Section 1 Overview

The logo for the RIVER resource.

FIGURE 1.1: The logo for the RIVER resource.

1.1 Unmet Needs

Most available interactions have focused on genes (or proteins), neglecting the study of regulatory interactions involving non-coding regions of the genome. As a result, there is a lack of dedicated resources and utilities in this area. The RIVER resource addresses these needs by providing manual curation of gene-directed regulatory interactions across varied contexts, such as organs, tissues, and cell types. More importantly, its web-server supports data mining that encompasses the non-coding genome.

1.2 Data Resource

The RIVER resource is specially designed to be an open and scalable platform for investigating gene-directed multimodal regulatory interactions. Currently, these interactions are organised into three modalities: Activity-By-Contact (ABC) for enhancer-gene maps (see this), Promoter Capture Hi-C (PCHiC) (see this), and Quantitative Trait Loci (QTL) (see this).

Genes involved in regulatory interactions are annotated with a range of ontologies on functions (Gene Ontology), phenotypes (Human Phenotype Ontology), diseases (Mondo Disease Ontology), protein domains including SCOP superfamily domains (SCOP), Pfam domains (Pfam), and InterPro domains (InterPro).

1.3 Data Mining

In response to the growing availability of summary-level epi/genomic datasets from cohort-scale studies, RIVER offers web-based data-mining capabilities that cover the non-coding genome. These capabilities include:

  • Mining - Search allows users to enter keywords to query the resource, which returns context-specific pages and gene-specific pages related to the query.

  • Mining - Browse allows users to navigate through different contexts such as organs, tissues, and cell types to interactively explore their regulatory interactions.

  • Mining - RI2Genes allows users to mine the resource to identify potential regulatory genes from their input data (see Example Output).