FANTOM

FANTOM maps promoter activities and transcriptional networks in mammalian genomes using cap analysis of gene expression (CAGE) and integrated high-throughput experiments to elucidate macrophage differentiation and discover novel transcriptome components.

Key Features:

• CAGE sequencing: Cap analysis of gene expression (CAGE) sequences mRNA 5'-ends using second-generation sequencers to quantify promoter activities, including in unannotated genomic regions.
• Short RNA sequencing and microarray profiling: Short RNA sequencing and microarray gene expression profiling are applied to large-scale perturbation studies in the THP-1 human leukemic cell line during differentiation.
• ChIP-chip assays: ChIP-chip assays map epigenetic modifications and transcription factor binding sites.
• Mammalian two-hybrid (M2H) assay: Large-scale M2H assays explore interactions between transcription factors.
• Quantitative RT-PCR: Quantitative RT-PCR analyses track expression profiles across human and mouse tissues to assess combinatorial effects of transcription factor regulation.
• Integrative annotation and analysis: Systematic annotation, integration, and combined analysis of multiple experimental data types are used to generate predictions and validate regulatory interactions.

Scientific Applications:

• Macrophage differentiation networks: Elucidating transcriptional networks governing macrophage differentiation using integrated CAGE and perturbation data.
• Novel transcriptome discovery: Identifying novel transcriptome components and promoters, including activity in previously unannotated regions.
• Transcription factor interaction analysis: Investigating combinatorial transcription factor regulation and protein–protein interactions via M2H and qRT-PCR.
• Epigenetic and binding site mapping: Mapping epigenetic modifications and transcription factor binding sites with ChIP-chip data.
• Regulatory prediction and validation: Producing published predictions and validated regulatory interactions to support studies of transcriptional regulation.

Methodology:

Data from CAGE, short RNA sequencing, microarray, ChIP-chip, M2H, and quantitative RT-PCR are analyzed individually and in combination and subjected to systematic annotation and integration to produce predictions and validated regulatory interactions.