ArticlePloS one2015
Differentially Expressed Genes and Signature Pathways of Human Prostate Cancer.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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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.
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Who cites it
19 citing papers in PubMed, 36 citations in OpenAlex.
- Trial
- Bridging Health Disparities: a Genomics and Transcriptomics Analysis by Race in Prostate Cancer.Journal of racial and ethnic health disparities · 2024Article
- Tumor microenvironment deconvolution identifies cell-type-independent aberrant DNA methylation and gene expression in prostate cancer.Clinical epigenetics · 2024Article
- Article
- Article
- Gene Regulation Network Analysis on Human Prostate Orthografts Highlights a Potential Role for theCancers · 2021Article
- Genome-wide analysis of therapeutic response uncovers molecular pathways governing tamoxifen resistance in ER+ breast cancer.EBioMedicine · 2020Article
- Choice of library size normalization and statistical methods for differential gene expression analysis in balanced two-group comparisons for RNA-seq studies.BMC genomics · 2020Article
- Suitability of ultrasound-guided fine-needle aspiration biopsy for transcriptome sequencing of the canine prostate.Scientific reports · 2019Article
- Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data.BMC bioinformatics · 2019Article
- GOTrapper: a tool to navigate through branches of gene ontology hierarchy.BMC bioinformatics · 2019Article
- Global Proteomic Response ofFrontiers in cellular and infection microbiology · 2019Article
- Systematic analysis reveals molecular characteristics of ERG-negative prostate cancer.Scientific reports · 2018Article
- Finding disagreement pathway signatures and constructing an ensemble model for cancer classification.Scientific reports · 2017Article
- Article
- A DEEP LEARNING APPROACH FOR CANCER DETECTION AND RELEVANT GENE IDENTIFICATION.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2017Article
- Stably Expressed Genes Involved in Basic Cellular Functions.PloS one · 2017Article
- Proteomic Upregulation of Fatty Acid Synthase and Fatty Acid Binding Protein 5 and Identification of Cancer- and Race-Specific Pathway Associations in Human Prostate Cancer Tissues.Journal of Cancer · 2016Article
- Trends in Gene Expression Profiling for Prostate Cancer Risk Assessment: A Systematic Review.Biomedicine hubReview
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genomic technologies including microarrays and next-generation sequencing have enabled the generation of molecular signatures of prostate cancer. Lists of differentially expressed genes between malignant and non-malignant states are thought to be fertile sources of putative prostate cancer biomarkers. However such lists of differentially expressed genes can be highly variable for multiple reasons. As such, looking at differential expression in the context of gene sets and pathways has been more robust. Using next-generation genome sequencing data from The Cancer Genome Atlas, differential gene expression between age- and stage- matched human prostate tumors and non-malignant samples was assessed and used to craft a pathway signature of prostate cancer. Up- and down-regulated genes were assigned to pathways composed of curated groups of related genes from multiple databases. The significance of these pathways was then evaluated according to the number of differentially expressed genes found in the pathway and their position within the pathway using Gene Set Enrichment Analysis and Signaling Pathway Impact Analysis. The "transforming growth factor-beta signaling" and "Ran regulation of mitotic spindle formation" pathways were strongly associated with prostate cancer. Several other significant pathways confirm reported findings from microarray data that suggest actin cytoskeleton regulation, cell cycle, mitogen-activated protein kinase signaling, and calcium signaling are also altered in prostate cancer. Thus we have demonstrated feasibility of pathway analysis and identified an underexplored area (Ran) for investigation in prostate cancer pathogenesis.
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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 Socratic graph.