GTRD

GTRD integrates uniformly annotated Next-Generation Sequencing (NGS) datasets including ChIP-seq, ChIP-exo, DNase-seq, MNase-seq, ATAC-seq, and RNA-seq to support analysis of transcription regulation and mapping of transcription factor binding sites, gene expression profiles, and regulatory elements.

Key Features:

• Uniform NGS annotation: Aggregates and uniformly annotates diverse NGS data types including ChIP-seq, ChIP-exo, DNase-seq, MNase-seq, ATAC-seq, and RNA-seq.
• Structured cell type dictionary: Systematically arranges cell types, encompassing both cell lines and tissues, into a structured dictionary linked to ontologies.
• Ontology integration: Links cell type annotations to BRENDA, Cell Ontology, Uberon, Cellosaurus, and Experimental Factor Ontology.
• Cross-references to regulatory databases: Connects integrated datasets with specialized resources such as FANTOM5, ENCODE, and GTEx.
• Regulatory annotations: Provides curated information on transcription factor binding sites, gene expression profiles, and regulatory elements.
• Custom table reports: Generates table reports focused on specific cell types, transcription factors, or genes for downstream analysis.

Scientific Applications:

• Transcription factor mapping: Mapping and comparative analysis of transcription factor binding sites across cell types and conditions.
• Regulatory mechanism analysis: Integrating multi-modal NGS data to investigate mechanisms of gene transcription regulation.
• Expression and regulatory element comparison: Comparative analysis of gene expression profiles and regulatory elements between cell lines and tissues.

Methodology:

Uniform annotation of NGS datasets (ChIP-seq, ChIP-exo, DNase-seq, MNase-seq, ATAC-seq, RNA-seq) and systematic arrangement of cell types into a dictionary linked to BRENDA, Cell Ontology, Uberon, Cellosaurus, Experimental Factor Ontology, with cross-references to FANTOM5, ENCODE, and GTEx; generation of table reports for selected cell types, transcription factors, or genes.