ArticleBiology2021
Oxford Nanopore MinION Direct RNA-Seq for Systems Biology.
Article in Biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 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
18 citing papers in PubMed, 26 citations in OpenAlex.
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- Plant oil complex: dual activation of peroxisome proliferator-activated receptors α andOpen life sciences · 2026Article
- Discovery of NovelGenes · 2025Article
- The Translatome Map: RNC-Seq vs. Ribo-Seq for Profiling of HBE, A549, and MCF-7 Cell Lines.International journal of molecular sciences · 2024Article
- Review
- Non-Targeted RNA Sequencing: Towards the Development of Universal Clinical Diagnosis Methods for Human and Veterinary Infectious Diseases.Veterinary sciences · 2024Review
- PHYH c.678+5G>T Leads to In-Frame Exon Skipping and Is Associated With Attenuated Refsum Disease.Investigative ophthalmology & visual science · 2024Article
- Identifying N6-Methyladenosine Sites in HepG2 Cell Lines Using Oxford Nanopore Technology.International journal of molecular sciences · 2023Article
- Article
- Comparative Transcriptomic Analysis of Three Common Liver Cell Lines.International journal of molecular sciences · 2023Article
- Exploiting Multi-Omics Profiling and Systems Biology to Investigate Functions of TOMM34.Biology · 2023Article
- The Transition from Cancer "omics" to "epi-omics" through Next- and Third-Generation Sequencing.Life (Basel, Switzerland) · 2022Review
- Decoding vesicle-based precision oncology in gliomas.Neuro-oncology advances · 2022Article
- A cohesin-associated gene score may predict immune checkpoint blockade in hepatocellular carcinoma.FEBS open bio · 2022Article
- Improved transcriptome assembly using a hybrid of long and short reads with StringTie.PLoS computational biology · 2022Article
- The Curious Case of the HepG2 Cell Line: 40 Years of Expertise.International journal of molecular sciences · 2021Review
- Microbial Single-Cell Analysis: What Can We Learn From Mammalian?Frontiers in cell and developmental biology · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
Long-read direct RNA sequencing developed by Oxford Nanopore Technologies (ONT) is quickly gaining popularity for transcriptome studies, while fast turnaround time and low cost make it an attractive instrument for clinical applications. There is a growing interest to utilize transcriptome data to unravel activated biological processes responsible for disease progression and response to therapies. This trend is of particular interest for precision medicine which aims at single-patient analysis. Here we evaluated whether gene abundances measured by MinION direct RNA sequencing are suited to produce robust estimates of pathway activation for single sample scoring methods. We performed multiple RNA-seq analyses for a single sample that originated from the HepG2 cell line, namely five ONT replicates, and three replicates using Illumina NovaSeq. Two pathway scoring methods were employed-ssGSEA and singscore. We estimated the ONT performance in terms of detected protein-coding genes and average pairwise correlation between pathway activation scores using an exhaustive computational scheme for all combinations of replicates. In brief, we found that at least two ONT replicates are required to obtain reproducible pathway scores for both algorithms. We hope that our findings may be of interest to researchers planning their ONT direct RNA-seq experiments.
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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.