# CisBP and CisBP-RNA: web resources for protein-DNA and protein-RNA binding models

> **NIH NIH U24** · CINCINNATI CHILDRENS HOSP MED CTR · 2024 · $573,116

## Abstract

Project Summary and Abstract
The processes underlying human health and disease are highly complex. This necessitates the
creation, organization, and dissemination of vast amounts of relevant scientific data. Organizing this
information into databases and user-friendly web sites and tools is therefore an integral component of
ongoing efforts to understand and ultimately improve human health.
Many human diseases are now appreciated to result from genetic and environmental perturbations to
gene regulatory mechanisms. As direct readers of genomic regulatory sequences, transcription factors
(TFs) and RNA-binding proteins (RBPs) are primary components of gene regulatory mechanisms.
Accordingly, the nucleic acid binding specificities of TFs and RBPs (henceforth, “specificities”) provide
foundational knowledge for understanding the processes underlying human health and disease states.
Comprehensive mapping of TF and RBP specificities is thus regarded as a major goal in the fields of
human genetics, functional genomics, and bioinformatics. We aim to ultimately achieve this goal and
disseminate the resulting data freely to the research community. To this end, we created the CisBP
and CisBP-RNA TF and RBP specificity databases over 10 years ago. Since then, we have improved
upon these resources through periodic updates incorporating new experimental data generated in our
labs and others. Since their creation, these unique resources have been heavily utilized by the research
community, with over 60,000 unique users and over 2,800 citations to date.
Our ongoing efforts to maintain and improve CisBP and CisBP-RNA have enabled the comprehensive
study of gene regulation in healthy and disease states in humans and other organisms relevant to
human health. In this proposal, we seek to build upon these powerful resources by improving the
database contents and underlying computational infrastructure (Aim 1), incorporating newly generated
specificity data for TFs and RBPs from human viruses and other important human pathogens (Aim 2),
and enhancing the user experience through improved web sites, web tools, and community outreach
efforts (Aim 3). Implementation of these improvements will directly lead to increased database update
frequencies, improved user experiences, a large and more knowledgeable user community, and new
data for studying the role of gene regulation in human healthy and disease states.

## Key facts

- **NIH application ID:** 10847161
- **Project number:** 1U24HG013078-01A1
- **Recipient organization:** CINCINNATI CHILDRENS HOSP MED CTR
- **Principal Investigator:** Timothy Hughes
- **Activity code:** U24 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $573,116
- **Award type:** 1
- **Project period:** 2024-06-24 → 2029-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10847161

## Citation

> US National Institutes of Health, RePORTER application 10847161, CisBP and CisBP-RNA: web resources for protein-DNA and protein-RNA binding models (1U24HG013078-01A1). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10847161. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*