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Fig. 2 | BMC Bioinformatics

Fig. 2

From: TCGA2BED: extracting, extending, integrating, and querying The Cancer Genome Atlas

Fig. 2

Interaction diagram of the TCGA2BED software architecture. It is composed of: a the controller, which executes the operations (e.g., download, conversion) specified either with a XML input configuration file or through the user interface; b TCGA retrieval system, which searches and retrieves TCGA genomic data of multiple types (i.e., CNV, DNA-seq, DNA-methylation, miRNA-seq, and RNA-seq V1, V2) and their associated clinical and biospecimen meta data; c the BioParser, which converts them in the tab-delimited BED format, and all their corresponding clinical and biospecimen meta data in tab-delimited attribute-value text format. Dashed blue and full green arrowed lines correspond to the paths of data download and conversion, respectively; from left to right, blue thick line rectangles refer to software components, green thin line ones represent the BioParser extensions with the links to the four external databases for additional genomic data retrieval (i.e., UCSC, HGNC, NCBI Entrez Gene, and miRBase). The roman (arabic) numbers refer to the sequence of download (conversion) operations that a user can perform

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