Nucleic Acids Research · 2015 · 111 citations · 32 references
Life SciencesCancer BiologyOncologyGene ExpressionMolecular OncologyTranscriptomicsCancer GenomicsCancer TranscriptomicsDifferential Gene Expression AnalysisNoncoding Rna TranscriptomicsRna Sequencing AnalysisTranscriptomic ProfilingCancer BioinformaticsCancer Genomics DatabasesCoexpression Network AnalysisDifferential Transcript ExpressionNon-coding Rna ProfilingNoncoding Rna Expression ProfilingRna SequencingTranscriptome Profiling
The genome-wide transcriptome profiling of cancerous and normal tissue samples can provide insights into the molecular mechanisms of cancer initiation and progression. RNA Sequencing (RNA-Seq) is a revolutionary tool that has been used extensively in cancer research. However, no existing RNA-Seq database provides all of the following features: (i) large-scale and comprehensive data archives and analyses, including coding-transcript profiling, long non-coding RNA (lncRNA) profiling and coexpression networks; (ii) phenotype-oriented data organization and searching and (iii) the visualization of expression profiles, differential expression and regulatory networks. We have constructed the first public database that meets these criteria, the Cancer RNA-Seq Nexus (CRN, http://syslab4.nchu.edu.tw/CRN). CRN has a user-friendly web interface designed to facilitate cancer research and personalized medicine. It is an open resource for intuitive data exploration, providing coding-transcript/lncRNA expression profiles to support researchers generating new hypotheses in cancer research and personalized medicine.
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Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Paul Shannon, Andrew Markiel, Owen Ozier et al. · Genome Research · 2003 · 54.3K citations · Full text