A comprehensive transcript index of the human genome generated using microarrays and computational approaches

Area of Science:

• Genomics
• Transcriptomics
• Human Biology

Background:

• Utilized computational and microarray-based experimental approaches to build a comprehensive human genome transcript index.
• Employed oligonucleotide probes from known and predicted transcript sequences for transcription surveys across 60 diverse human tissues and cell lines.
• Assessed expression activity using genomic tiling arrays on chromosomes 20 and 22.

Purpose of the Study:

• To generate an experimentally supported transcript set for the human genome.
• To investigate transcriptional activity outside of annotated genomic regions.
• To provide an atlas of human gene expression.

Main Methods:

• Ink-jet microarrays for surveying transcription in 60 tissues/cell lines.
• Genomic tiling arrays for assessing expression activity across conditions.
• Integration of microarray data with genome annotations.

Main Results:

• Identified 28,456 experimentally supported transcripts, representing the first experimentally driven human genome annotation.
• Genomic tiling revealed substantial transcription outside annotated genomic regions.
• Demonstrated a genome-wide method for measuring unannotated transcriptional activity.

Conclusions:

• The study provides one of the most comprehensive assessments of human transcriptional activity to date.
• The generated data serves as an atlas of human gene expression.
• Further characterization of unannotated transcriptional activity is necessary for complete human genome annotation.