{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Illumina Infinium HumanMethylation 450K - GenomeStudio"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00010000482"],"sample_count":["1"],"description":["EGA dataset EGAD00010000482"],"repository":["EGA"],"title":["Title not provided"],"pubmed_abstract":["Recent comprehensive assessments of RNA-seq technology support its utility in quantifying gene expression in various samples. The next step of rigorously quantifying differences between sample groups, however, still lacks well-defined best practices. Although a number of advanced statistical methods have been developed, several studies demonstrate that their performance depends strongly on the data under analysis, which compromises practical utility in real biomedical studies. As a solution, we propose to use a data-adaptive procedure that selects an optimal statistic capable of maximizing reproducibility of detections. After demonstrating its improved sensitivity and specificity in a controlled spike-in study, the utility of the procedure is confirmed in a real biomedical study by identifying prognostic markers for clear cell renal cell carcinoma (ccRCC). In addition to identifying several genes previously associated with ccRCC prognosis, several potential new biomarkers among genes regulating cell growth, metabolism and solute transport were detected."],"pubmed_title":["ROTS: reproducible RNA-seq biomarker detector-prognostic markers for clear cell renal cell cancer."],"pubmed_authors":["Seyednasrollah Fatemeh F, Rantanen Krista K, Jaakkola Panu P, Elo Laura L LL"],"name_synonyms":["clear cell renal cell carcinoma, methylation, Methylations., clear cell renal cell adenocarcinoma, CCRCC"],"pubmed_title_synonyms":["Biological Markers, Viral Marker, Viral, Surrogate Endpoints, Surrogate Endpoint, Clinical Markers, Laboratory, renal clear cell adenocarcinoma, Clinical Marker, Serum Markers, clear cell carcinoma of the kidney, kidney, Biochemical, End Point, RNA-seq, Endpoint, Biochemical Markers, clear cell kidney carcinoma, Serum, conventional renal cell carcinoma, Grawitz tumor, Biologic Marker, clear-cell metastatic renal cell carcinoma, Immune Marker, Surrogate End Points, Surrogate Markers, Laboratory Markers, Marker, Biological, Surrogate End Point, clear cell renal cell cancer, Whole Transcriptome Shotgun Sequencing, clear cell adenocarcinoma of the kidney, RCC, clear cell renal carcinoma., hypernephroma, Biologic Markers, Biomarker, Serum Marker, Clinical, End Points, conventional (clear cell) renal cell carcinoma, Surrogate, kidney clear cell carcinoma, Biological Marker, Endpoints, conventional (clear cell) renal cell adenocarcinoma, clear cell adenocarcinoma, clear cell adenocarcinoma of kidney, Immunologic, Laboratory Marker, Surrogate Marker, clear cell renal cell carcinoma, Immunologic Markers, Immune, Markers, Biochemical Marker, Viral Markers, clear cell carcinoma of kidney, kidney clear cell adenocarcinoma, renal cell carcinoma, renal clear cell carcinoma, Immunologic Marker, Biologic, Immune Markers"],"description_synonyms":["clear cell renal cell carcinoma, methylation, clear cell renal cell adenocarcinoma, microarray., Methylations, CCRCC"],"pubmed_abstract_synonyms":["biochemical pathways, dmBest1, Biological Markers, Viral Marker, Metabolic Process, Materials, Collecting Duct, clear cell renal cell adenocarcinoma, Surrogate Endpoints, determination, Laboratory, Metabolic Concepts, Biochemical, Endpoint, Tumor, Serum, Papillary Renal Cell Carcinoma, DmelCG6264, CCRCC, Techniques, Laboratory