A single-page web tool to analyze chromosomal Copy Number Variation (CNV) regions and identify intersecting genes. The tool queries the Ensembl (hg38/GRCh38) database to provide detailed information about how a given CNV affects overlapping genes.
This application provides a user-friendly interface to input one or more genomic regions and receive a detailed analysis of gene overlap. For each gene, it determines the type of intersection (e.g., fully contained, partial overlap) and can perform a deeper analysis on partially-affected genes to check if the CNV breakpoints disrupt coding sequences or specific exons.
This tool is designed for researchers and bioinformaticians who need a quick way to assess the potential impact of CNVs on gene function without complex command-line workflows.
- Simple Interface: Clean, single-page application that runs in any modern web browser.
- Batch Processing: Analyze multiple CNV regions in a single submission.
- Detailed Gene Analysis: Determines the relationship between the CNV and each overlapping gene.
- Breakpoint Analysis: For partial overlaps, it checks if breakpoints fall within a gene's coding region (CDS).
- Exon-Level Detail: Optional analysis to identify specific exons contained within the CNV or hit by a breakpoint.
- Clear Output:
- A primary, tab-separated output for easy copy-pasting into spreadsheets or other software.
- Detailed, collapsible logs for each region, showing the step-by-step analysis logic and raw API responses for transparency.
- Robust API Handling: Automatically handles Ensembl API rate-limiting by waiting and retrying requests.
- Save the Code: Copy the entire HTML code from the
cnv-gene-analyzer.htmlfile. - Open in Browser: Save the code as an HTML file (e.g.,
analyzer.html) and open it with a web browser like Chrome, Firefox, or Edge. - Enter Regions: In the "CNV Regions" text area, enter one or more genomic regions.
- Select Options: Check the boxes under "Include in summary" if you want to see details about exons within the CNV or at the breakpoint for partially affected genes.
- Analyze: Click the "Analyze Regions" button. The results and logs will appear below.
Regions should be provided in the format [chrom]:[start]-[end], based on the hg38/GRCh38 human genome assembly.
You can enter multiple regions separated by a newline or a comma.
Example Input:
7:140719331-140783331
13:32315474-32335474
X:155019803-155029803
The main results are presented in a text area, with each line formatted as:
[region] [gene1(details),gene2(details),...]
Example:
3:12430001-12830000 PPARG(partial,coding_breakpoint;intronic_breakpoint),CAND2(partial,coding_breakpoint;exon_at_breakpoint:ENSE00000966695|ENSE00000966696)
Annotation Details:
(contained): The gene is fully inside the CNV.(contains_CNV): The CNV is fully inside the gene (e.g., in an intron).(adjacent): The CNV and gene are next to each other but do not overlap.(partial,coding_breakpoint): A CNV breakpoint falls within the gene's coding sequence (CDS).(partial,non-coding_breakpoint): A CNV breakpoint falls within the gene's non-coding sequence (e.g., an intron outside the CDS).;exons_inside:[id1|id2]: (Optional) Lists exons fully inside the CNV.;exon_at_breakpoint:[id1|id2]: (Optional) Lists exons physically hit by a breakpoint.;intronic_breakpoint: (Optional) Indicates a coding breakpoint occurred in an intron, not within an exon's boundaries.
For each region analyzed, a collapsible log is generated. This provides a step-by-step trace of the analysis, including:
- The coordinates being checked.
- The logic used to determine the breakpoint type.
- The full JSON response from the Ensembl API for detailed gene lookups, allowing for manual verification.
- Frontend: Plain HTML, JavaScript, and Tailwind CSS for styling. No server-side component is needed.
- API: Uses the public Ensembl REST API (
https://rest.ensembl.org) for all genomic data. - Genome Assembly: All coordinates and gene models are based on GRCh38 (hg38) as defined by Ensembl.