used high-throughput RNA sequencing and mass spectrometry (MS)-based proteomic...
ORGANISM(S): Homo sapiens (Human) 
2019-10-14 | PXD012556 | Pride
Human Proteoforms Alternative splicing Nanolc-ms/ms Proteome Jurkat t cells Rna-seq 
UnknownSTON: exploring biological pathways using the SBGN standard and graph databases.
Not available
S-EPMC5139139 | biostudies-literature
ProteomicsGeneration of ENSEMBL-based proteogenomics databases boost the identification of novel peptides
A novel bioinformatics tool pypgatk and the pgdb workflow is presented in study to create proteogenomics databases based on ENSEMBL resources. The tools allow the generation of protein sequences from novel protein-coding transcripts by performing a three-frame translation of pseudogenes, lncRNAs, an...
ORGANISM(S): Homo sapiens (Human) 
2021-10-26 | PXD029360 | Pride
Ensembl Reanalysis Proteogenomics 
ProteomicsnextPP for chromosome-based proteomic research using neXtProt and GENCODE databases
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.
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-07-25 | MSV000081385 | MassIVE
ProteomicsDe novo assembled databases allow species-specific protein-based stable isotope probing of microbiomes without prior knowledge of the community composition
Dataset generated and used in "De novo assembled databases allow species-specific protein-based stable isotope probing of microbiomes without prior knowledge of the community composition". For more information, see SDRF.sdrf.tsv
ORGANISM(S): Candidatus Kuenenia stuttgartiensis Bacteria 
2025-09-08 | PXD057215 | Pride
De novo peptide sequencing Protein-based stable isotope probing 
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