The gene expression profiles of four independent datasets deposited in the Gene Expression Omnibus (GEO) (accession numbers GSE7929, GSE7956, GSE8401, and GSE19234) were analyzed [7,8]. Microarray platforms used in these datasets were HU133A Affymetrix DNA chips (GSE7929, GSE7956, GSE8401) and Illumina HumanWG-6 v2 E/HumanWG HT12 Expression Beadchip (GSE19234).
The GSE7929 comprises the gene expression microarray data of 32 human melanoma cells samples including 11 replicas of parental melanoma cell line A375 (LeiATCC) and 21 derived cell lines with different metastatic potentials selected based on a xenotransplant metastasis model . The GSE7956 dataset comprises whole-genome mRNA expression data of 39 human melanoma cell samples, including 10 replicas of parental melanoma cell line A375 (LeiFidler) and 29 derived cell lines with different metastatic potentials generated by two or three rounds of selection in immunodeficient mice .
The GSE8401 dataset was generated from 83 melanoma samples (31 primary and 52 metastatic tumors) that were collected from patients undergoing surgery were collected from 1992 to 2001 at the Massachusetts General Hospital and Harvard Medical School as a part of the diagnostic workup or planning of therapy . Fifty-two of these metastatic melanoma samples were of superficially spreading type, 19 nodular, and 5 acral lentiginous; the types are not available for the remaining. Most of the primary melanomas were TNM stage I-II, the metastatic melanoma group includes 17 stage III and 35 stage IV tumors .
The GSE19234 dataset comprises 44 melanoma tumors with metastasis were collected at the New York University Medical Center from 1988 to 1997 . Five cases received immunotherapy. Fifteen cases showed CD3 positive. Among these tumors, 4 cases were at stage IIIA tumors,23 at stage IIIB, 12 at stage IIIC, and 5 at stage IV .
As claimed in the original publications, all the studies on these datasets had been approved by the local ethical committees and samples were collected with written informed consent from the patients.