ArticleBMC cancer2021
Reference-free transcriptome signatures for prostate cancer prognosis.
Article in BMC cancer, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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
11 citing papers in PubMed.
- Article
- Reference-free RNA profiling predicts triple negative breast cancer chemoresistance to neoadjuvant treatment.NAR cancer · 2025Article
- Spatial multi-omics identifies aggressive prostate cancer signatures highlighting pro-inflammatory chemokine activity in the tumor microenvironment.Nature communications · 2025Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- Genomic strategies for drug repurposing.Journal of the Egyptian National Cancer Institute · 2024Review
- A Novel Nomogram for Identifying the Patients at Risk for Rapid Progression of Advanced Hormone-Sensitive Prostate Cancer.Cancer management and research · 2023Article
- Replicability in cancer omics data analysis: measures and empirical explorations.Briefings in bioinformatics · 2022Article
- The contribution of uncharted RNA sequences to tumor identity in lung adenocarcinoma.NAR cancer · 2022Article
- Identification and validation of an immune-related gene pairs signature for three urologic cancers.Aging · 2022Article
- Gene expression analysis reveals a 5-gene signature for progression-free survival in prostate cancer.Frontiers in oncology · 2022Article
- Article
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
backgroundRNA-seq data are increasingly used to derive prognostic signatures for cancer outcome prediction. A limitation of current predictors is their reliance on reference gene annotations, which amounts to ignoring large numbers of non-canonical RNAs produced in disease tissues. A recently introduced kind of transcriptome classifier operates entirely in a reference-free manner, relying on k-mers extracted from patient RNA-seq data.
methodsIn this paper, we set out to compare conventional and reference-free signatures in risk and relapse prediction of prostate cancer. To compare the two approaches as fairly as possible, we set up a common procedure that takes as input either a k-mer count matrix or a gene expression matrix, extracts a signature and evaluates this signature in an independent dataset.
resultsWe find that both gene-based and k-mer based classifiers had similarly high performances for risk prediction and a markedly lower performance for relapse prediction. Interestingly, the reference-free signatures included a set of sequences mapping to novel lncRNAs or variable regions of cancer driver genes that were not part of gene-based signatures.
conclusionsReference-free classifiers are thus a promising strategy for the identification of novel prognostic RNA biomarkers.
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.