Housekeeping and Reference Transcript Atlas

Housekeeping and Reference Transcript Atlas provides a curated atlas of human and mouse housekeeping genes and candidate reference transcripts for calibrating gene expression analyses and selecting qPCR reference transcripts.

Key Features:

• Extensive Data Mining: Mined RNA-seq datasets comprising 11,281 high-quality samples from 52 non-disease human tissues/cells and 507 samples from 14 healthy tissues/cells of C57BL/6 wild type mice.
• Accurate Identification: Reports 2,158 human housekeeping transcripts derived from 2,176 housekeeping genes and 3,024 mouse housekeeping transcripts from 3,277 housekeeping genes.
• Candidate Reference Transcripts: Provides stable, tissue-selective candidate reference transcripts suitable for normalizing quantitative PCR (qPCR) experiments.
• Primer Design and Predicted Modifiers: Includes specific primers and predicted modifiers of gene expression for some housekeeping transcripts.
• Integration with Regulatory Elements: Integrated with a regulatory elements resource from the Epiregio server.

Scientific Applications:

• Gene Expression Calibration: Enables selection of housekeeping transcripts for calibration of gene expression measurements across tissues and experiments.
• qPCR Normalization: Supplies candidate reference transcripts and primers to improve normalization in quantitative PCR assays.
• Genomic and Evolutionary Analyses: Supports comparative studies of housekeeping gene conservation and evolutionary patterns in human and mouse.
• Molecular Diagnostics: Provides validated housekeeping transcript sets that can serve as controls in diagnostic gene expression assays.
• Regulatory Element Analysis: Facilitates exploration of regulatory elements associated with housekeeping genes via integration with Epiregio.

Methodology:

Mined RNA-seq datasets (11,281 human samples from 52 non-disease tissues/cells; 507 mouse samples from 14 healthy tissues/cells of C57BL/6 wild type) and integrated results with the Epiregio regulatory elements resource.