# Resource Informatics Core

> **NIH NIH U41** · UNIVERSITY OF WASHINGTON · 2020 · $593,675

## Abstract

C. Informatics Core
Summary
The informatics core will continue to deliver to the community high quality, well-structured datasets with
complete metadata along with comprehensive data analysis. To achieve this, we have developed
bioinformatics pipelines to process and validate our ChIP-seq and RNA-seq data and worked extensively
with the ENCODE DCC to curate our metadata to make our data easily accessible. The ChIP-seq pipeline
has been used to call both narrow and broad peaks and to annotate HOT regions and TF binding sites in
worm and fly across varying samples and stages; the RNA-seq pipeline has been used to identify
differentially expressed genes under various conditions, such as different developmental stages and TF
mutants, and we will evaluate TF binding sites associated with these genes. Although these pipelines have
been set up and tested thoroughly, we aim to further optimize them; for instance, a new method is being
developed to call ChIP-seq peaks using multiple types of controls. To our knowledge, no such peak caller
exists. To integrate and analyze our data, we will develop a mini-encyclopedia with three levels of
annotations, similar to the encyclopedia developed through the ENCODE project. The ground level will
consist of the gene expression, TF binding and histone modification data in worm and fly. Based on our
preliminary results, we have developed advanced statistical models to identify functional genomic regions,
such as enhancers and HOT regions, etc. We will deposit these results into the middle annotation level.
The top level will contain linkages of genes and their regulators, predicted by our models. The regulators
include both cis- and trans-regulatory elements, such as enhancers and TFs. Moreover, the linkages will be
integrated to form temporal or spatial networks. We aim to identify key regulatory factors by comparing the
structure of the networks. We will share all of our datasets, analysis results, and worm and fly strains with
the community through the appropriate public databases.

## Key facts

- **NIH application ID:** 9944662
- **Project number:** 5U41HG007355-07
- **Recipient organization:** UNIVERSITY OF WASHINGTON
- **Principal Investigator:** ROBERT H WATERSTON
- **Activity code:** U41 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $593,675
- **Award type:** 5
- **Project period:** — → —

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9944662

## Citation

> US National Institutes of Health, RePORTER application 9944662, Resource Informatics Core (5U41HG007355-07). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9944662. Licensed CC0.

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