ArticleProteomics2014
Leveraging the complementary nature of RNA-Seq and shotgun proteomics data.
Article in Proteomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 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
54 citing papers in PubMed.
- Proteoform medicine: characterizing and targeting protein forms in human disease.Nature reviews. Genetics · 2026Review
- Opportunities for RNA sequencing in physiology: from big data to understanding homeostasis and heterogeneity.Function (Oxford, England) · 2026Review
- A Mouse Photoreceptor Proteome Resource Identifies PALS2/MPP6 as a Novel Pan-Cone Photoreceptor Marker.Investigative ophthalmology & visual science · 2025Article
- Investigation of the global translational response to oxidative stress in the model archaeonmSphere · 2025Article
- Disruption of oocyte SUMOylation impacts critical regulatory processes during folliculogenesis in mice†.Biology of reproduction · 2025Article
- Proteomic Profiling Towards a Better Understanding of Genetic Based Muscular Diseases: The Current Picture and a Look to the Future.Biomolecules · 2025Review
- Moving Toward Metaproteogenomics: A Computational Perspective on Analyzing Microbial Samples via Proteogenomics.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Exploring G Protein-Coupled Receptors in Hematological Cancers.ACS pharmacology & translational science · 2024Article
- Comprehensive immune cell spectral library for large-scale human primary T, B, and NK cell proteomics.Scientific data · 2024Article
- A multiomic atlas of the aging hippocampus reveals molecular changes in response to environmental enrichment.Nature communications · 2024Article
- RNA-seq reveals role of cell-cycle regulating genes in the pathogenicity of a field very virulent infectious bursal disease virus.Frontiers in veterinary science · 2024Article
- Multi-omics reveals largely distinct transcript- and protein-level responses to the environment in an intertidal mussel.The Journal of experimental biology · 2023Article
- Current perspectives on mass spectrometry-based immunopeptidomics: the computational angle to tumor antigen discovery.Journal for immunotherapy of cancer · 2023Review
- Integrative multi-omics and systems bioinformatics in translational neuroscience: A data mining perspective.Journal of pharmaceutical analysis · 2023Review
- Synaptic resilience is associated with maintained cognition during ageing.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2023Article
- Discovery of Novel Effector Protein Candidates Produced in the Dorsal Gland of Adult Female Root-Knot Nematodes.Molecular plant-microbe interactions : MPMI · 2023Article
- Transcriptome and Proteome Profiling of Primary Human Gastric Interstitial Cells of Cajal Predicts Pacemaker Networks.Journal of neurogastroenterology and motility · 2023Article
- CRISPR-Cas9 editing of a TNPO3 mutation in a muscle cell model of limb-girdle muscular dystrophy type D2.Molecular therapy. Nucleic acids · 2023Article
- Integrative Analysis of Transcriptome, Proteome, and Phosphoproteome Reveals Potential Roles of Photosynthesis Antenna Proteins in Response to Brassinosteroids Signaling in Maize.Plants (Basel, Switzerland) · 2023Article
- Overview and considerations in bottom-up proteomics.The Analyst · 2023Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
RNA sequencing (RNA-Seq) and MS-based shotgun proteomics are powerful high-throughput technologies for identifying and quantifying RNA transcripts and proteins, respectively. With the increasing affordability of these technologies, many projects have started to apply both to the same samples to achieve a more comprehensive understanding of biological systems. A major analytical challenge for such integrative projects is how to effectively leverage the complementary nature of RNA-Seq and shotgun proteomics data. RNA-Seq provides comprehensive information on mRNA abundance, alternative splicing, nucleotide variation, and structure alteration. Sample-specific protein databases derived from RNA-Seq data can better approximate the real protein pools in cell and tissue samples and thus improve protein identification. Meanwhile, proteomics data provide essential confirmation of the validity and functional relevance of novel findings from RNA-Seq data. At the quantitative level, mRNA and protein levels are only modestly correlated, suggesting strong involvement of posttranscriptional regulation in controlling gene expression. Here, we review recent studies at the interface of RNA-Seq and proteomics data. We discuss goals, accomplishments, and challenges in RNA-Seq-based proteogenomics. We also examine the current status and future potential of parallel transcriptome and proteome quantification in revealing posttranscriptional regulatory mechanisms.
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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.