FC-R2

FC-R2 provides a comprehensive expression atlas of the human transcriptome, quantifying expression for over 109,000 coding and noncoding genes to support analysis of long noncoding RNA (lncRNA) roles across tissues and diseases.

Key Features:

• Data content: Expression profiles cover over 109,000 coding and noncoding genes across more than 70,000 samples.
• Source annotations: Gene models and transcript annotations are derived from the FANTOM CAGE-Associated Transcriptome (FANTOM-CAT).
• Recount2 integration: Gene annotations expand and build upon the original recount2 resource.
• lncRNA focus: Systematic quantification and characterization of long noncoding RNAs, including enhancer lncRNAs.
• Tissue-specific profiling: Identification of distinct transcription profiles for classes of coding and noncoding genes across tissues.
• Differential expression analysis: Performed across thirteen cancer types to detect differentially expressed noncoding and coding genes.
• Prognostic marker assessment: Evaluation and confirmation of prognostic significance for several enhancer lncRNAs in cancer.
• Reproducibility and discovery: Capability to reproduce key findings from large-scale studies and generate novel insights in normal and diseased samples.

Scientific Applications:

• Tissue-specific transcription profiling: Characterizing expression patterns of coding and noncoding gene classes across diverse human tissues.
• Cancer differential expression: Identifying differentially expressed genes, including novel noncoding candidates, across thirteen cancer types.
• Prognostic biomarker evaluation: Assessing the prognostic value of enhancer lncRNAs in cancer cohorts.
• lncRNA functional characterization: Systematic investigation of lncRNA expression to inform studies of phenotype determination and disease pathogenesis.
• Large-scale study validation: Reproducing and contextualizing findings from large transcriptomic datasets.

Methodology:

Expression quantification and annotations derived from FANTOM CAGE-Associated Transcriptome (FANTOM-CAT), expanded on recount2 gene annotations, with differential expression analyses performed across thirteen cancer types using aggregated expression data from over 70,000 samples.