ArticleAlgorithms for molecular biology : AMB2008
A weighted average difference method for detecting differentially expressed genes from microarray data.
Article in Algorithms for molecular biology : AMB, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 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
56 citing papers in PubMed.
- FOXP4 inhibits squamous differentiation of atypical cells in cervical intraepithelial neoplasia via an ELF3-dependent pathway.Cancer science · 2022Article
- DiffChIPL: a differential peak analysis method for high-throughput sequencing data with biological replicates based on limma.Bioinformatics (Oxford, England) · 2022Article
- Uterine Deletion ofInternational journal of molecular sciences · 2022Article
- Effect of matcha consumption on gut microbiota in healthy Japanese individuals: study protocol for a double-blind crossover interventional study.Journal of clinical biochemistry and nutrition · 2022Article
- Extracellular lipidome change by an SGLT2 inhibitor, luseogliflozin, contributes to prevent skeletal muscle atrophy in db/db mice.Journal of cachexia, sarcopenia and muscle · 2022Article
- Neurodegenerative processes accelerated by protein malnutrition and decelerated by essential amino acids in a tauopathy mouse model.Science advances · 2021Article
- Differential expression analysis using a model-based gene clustering algorithm for RNA-seq data.BMC bioinformatics · 2021Article
- Transcriptome profiling implicated in beneficiary actions of kimchi extracts againstJournal of clinical biochemistry and nutrition · 2021Article
- Activation-induced cytidine deaminase is a possible regulator of cross-talk between oocytes and granulosa cells through GDF-9 and SCF feedback system.Scientific reports · 2021Article
- Let-7e-5p Regulates IGF2BP2, and Induces Muscle Atrophy.Frontiers in endocrinology · 2021Article
- The prognostic significance of interferon-stimulated gene 15 (ISG15) in invasive breast cancer.Breast cancer research and treatment · 2021Article
- Trans Fatty Acid Intake Induces Intestinal Inflammation and Impaired Glucose Tolerance.Frontiers in immunology · 2021Article
- Intake of sucrose affects gut dysbiosis in patients with type 2 diabetes.Journal of diabetes investigation · 2020Article
- The Effects of Metformin on the Gut Microbiota of Patients with Type 2 Diabetes: A Two-Center, Quasi-Experimental Study.Life (Basel, Switzerland) · 2020Article
- Targetable ERBB2 mutation status is an independent marker of adverse prognosis in estrogen receptor positive, ERBB2 non-amplified primary lobular breast carcinoma: a retrospective in silico analysis of public datasets.Breast cancer research : BCR · 2020Article
- Pharmacologically targetable vulnerability in prostate cancer carrying RB1-SUCLA2 deletion.Oncogene · 2020Article
- Peripubertal high-fat diet promotes c-Myc stabilization in mammary gland epithelium.Cancer science · 2020Article
- Article
- The prognostic significance of wild-type isocitrate dehydrogenase 2 (IDH2) in breast cancer.Breast cancer research and treatment · 2020Article
- Initiation of Supporting Cell Activation for Hair Cell Regeneration in the Avian Auditory Epithelium: An Explant Culture Model.Frontiers in cellular neuroscience · 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
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIdentification of differentially expressed genes (DEGs) under different experimental conditions is an important task in many microarray studies. However, choosing which method to use for a particular application is problematic because its performance depends on the evaluation metric, the dataset, and so on. In addition, when using the Affymetrix GeneChip(R) system, researchers must select a preprocessing algorithm from a number of competing algorithms such as MAS, RMA, and DFW, for obtaining expression-level measurements. To achieve optimal performance for detecting DEGs, a suitable combination of gene selection method and preprocessing algorithm needs to be selected for a given probe-level dataset.
resultsWe introduce a new fold-change (FC)-based method, the weighted average difference method (WAD), for ranking DEGs. It uses the average difference and relative average signal intensity so that highly expressed genes are highly ranked on the average for the different conditions. The idea is based on our observation that known or potential marker genes (or proteins) tend to have high expression levels. We compared WAD with seven other methods; average difference (AD), FC, rank products (RP), moderated t statistic (modT), significance analysis of microarrays (samT), shrinkage t statistic (shrinkT), and intensity-based moderated t statistic (ibmT). The evaluation was performed using a total of 38 different binary (two-class) probe-level datasets: two artificial "spike-in" datasets and 36 real experimental datasets. The results indicate that WAD outperforms the other methods when sensitivity and specificity are considered simultaneously: the area under the receiver operating characteristic curve for WAD was the highest on average for the 38 datasets. The gene ranking for WAD was also the most consistent when subsets of top-ranked genes produced from three different preprocessed data (MAS, RMA, and DFW) were compared. Overall, WAD performed the best for MAS-preprocessed data and the FC-based methods (AD, WAD, FC, or RP) performed well for RMA and DFW-preprocessed data.
conclusionWAD is a promising alternative to existing methods for ranking DEGs with two classes. Its high performance should increase researchers' confidence in microarray analyses.
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.