ArticleAMIA ... Annual Symposium proceedings. AMIA Symposium2019
Interpretation of 'Omics dynamics in a single subject using local estimates of dispersion between two transcriptomes.
Article in AMIA ... Annual Symposium proceedings. AMIA Symposium, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 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
9 citing papers in PubMed.
- Oncogenic potential of truncated-Gli3 via the Gsk3β/Gli3/AR-V7 axis in castration-resistant prostate cancer.Oncogene · 2025Article
- Lung Epithelial Cells from Obese Patients Have Impaired Control of SARS-CoV-2 Infection.International journal of molecular sciences · 2023Article
- The Architecture of a Precision Oncology Platform.Advances in experimental medicine and biology · 2022Review
- A versatile genetic toolbox for Prevotella copri enables studying polysaccharide utilization systems.The EMBO journal · 2021Article
- 'Single-subject studies'-derived analyses unveil altered biomechanisms between very small cohorts: implications for rare diseases.Bioinformatics (Oxford, England) · 2021Article
- Personalized beyond Precision: Designing Unbiased Gold Standards to Improve Single-Subject Studies of Personal Genome Dynamics from Gene Products.Journal of personalized medicine · 2020Article
- Case report: 16-yr life history and genomic evolution of an ERCold Spring Harbor molecular case studies · 2020Article
- binomialRF: interpretable combinatoric efficiency of random forests to identify biomarker interactions.BMC bioinformatics · 2020Article
- Transcriptome changes in reciprocal grafts involving watermelon and bottle gourd reveal molecular mechanisms involved in increase of the fruit size, rind toughness and soluble solids.Plant molecular biology · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
Calculating Differentially Expressed Genes (DEGs) from RNA-sequencing requires replicates to estimate gene-wise variability, a requirement that is at times financially or physiologically infeasible in clinics. By imposing restrictive transcriptome-wide assumptions limiting inferential opportunities of conventional methods (edgeR, NOISeq-sim, DESeq, DEGseq), comparing two conditions without replicates (TCWR) has been proposed, but not evaluated. Under TCWR conditions (e.g., unaffected tissue vs. tumor), differences of transformed expression of the proposed individualized DEG (iDEG) method follow a distribution calculated across a local partition of related transcripts at baseline expression; thereafter the probability of each DEG is estimated by empirical Bayes with local false discovery rate control using a two-group mixture model. In extensive simulation studies of TCWR methods, iDEG and NOISeq are more accurate at 5%<DEGs<20% (precision>90%, recall>75%, false_positive_rate<1%) and 30%<DEGs<40% (precision=recall~90%), respectively. The proposed iDEG method borrows localized distribution information from the same individual, a strategy that improves accuracy to compare transcriptomes in absence of replicates at low DEGsconditions. http://www.lussiergroup.org/publications/iDEG.
Indexed as
Identifiers
32308852PMC7153139What 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.