ArticleScientific reports2013
Soft truncation thresholding for gene set analysis of RNA-seq data: application to a vaccine study.
Article in Scientific reports, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers, 1 of them a synthesis that pooled it.
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
11 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Statistical genomics in rare cancer.Seminars in cancer biology · 2020Pooled it
- Fifteen Years of Gene Set Analysis for High-Throughput Genomic Data: A Review of Statistical Approaches and Future Challenges.Entropy (Basel, Switzerland) · 2020Review
- DOT: Gene-set analysis by combining decorrelated association statistics.PLoS computational biology · 2020Article
- Ontogeny-related pharmacogene changes in the pediatric liver transcriptome.Pharmacogenetics and genomics · 2018Article
- Gene signatures associated with adaptive humoral immunity following seasonal influenza A/H1N1 vaccination.Genes and immunity · 2016Article
- Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline.Briefings in bioinformatics · 2016Article
- Gene signatures related to HAI response following influenza A/H1N1 vaccine in older individuals.Heliyon · 2016Article
- Article
- Comparative evaluation of gene set analysis approaches for RNA-Seq data.BMC bioinformatics · 2014Article
- GSAASeqSP: a toolset for gene set association analysis of RNA-Seq data.Scientific reports · 2014Article
- The personal touch: strategies toward personalized vaccines and predicting immune responses to them.Expert review of vaccines · 2014Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Gene set analysis (GSA) has been used for analysis of microarray data to aid the interpretation and to increase statistical power. With the advent of next-generation sequencing, the use of GSA is even more relevant, as studies are often conducted on a small number of samples. We propose the use of soft truncation thresholding and the Gamma Method (GM) to determine significant gene set (GS), where a generalized linear model is used to assess per-gene significance. The approach was compared to other methods using an extensive simulation study and RNA-seq data from smallpox vaccine study. The GM was found to outperform other proposed methods. Application of the GM to the smallpox vaccine study found the GSs to be moderately associated with response, including focal adhesion (p = 0.04) and extracellular matrix receptor interaction (p = 0.05). The application of GSA to RNA-seq data will provide new insights into the genomic basis of complex traits.
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.