Markers, Adenocarcinoma Of Kidneys, Renal Cell Adenocarcinomas, Method, Biological, GRP1, Grp1, ARB, Concepts, Metabolism Concept, Phenomenon, Hypernephromas, Prognoses, Gene Expressions, reference sample, catabolism, non-developmental growth of a unicellular organism, PTPSTEP, metabolic process resulting in cell growth, procedures, SURGICAL AND MEDICAL PROCEDURES, clear cell renal cell carcinoma, Immune, Markers, Methodological Studies, l(2)k08110, Viral Markers, sample, biotransformation, Renal Collecting Duct Carcinoma, Catabolism, GPH, Carcinoma, Adenocarcinoma Of, single-organism transport., Viral, CG6264, Surrogate Endpoint, Process, Arts, metabolism resulting in cell growth, RNA-seq, Renal Cell Adenocarcinoma, Biochemical Markers, Adenocarcinoma Of Kidney, Procedure, Biologic Marker, Renal Cell Carcinoma, Adenocarcinomas, Collecting Duct Carcinoma of the Kidney, Clear Cell Renal Cell Carcinoma, Marker, non-developmental cell growth, 3.1.3.48, Genetic Materials, secretion, TU15B, Hypernephroma, Genetic Material, dBest1, Carcinomas, Industrial, Factors, Industrial Arts, End Points, Step, CG11628, Kidney, Prognostic, dbest1, Striatum-enriched protein-tyrosine phosphatase, Methodological, Immunologic, Nephroid, Laboratory Marker, Clear-cell metastatic renal cell carcinoma, Methodological Study, Renal Cell Cancer, Papillary, Specificity and Sensitivity, STEP, Material, Biochemical Marker, Collecting Duct Carcinoma (Kidney), Cistron, Nephroid Carcinoma, Clear Cell Renal Carcinoma, Prognostic Factor, Adenocarcinoma, GRP1/cytohesin 1, Procedures, Clinical Markers, Processes, Clinical Marker, number, Renal Cell Cancers, Gene, Prognostic Factors, Renal Adenocarcinomas, Metabolic Processes, anon-WO0118547.380, Intervention or Procedure, Surrogate End Points, CG11633, cytohesin/GRP1, Surrogate Markers, Hypernephroid, Metabolism, Sarcomatoid Renal Cell Carcinoma, Studies, Whole Transcriptome Shotgun Sequencing, Hypernephroid Carcinomas, Renal Carcinomas, Hypernephroid Carcinoma, Metabolism Phenomena, Technique, Grawitz Tumor, study, Biomarker, Genetic, Clinical, interventionDescription, VMD2, Collecting Duct Carcinoma, Biological Marker, l(2)SH2 0323, Interventional, Metabolic Concept, Renal, BMD, Expressions, Solution, Study, Immunologic Markers, Neural-specific protein-tyrosine phosphatase, Sensitivity, Expression, Collecting Duct Carcinomas (Kidney), Immunologic Marker, Biologic, Controlled, RP50, Grawitz, Cancer, Intervention Strategies, Controlling, degradation, Chromophil Renal Cell Carcinoma, Collecting Duct Carcinomas, Serum Markers, Renal Cell Carcinomas, End Point, stepk, Factor, Renal Adenocarcinoma, Cistrons, Immune Marker, Concept, Metabolic Phenomena, Chromophobe Renal Cell Carcinoma, cell expansion, Metabolism Concepts, Surrogate End Point, chemical analysis, Phenomena, Nephroid Carcinomas, techniques, l(2)SH0323, metabolism, Metabolic Phenomenon, Biologic Markers, CYH1, Intervention, Dbest, multicellular organism metabolic process, Serum Marker, biodegradation, best, Metabolic, Surrogate, Renal Cell, Renal Carcinoma, Endpoints, Specificity, sample population, Surrogate Marker, DmelCG11628, Collecting Duct (Kidney), cardinality, assay, BEST, methodology, Immune Markers, Anabolism"],"additional_accession":[]},"is_claimable":false,"name":"ccRCC_methylation - samples","description":"ccRCC case samples using methylation array","dates":{"updated":"2017-07-26 15:39:25"},"accession":"EGAD00010000482","cross_references":{"TAXONOMY":["9606"],"pubmed":["26264667"],"EGA":["EGAC00001000109","EGAS00001000509"]}}