FunCirc - Functional Circular RNA Database

A web application for querying circRNA essentiality and clinical expression data from multiple studies.

Overview

FunCirc integrates data from multiple circRNA screening studies and clinical datasets, enabling researchers to:

• Query circRNA Essentiality: Visualize MAGeCK screen results showing which circRNAs are essential for cell viability across different cancer cell lines
• Query Clinical Expression: Explore circRNA expression patterns across patient cohorts and cancer types

Technology Stack

Layer	Technology
Frontend	React 18, TypeScript, Vite
State Management	Zustand
Data Fetching	TanStack Query (React Query)
Visualizations	Recharts, D3.js, Custom SVG
Backend	Node.js, Express, TypeScript
Data Format	JSON (converted from R RDS files)

Project Structure

db_react/
├── client/                 # React frontend
│   ├── src/
│   │   ├── components/     # Reusable UI components
│   │   ├── pages/          # Page components (Home, Essentiality, Clinical)
│   │   ├── hooks/          # Custom React hooks
│   │   ├── store/          # Zustand state management
│   │   └── App.tsx         # Main application component
│   ├── public/             # Static assets (images)
│   ├── index.html
│   ├── vite.config.ts
│   └── package.json
│
├── server/                 # Express backend
│   ├── src/
│   │   ├── routes/         # API endpoints
│   │   │   ├── studies.ts  # Essentiality data endpoints
│   │   │   ├── clinical.ts # Clinical expression endpoints
│   │   │   └── search.ts   # Gene search endpoint
│   │   ├── types.ts        # TypeScript type definitions
│   │   └── index.ts        # Server entry point
│   ├── data/               # JSON data files (see Data Setup)
│   └── package.json
│
├── scripts/                # Data conversion utilities
│   └── convert_data.js     # Convert R RDS to JSON
│
├── data/                   # Shared data directory
└── package.json            # Root package.json

Installation

Prerequisites

• Node.js v18 or higher
• npm v9 or higher

Setup

1. Clone the repository

   git clone https://github.com/HansenHeLab/FunCirc-React.git
   cd FunCirc-React

2. Install dependencies

   # Install root dependencies (optional, for workspace management)
   npm install
   
   # Install client dependencies
   cd client
   npm install
   cd ..
   
   # Install server dependencies
   cd server
   npm install
   cd ..

3. Set up data files

   The application requires JSON data files in server/data/. These should be converted from the original R RDS files using the scripts in scripts/.

   Expected data structure:

   server/data/
   ├── her-et-al/
   │   ├── annotations.json
   │   ├── screen_data.json
   │   └── genes.json
   ├── chen-et-al/
   │   ├── annotations.json
   │   ├── circ_data.json
   │   ├── genes.json
   │   └── linear_data.json
   ├── liu-et-al/
   │   ├── ht29/
   │   ├── 293ft/
   │   └── hela/
   ├── li-et-al/
   │   ├── colon/
   │   ├── pancreas/
   │   ├── brain/
   │   └── skin/
   └── clinical/
       ├── split/
       ├── arul-et-al.json
       ├── cpcg.json
       └── breast-cohort.json
   ├── gene-search-index.json
   

Running the Application

Development Mode

Open two terminal windows:

Terminal 1 - Start the backend server:

cd server
npm run dev

Server will run on http://localhost:3001

Terminal 2 - Start the frontend:

cd client
npm run dev

Frontend will run on http://localhost:5173

Production Build

# Build client
cd client
npm run build

# Build server
cd ../server
npm run build

API Endpoints

Endpoint	Description
GET /api/studies	List all available studies
GET /api/studies/:id/genes	Get genes for a study
GET /api/studies/:id/annotations	Get circRNA annotations
GET /api/studies/:id/essentiality	Get essentiality dotmap data
GET /api/clinical/datasets	List clinical datasets
GET /api/clinical/:id/expression	Get clinical expression data
GET /api/search?q=...	Search genes across studies

Data Sources

Screening Studies

• Her et al. – shRNA genome-wide circRNA screen (7 cancer cell lines)
• Liu et al. – shRNA-based circRNA screen (18 cell lines, 4 tissue types)
• Li et al. – CRISPR-RfxCas13d circRNA screen (Colon, Pancreas, Brain, Skin)
• Chen et al. – shRNA circRNA screen in prostate cancer (LNCaP, V16A, 22Rv1, PC-3)

Clinical Datasets

• Arul et al. (Vo et al.) – The landscape of circular RNA in cancer
• CPCG (Fraser et al.) – Canadian Prostate Cancer Genome Network
• In-house Breast Cohort – Breast cancer subtypes

This project is for research purposes. Please cite the original studies when using this database.

Contact

He Lab @ UHN