ArticleFrontiers in genetics2018
DECtp: Calling Differential Gene Expression Between Cancer and Normal Samples by Integrating Tumor Purity Information.
Article in Frontiers in genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed.
- STLBRF: an improved random forest algorithm based on standardized-threshold for feature screening of gene expression data.Briefings in functional genomics · 2025Article
- Identifying the key hub genes linked with lung squamous cell carcinoma by examining the differentially expressed and survival genes.Molecular genetics and genomics : MGG · 2024Article
- Automated Prognosis Marker Assessment in Breast Cancers Using BLEACH&STAIN Multiplexed Immunohistochemistry.Biomedicines · 2023Article
- IRF4 as a novel target involved in malignant transformation of oral submucous fibrosis into oral squamous cell carcinoma.Scientific reports · 2023Article
- Agent Repurposing for the Treatment of Advanced Stage Diffuse Large B-Cell Lymphoma Based on Gene Expression and Network Perturbation Analysis.Frontiers in genetics · 2021Article
- A novel single-cell based method for breast cancer prognosis.PLoS computational biology · 2020Article
- Pan-cancer transcriptomic analysis dissects immune and proliferative functions of APOBEC3 cytidine deaminases.Nucleic acids research · 2019Article
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Authors and funding
4 authors.
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Abstract
Identifying differentially expressed genes (DEGs) between tumor and normal samples is critical for studying tumorigenesis, and has been routinely applied to identify diagnostic, prognostic, and therapeutic biomarkers for many cancers. It is well-known that solid tumor tissue samples obtained from clinical settings are always mixtures of cancer and normal cells. However, the tumor purity information is more or less ignored in traditional differential expression analyses, which might decrease the power of differential gene identification or even bias the results. In this paper, we have developed a novel differential gene calling method called DECtp by integrating tumor purity information into a generalized least square procedure, followed by the Wald test. We compared DECtp with popular methods like
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