ArticleBioData mining2017
RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study.
Article in BioData mining, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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
14 citing papers in PubMed.
- Functional diversity and molecular interactions of small membrane proteins in bacteria.microLife · 2025Review
- Type I toxin-antitoxin systems in bacteria: from regulation to biological functions.EcoSal Plus · 2024Review
- Article
- Relevance of charged and polar amino acids for functionality of membrane toxin TisB.Scientific reports · 2024Article
- Article
- Article
- An Easy-to-Use Plasmid Toolset for Efficient Generation and Benchmarking of Synthetic Small RNAs in Bacteria.ACS synthetic biology · 2022Article
- A Shift in Perspective: A Role for the Type I Toxin TisB as Persistence-Stabilizing Factor.Frontiers in microbiology · 2022Article
- ThemSphere · 2021Article
- Cross-species RNA-seq for deciphering host-microbe interactions.Nature reviews. Genetics · 2021Review
- Elevated Expression of Toxin TisB Protects Persister Cells against Ciprofloxacin but Enhances Susceptibility to Mitomycin C.Microorganisms · 2021Article
- An RNA pseudoknot is essential for standby-mediated translation of the tisB toxin mRNA in Escherichia coli.Nucleic acids research · 2020Article
- Type I toxin-dependent generation of superoxide affects the persister life cycle of Escherichia coli.Scientific reports · 2019Article
- Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration.Nature communications · 2017Article
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
backgroundMeasuring how gene expression changes in the course of an experiment assesses how an organism responds on a molecular level. Sequencing of RNA molecules, and their subsequent quantification, aims to assess global gene expression changes on the RNA level (transcriptome). While advances in high-throughput RNA-sequencing (RNA-seq) technologies allow for inexpensive data generation, accurate post-processing and normalization across samples is required to eliminate any systematic noise introduced by the biochemical and/or technical processes. Existing methods thus either normalize on selected known reference genes that are invariant in expression across the experiment, assume that the majority of genes are invariant, or that the effects of up- and down-regulated genes cancel each other out during the normalization.
resultsHere, we present a novel method,
conclusionsThe proposed RNA-seq normalization method,
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.