ArticlePeerJ2013
A new 12-gene diagnostic biomarker signature of melanoma revealed by integrated microarray analysis.
Article in PeerJ, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers, 3 of them syntheses that pooled it.
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Who cites it
37 citing papers in PubMed, 3 syntheses or guidelines pooled it, 69 citations in OpenAlex.
- KLHL21, a novel gene that contributes to the progression of hepatocellular carcinoma.BMC cancer · 2016Pooled it
- Meta-analysis of gene expression profiles indicates genes in spliceosome pathway are up-regulated in hepatocellular carcinoma (HCC).Medical oncology (Northwood, London, England) · 2015Pooled it
- Gene Network Rewiring to Study Melanoma Stage Progression and Elements Essential for Driving Melanoma.PloS one · 2015Pooled it
- Tertiary lymphoid structures in gastrointestinal cancer: orchestrating tumour microenvironmental immune subcycles to elegantly amplify the cancer immunity cycle.Annals of medicine · 2026Review
- PPP2R2C promotes aerobic glycolysis and mediates pemetrexed resistance in lung adenocarcinomas by upregulating TCP1-dependent protein folding of glycolytic enzymes.Respiratory research · 2026Article
- Bile acids enrichment fuel tumor aerobic glycolysis and immune evasion via stabilizing FXR-RARα.Frontiers in immunology · 2026Article
- Proteomic and metabolomic profiles of plasma-derived Extracellular Vesicles differentiate melanoma patients from healthy controls.Translational oncology · 2024Article
- Bladder cancer: non-coding RNAs and exosomal non-coding RNAs.Functional & integrative genomics · 2024Review
- Role of gene signature regulation in tumor immune microenvironment on the mechanism of uveal melanoma metastasis.Cancer biomarkers : section A of Disease markers · 2023Article
- Experimental assessment of robust reference genes for qRT-PCR in lung cancer studies.Frontiers in oncology · 2023Article
- Melanoma molecular subtyping and scoring model construction based on ligand-receptor pairs.Frontiers in genetics · 2023Article
- Biomarker Discovery for Meta-Classification of Melanoma Metastatic Progression Using Transfer Learning.Genes · 2022Article
- Genome-wide promoter methylation profiling in a cellular model of melanoma progression reveals markers of malignancy and metastasis that predict melanoma survival.Clinical epigenetics · 2022Article
- A decade of checkpoint blockade immunotherapy in melanoma: understanding the molecular basis for immune sensitivity and resistance.Nature immunology · 2022Review
- Feature selection and classification over the network with missing node observations.Statistics in medicine · 2022Article
- The Research on the Treatment of Metastatic Skin Cutaneous Melanoma by Huanglian Jiedu Decoction Based on the Analysis of Immune Infiltration Analysis.Evidence-based complementary and alternative medicine : eCAM · 2021Article
- Cutaneous Melanoma: Mutational Status and Potential Links to Tertiary Lymphoid Structure Formation.Frontiers in immunology · 2021Review
- MicroRNAs and target molecules in bladder cancer.Medical oncology (Northwood, London, England) · 2020Review
- Insights Into the Albinism Mechanism for Two Distinct Color Morphs of Northern Snakehead,Frontiers in genetics · 2020Article
- Expression of Neural Crest Markers GLDC and ERRFI1 is Correlated with Melanoma Prognosis.Cancers · 2019Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome-wide microarray technology has facilitated the systematic discovery of diagnostic biomarkers of cancers and other pathologies. However, meta-analyses of published arrays often uncover significant inconsistencies that hinder advances in clinical practice. Here we present an integrated microarray analysis framework, based on a genome-wide relative significance (GWRS) and genome-wide global significance (GWGS) model. When applied to five microarray datasets on melanoma published between 2000 and 2011, this method revealed a new signature of 200 genes. When these were linked to so-called 'melanoma driver' genes involved in MAPK, Ca(2+), and WNT signaling pathways we were able to produce a new 12-gene diagnostic biomarker signature for melanoma (i.e., EGFR, FGFR2, FGFR3, IL8, PTPRF, TNC, CXCL13, COL11A1, CHP2, SHC4, PPP2R2C, and WNT4). We have begun to experimentally validate a subset of these genes involved in MAPK signaling at the protein level, including CXCL13, COL11A1, PTPRF and SHC4 and found these to be over-expressed in metastatic and primary melanoma cells in vitro and in situ compared to melanocytes cultured from healthy skin epidermis and normal healthy human skin. While SHC4 has been reported previously to be associated to melanoma, this is the first time CXCL13, COL11A1, and PTPRF have been associated with melanoma on experimental validation. Our computational evaluation indicates that this 12-gene biomarker signature achieves excellent diagnostic power in distinguishing metastatic melanoma from normal skin and benign nevus. Further experimental validation of the role of these 12 genes in a new signaling network may provide new insights into the underlying biological mechanisms driving the progression of melanoma.
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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.