OGI Index Calculator

Transcriptome-Based Predictive Modeling Tool for Immunotherapy Response

About this tool

The OGI Index Analysis Tool provides an easy-to-use platform for predicting immunotherapy sensitivity in hepatocellular carcinoma using transcriptome data. By uploading expression files, users can obtain OGI scores, response classifications, and immune features.

OGI intro modules
Format notes: The first column must be gene symbols (Gene). If a header exists, sample names start from column 2. If there is no header, sample names will be auto-generated as Sample1..SampleN. CSV / TSV / TXT are supported (separator auto-detected).

Analysis

Run OGI scoring and view results

Upload expression matrix (Auto-detect mode)

Click to upload CSV / TSV / TXT
Column 1: Gene; remaining columns: expression values (header optional).
Paste expression matrix (optional)
Supports CSV / TSV / TXT (delimiter auto-detected). First column must be Gene. Click Fill example to insert a demo template, or Use pasted data to parse and detect mode.
The same method is used to compute OGI1/OGI2/OGI. Mode is decided by sample count.
Input tips:
  • Single-sample: ideally upload 2 columns (Gene + one sample).
  • Cohort: preferably include a header row (Gene, Sample1, Sample2, ...).
  • Expression values can be TPM / FPKM / counts / log2, etc.
  • Note: this frontend also sends built-in OGI1/OGI2 gene sets to backend (see Help page).

Analyzing... Please wait...

OGI Results

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Tip: click table headers to sort. Search applies to all columns. Pagination updates automatically.

Visualization

Note: "Download image" exports the first plot (bar) by default.

Statistics

User Guide

1. Overview

The OGI Index Calculator is a transcriptomic analysis tool (GSVA/Z-score) designed to compute OGI (OKI Gene-derived Index), which summarizes activity differences between drug-response-related gene sets.

2. Input format

File types

CSV / TSV / TXT files are supported.

Data structure

The first column must be Gene; remaining columns are sample expression values (header row recommended).

Example file

You can download an example file to confirm the expected format:

Download sample_data.csv

3. Parameters

  • Method: Choose GSVA or Z-score
  • Min gene set size: Default 10
  • Max gene set size: Default 1000

4. Visualization (cohort mode)

  • The Plot tab will render all plots after you click Run analysis:
  • Bar plot: OGI by sample (demo threshold OGI=1)
  • Boxplot: distribution
  • Violin plot: density
  • Scatter plot: OGI1 vs OGI2

5. Interpreting results

  • OGI1: gene set activity score 1
  • OGI2: gene set activity score 2
  • OGI: computed as 2^(OGI1-OGI2)

Gene signatures used in OGI

This frontend includes built-in OGI1/OGI2 gene sets and sends them to backend in the analysis request (params.geneSets).

Copy / Preview gene sets
Tip: click buttons to copy to clipboard.
Preview shows first 80 genes per set to keep the page responsive.

Frequently Asked Questions

OGI (OKI Gene-derived Index) is a transcriptome-based surrogate of the functional PDOTS readout OKI (Organoid Killing Index).

In our study, OGI was derived from two gene signatures: sensitive-like and resistant-like. Signature activity scores are computed (e.g., GSVA) and integrated into a composite index.

This tool accepts CSV / TSV / TXT. The first column must be gene symbols and the remaining columns are expression values.

  • Header recommended: Gene, Sample1, Sample2, ...
  • No header: sample columns will be named Sample1..SampleN automatically.

Please check:

  • First column is gene symbols.
  • Delimiter is consistent.
  • Expression columns are numeric.
  • No extra annotation columns between Gene and expression values.

In this demo frontend, we use a simple OGI ≥ 1 rule to display a badge. Calibrate cutoffs for real-world use.

Data is used for computation only in your current session. Upload de-identified data whenever possible.

Contact Us

If you encounter issues (format errors, interpretation questions, runtime problems), please contact the authors below.

First Author

Name: Fei Song
Affiliation: Liver Cancer Institute & Department of Liver Surgery and Transplantation, Zhongshan Hospital, Fudan University, Shanghai, China
Department of Hepatobiliary Surgery, Affiliated Hospital of Nantong University, Nantong, China
Role: Software · Data curation · Formal analysis · Investigation · Visualization · Methodology · Writing – original draft & review/editing
ORCID

Corresponding Author

Name: Xin-Rong Yang, MD, PhD
Affiliation: Liver Cancer Institute & Department of Liver Surgery and Transplantation, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
Role: Conceptualization · Supervision · Funding acquisition
ORCID

Terms of Use

1. Service terms

Welcome to the OGI Index Calculator. By accessing and using this platform, you agree to the following terms and conditions. If you do not agree, please do not use this service.

2. Data privacy

  • Uploaded data is used only for OGI computation.
  • Data processing is performed on the local server and is not sent to third parties.
  • Temporary files are deleted after analysis (backend-dependent).
  • No personally identifiable information is collected or stored.

3. Usage limitations

  • Maximum file size: 100 MB.
  • Recommended maximum genes per run: 50,000.
  • Do not upload malicious code or virus files.
  • Any actions that may compromise system security are prohibited.

4. Academic use

  • Academic research use is encouraged.
  • Please cite appropriately when publishing results.
  • Commercial use requires prior permission.

5. Disclaimer

  • Results are for reference only and do not constitute medical or scientific advice.
  • Users are responsible for the legality and accuracy of uploaded data.
  • The platform is not liable for losses arising from use of this service.
  • The service may be temporarily unavailable for maintenance or upgrades.

6. Updates

We reserve the right to modify these terms at any time. Updates will be posted on this page.

Last updated: November 21, 2025