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ProteomicsEvaluating False Transfer Rates from the Match-Between-Runs algorithm with a two-proteome model
Stochasticity between independent LC-MS/MS runs is a challenging problem in the field of proteomics resulting in significant missing values (i.e., abundance measurements) among observed peptides. To address this issue, several approaches have been developed including computational methods such as Ma...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2019-09-25 | PXD014415 | Pride
False transfer rate Match-between-runs Label-free quantitation Two-proteome mixture 
no omics definedTranscription profiling in primary mouse hepatocytes discriminates between true and false genotoxic compounds
Primary mouse hepatocytes are applied in this study as an in vitro system to discriminate false positive GTX compounds from true GTX compounds.
ORGANISM(S): Mus musculus 
2011-01-11 | E-MEXP-2539 | biostudies-arrayexpress
UnknownTransfer Learning in Large-scale Gaussian Graphical Models with False Discovery Rate Control.
Not available
S-EPMC10746133 | biostudies-literature
GenomicsBioinformatic identification of Lentivirus transfer plasmid in HIV-positive NAT results
Bioinformatic identification of Lentivirus transfer plasmid Contamination causing False positive HIV NAT results in a High-Throughput Molecular Screening Laboratory
PRJEB101388 | ENA
TranscriptomicsGene expression patterns within cell lines are predictive of chemosensitivity
We generated RNA's and measured expression of 40000 genes using spotted cDNA microarrays from the fifty nine publicly available cell lines of the NCI Developmental Therapeutics Program's NCI60 studies and an additional set of seven cell lines for which GI50 compound sensitivity data were available. ...
ORGANISM(S): Homo sapiens 
2008-02-07 | E-GEOD-7947 | biostudies-arrayexpress
ProteomicsMapping physiological ADP-ribosylation using Activated Ion Electron Transfer Dissociation (AI-ETD)
ADP-ribosylation (ADPr) is a post-translational modification that plays pivotal roles in a wide range of cellular processes. Mass spectrometry (MS)-based analysis of ADPr under physiological conditions, without relying on genetic or chemical perturbation, has been hindered by technical limitations. ...
ORGANISM(S): Homo sapiens (Human) 
2020-09-23 | PXD017417 | Pride
Activated ion electron transfer dissociation Post-translational modification Adpr Ptm Parp Ai-etd Adp-ribosylation 
TranscriptomicsTranscriptomic study (RNAseq) of Brachypodium distachyon ecotypes Bd21 and Bd2-3 under submergence stress
Purpose: The goal of this study is to compare the transcriptomes expressed during submergence stress of two Brachypodium distachyon ecotypes with contrasting survival under this stress. Bd21 is a submergence sensitive ecotype with EC50 of 2.5 days and Bd2-3 is a tolerant ecotype with EC50 of 4 days....
ORGANISM(S): Brachypodium distachyon 
2016-01-04 | E-GEOD-74222 | biostudies-arrayexpress
ProteomicsRcgA and RcgR, two novel proteins involved in conjugative transfer of rhizobial plasmids
Rhizobia are gram-negative bacteria able to establish a symbiotic interaction with leguminous plants. Due to their nitrogen fixing capacity, the study of these microorganisms has acquired great relevance for the agriculture. Rhizobia usually harbor many plasmids in their genome which can be transfer...
ORGANISM(S): Rhizobium favelukesii 
2022-08-29 | PXD033583 | Pride
Conjugation Rhizobia Plasmid 
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
ProteomicsPlasma Protein Corona on Polystyrene Nanoparticles Facilitates their Transfer across the Human Placenta
Nanoparticles exposed to biological fluids are rapidly surrounded by proteins. It is known that this formed protein corona influences the interplay of nanoparticles with cells or tissue barriers. In this study, we report the impact of a formed human plasma protein corona on the transfer of 80 nm pol...
ORGANISM(S): Homo sapiens (Human) 
2020-08-19 | PXD018160 | Pride
Dual ex vivo placental perfusion Polystyrene Biocorona Nanoparticle Human placenta Plasma proteins Transfer 
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