ArrayExpress Uploader0human79not applicablenot applicablemnot applicablenot applicableNORMAL SKIN47not applicablenot applicablemnot applicablenot applicableNORMAL SKIN44not applicablenot applicablefnot applicablenot applicableNORMAL SKIN85not applicablenot applicablemnot applicablenot applicableNORMAL SKIN39not applicablenot applicablemnot applicablenot applicableNORMAL SKIN41not applicablenot applicablemnot applicablenot applicableNORMAL SKIN50not applicablenot applicablemnot applicablenot applicableNORMAL SKIN44not applicablenot applicablemnot applicablenot applicableNORMAL SKIN74not applicablenot applicablemnot applicablenot applicableNORMAL SKIN56not applicablenot applicablemnot applicablenot applicableNORMAL SKIN73not applicablenot applicablefnot applicablenot applicableNORMAL SKIN58not applicablenot applicablemnot applicablenot applicableNORMAL SKIN20not applicablenot applicablefnot applicablenot applicableNORMAL SKIN62not applicablenot applicablemnot applicablenot applicableNORMAL SKIN55not applicablenot applicablemnot applicablenot applicableNORMAL SKIN52not applicablenot applicablemnot applicablenot applicableNORMAL SKIN66NOWTmWTNODESMOPLASTIC MELANOMA60YESWTmWTYESSSM76YESQ61RmWTNOSSM50NOWTmWTNOSSM59not specifiedWTmV600Rnot specifiedSSM63NOWTmWTNOSSM47not specifiedWTmWTnot specifiedNODULAR MELANOMA44NOWTfV600EYESSSM42YESWTmV600ENOSSM81NOWTfWTYESSSM83NOWTmV600ENOMIS80NOQ61RmWTNONODULAR MELANOMA72YESWTfV600EYESSSM61NOWTmV600ENOSPINDLE CELL MELANOMA55NOQ61KfWTNOACRAL MELANOMA41NOWTmL597SNOSSM50not specifiedWTmV600EYESSSM50not specifiedWTmV600EYESSSM33YESWTfWTYESNODULAR MELANOMA76NOWTmWTNOSSM45NOWTfWTNOSSM51YESWTfV600EYESACRAL MELANOMA74YESWTmWTNOSSM79NOWTmWTNOSSM56YESWTmV600EYESNODULAR MELANOMA44NOWTmWTNOSSM33NOWTfWTNOMIS73NOWTfWTNOSSM20NOWTfV600ENOSSM70NOWTfWTNOACRAL MELANOMA62not specifiedWTmV600Knot specifiedSSM55NOWTmV600KNOSSM67NOQ61RmWTYESNODULAR MELANOMA43YESWTmV600EYESDERMAL MELANOMA48YESWTmV600EYESPOLYPOID MELANOMA70NOWTmWTNOSSM52NOWTmV600ENOSSM36NOWTmV600ENONODULAR MELANOMA87NOWTfWTNOSSM92NOQ61LfWTYESNODULAR MELANOMA66YESWTmV600EYESSSM42NOWTmWTNOSSM45NOWTmWTNOSSM80YESWTmWTnot specifiedLMM87NOQ61LfWTYESNODULAR MELANOMA64YESWTmL597RNOSSM40YESWTmV600EYESREGIONAL LYMPH NODE METASTASIS66YESQ61KfWTnot specifiedREGIONAL LYMPH NODE METASTASIS55YESWTmV600Enot specifiedDISTANT METASTASIS27YESWTfV600Enot specifiedREGIONAL LYMPH NODE METASTASIS33YESWTmV600Enot specifiedDISTANT METASTASIS71YESWTmV600Knot specifiedREGIONAL LYMPH NODE METASTASIS36NOWTmV600EYESREGIONAL LYMPH NODE METASTASIS77NOWTfWTYESSUBCUTANIOUS SOFT TISSUE METASTASIS90NOQ61KfWTYESREGIONAL LYMPH NODE METASTASIS71YESWTfV600EYESREGIONAL LYMPH NODE METASTASIS53YESWTmWTYESSUBCUTANIOUS SOFT TISSUE METASTASIS89YESWTfV600EYESREGIONAL LYMPH NODE METASTASIS3247arrayexpress_sid4The identification of novel tumor-specific markers may improve understanding of melanoma progression and prognostic accuracy. Whole...E-GEOD-15605/profile/8773/arrayexpressuploader774diseasegenomeinferiorintestineliquidlymphmelanomaskinsmall intestinespleenDec.12, 2014FalseE-GEOD-15605_A-AFFY-44transcriptome-profiling-identifies-hmga2-as-a-noveTranscriptome profiling identifies HMGA2 as a novel gene in melanoma progressionSep.12, 2014The identification of novel tumor-specific markers may improve understanding of melanoma progression and prognostic accuracy. Whole genome expression profiling of 46 primary melanomas, 12 metastases, and 16 normal skin samples using Affymetrix U133 PLUS 2.0 array generated gene lists including both known and new melanoma genes. The molecular genetic alterations contributing to the pathogenesis of melanoma are incompletely defined and few independent prognostic features have been identified beyond the pathologic characteristics of the primary tumor. Early stage melanoma is frequently curable, in contrast to the inferior prognosis of melanomas with regional lymph nodes involvement and the incurability of distant metastatic disease. The identification of novel tumor-specific markers may improve our understanding of melanoma progression and prognostic accuracy. To find differentially expressed genes that can distinguish melanoma from normal tissue, we performed a whole genome expression profiling of 46 primary melanoma samples, 12 regional or distant metastases, and 16 normal skin samples using Affymetrix U133 2.0 Plus array. Our study generated lists of differentially expressed genes in melanoma and identified novel prognostic marker HMGA2. It is a novel, highly overexpressed melanoma gene associated with poor prognosis. The overexpression of HMGA2 is strongly associated with regional and distant metastases and serves as an independent predictor of disease-free survival and overall survival in melanoma. Melanoma samples were obtained through an IRB-approved protocol using informed consent at the University of Michigan Multidisciplinary Melanoma Clinic. A portion of pigmented lesions clinically suspicious for melanoma and known melanoma were sampled by punch biopsy at the time of excision. The punch biopsy was bisected; half was sent to for clinical diagnosis and the other half along with adjacent normal skin when available immediately snap-frozen in liquid nitrogen. Snap-frozen tissue was embedded in OCT (TissueTek) followed by frozen sectioning and H&E slide preparation. The slides were evaluated by dermatopathologist who identified areas with greater than 70% tumor cellularity, which were sampled for RNA extraction. Primary melanomas and melanoma metastases were derived from different patients. Metastatic samples included lymph nodes (n=8), subcutaneous soft tissue (n=2), spleen (n=1), and small intestine (n=1).http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-15605http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-15605/samples/