# IMAT-ITCR Collaboration: A NOVEL METHODOLOGY AND WEB APPLICATION FOR REPRESENTING PROTOFORM DIVERSITY IN CANCER NETWORK MODELS

> **NIH NIH U24** · UNIVERSITY OF CALIFORNIA, SAN DIEGO · 2024 · $79,500

## Abstract

ABSTRACT
A single gene can give rise to several alternatively spliced protein isoforms (i.e., proteoforms) that acquire
cancer-promoting functions. These cancer-associated proteoforms, compared to their normal counterparts, can
exhibit differential binding to protein partners that lead to the “rewiring” of cellular networks. To derive insight
into cancer cellular systems, network biology tools, such as Cytoscape, has been developed to visualize and
analyze cancer from a network biology framework. However, the molecular diversity of proteoforms is not
reflected in cancer interactome models. A limitation to progress in this area is conceptually simple. In nearly all
biological network models, ‘nodes’ represent proteins and ‘edges’ connect pairs of proteins that exhibit a
functional interaction. This is a problem because a gene may have a canonical annotated function, but the
cancer-associated proteoform can exhibit entirely different functions. Rather than conflating all proteoforms into
one gene representation, in this proposal, the IMAT and ITCR team will create a formal representation of
proteoforms in a network biology framework, based on the Cytoscape eXchange (CX) schema that underlies
all NDEx network resources. At the project’s end, the IMAT and ITCR teams will release the new proteoform
data specification (PCX), proteoform networks in the public NDEx database, and an NDEx-compatible
Cytoscape web analysis module based on PCX to analyze proteoform networks. This project will catalyze new
end-user applications that the NDEx resource will serve, as well as provide for the IMAT team advanced
network analysis that can be performed on experimentally generated cancer interactomes.

## Key facts

- **NIH application ID:** 11135124
- **Project number:** 3U24CA269436-02S1
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN DIEGO
- **Principal Investigator:** Dexter Pratt
- **Activity code:** U24 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $79,500
- **Award type:** 3
- **Project period:** 2023-04-15 → 2028-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/11135124

## Citation

> US National Institutes of Health, RePORTER application 11135124, IMAT-ITCR Collaboration: A NOVEL METHODOLOGY AND WEB APPLICATION FOR REPRESENTING PROTOFORM DIVERSITY IN CANCER NETWORK MODELS (3U24CA269436-02S1). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/11135124. Licensed CC0.

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