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cerna-analysis

Build a ceRNA regulatory network from a key gene list using miRNA-mRNA and miRNA-lncRNA reference tables, with CSV exports and PDF visualization. The ModelScope package requires reference data obtained from the canonical source repository.

personAuthor: OpenScientificSkillshubOpenAPI
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ceRNA Analysis

When to Use

Use this skill when you need to construct a ceRNA regulatory network from a known key-gene list using miRNA-mRNA and miRNA-lncRNA reference tables.

ModelScope distribution note: the reference tables exceed the platform package-size limit and are not embedded in this distribution. Obtain references/database/ from the canonical source repository, then pass its location with --reference_dir.

Use it for:

  • Building a ceRNA network from one gene list and exporting flat CSV plus PDF outputs
  • Comparing supported miRNA source modes such as combined, starbase, or pairwise overlaps
  • Re-running the same local workflow with different lncRNA strictness, layout, or plotting parameters

Do not use it for:

  • Differential expression, single-cell, enrichment, or survival analysis
  • Workflows that do not start from a key gene list
  • Cases where you want a miRNA-mRNA-only graph without a retained lncRNA ceRNA layer

Input Validation

This skill accepts:

  • A key gene list as a plain-text file (one gene symbol per line) or as a comma-separated string on the CLI
  • Optional parameter overrides for dataset mode, lncRNA strictness, layout, colors, and timeout

If the user's request does not involve building a ceRNA regulatory network from a key gene list — for example, asking to run differential expression, enrichment analysis, single-cell workflows, or survival analysis — do not proceed with the workflow. Instead respond:

"ceRNA Analysis is designed to construct a ceRNA regulatory network from a key gene list using bundled miRNA-mRNA and miRNA-lncRNA reference databases. Your request appears to be outside this scope. Please provide a key gene list and specify a supported miRNA dataset mode, or use a more appropriate skill for differential expression, enrichment analysis, or single-cell workflows."

When to Read External Files

| Situation | File to Read | Purpose | |-----------|--------------|---------| | Need algorithm details | references/algorithm.md | ceRNA construction logic, dataset combinations, filtering rules. Includes worked examples of pairwise intersection network size vs combined mode. | | Need to run analysis | scripts/main.R | Execute: Rscript scripts/main.R --key_genes ... --output_dir .... Note: --help requires igraph to be installed. | | Encounter errors | references/troubleshooting.md | Common errors and solutions | | Need CLI examples | references/cli-guide.md | Detailed local run examples with measured outputs | | Need test data | tests/data/ | Sample key-gene input for testing |

Usage

Rscript scripts/main.R \
  --key_genes tests/data/gene.txt \
  --output_dir ./output/ \
  --mirna_dataset combined \
  --lncrna_strictness High \
  --lncrna_freq_thresh 0 \
  --timeout_seconds 600 \
  --seed 42

Dependency note: --help and all analysis modes require igraph to be installed. Install igraph before running any command. Use references/troubleshooting.md for installation guidance.

Arguments

Main Analysis: scripts/main.R

| Short | Long | Type | Default | Description | |-------|------|------|---------|-------------| | -i | --key_genes | character | required | Key gene file path or comma-separated gene names | | -o | --output_dir | character | ./output/ | Output directory | | -m | --mirna_dataset | character | combined | Dataset: combined, starbase, mirdb, mirtarbase, starbase+mirdb, starbase+mirtarbase, mirdb+mirtarbase | | -l | --lncrna_strictness | character | High | lncRNA interaction strictness: Low, Median, High | | -f | --lncrna_freq_thresh | integer | 0 | Minimum retained lncRNA frequency | | -r | --reference_dir | character | file.path(script_dir, "..", "references", "database") | Database directory | | | --plot_width | double | 12 | PDF width in inches | | | --plot_height | double | 8 | PDF height in inches | | | --layout_type | character | kk | Layout: kk, fr, nicely, circle, grid, randomly | | | --mrna_color | character | #D16BA5 | mRNA node color | | | --lncrna_color | character | #008dcd | lncRNA node color | | | --mirna_color | character | #00c9a7 | miRNA node color | | | --node_size_base | double | 15 | Base node size | | | --label_size | double | 0.8 | Node label size | | | --show_legend | logical | TRUE | Show legend in the PDF | | -t | --timeout_seconds | integer | 3600 | Elapsed timeout limit | | -s | --seed | integer | 42 | Random seed for reproducibility |

Input Format

Key Genes (key_genes)

Plain-text input with one gene symbol per line, or a comma-separated string passed directly on the CLI.

TP53
BRCA1
MYC

Rules:

  • Blank lines are ignored
  • Lines starting with # are ignored
  • Duplicate genes are removed
  • At least one valid gene is required

Database Directory (reference_dir)

The bundled database directory is references/database/. Required files depend on the selected mirna_dataset plus the selected lncRNA strictness file.

  • combined: miRNA_mRNA.csv
  • starbase: starbase_miRNA_mRNA.csv
  • mirdb: miRDB_miRNA_mRNA.csv
  • mirtarbase: miRTarbase_miRNA_mRNA.csv
  • starbase+mirdb: starbase_miRNA_mRNA.csv and miRDB_miRNA_mRNA.csv
  • starbase+mirtarbase: starbase_miRNA_mRNA.csv and miRTarbase_miRNA_mRNA.csv
  • mirdb+mirtarbase: miRDB_miRNA_mRNA.csv and miRTarbase_miRNA_mRNA.csv
  • lncRNA file: one of starbase_miRNA_lncRNA_High.csv, starbase_miRNA_lncRNA_Median.csv, or starbase_miRNA_lncRNA_Low.csv

Output Files

| File | Description | |------|-------------| | ceRNA_network_edges.csv | Edge table with node1,node2 columns | | ceRNA_network_nodes.csv | Node table with node,type,degree columns | | ceRNA_network.pdf | ceRNA network visualization | | session_info.txt | R session details and loaded package versions |

Workflow

Step 1: Validate Input

  • Check key-gene input existence or parse comma-separated genes
  • Validate parameter choices, numeric limits, timeout, and colors
  • Verify the database directory and required files

Step 2: Load Interaction Data

  • Load the selected miRNA-mRNA dataset
  • Load the selected miRNA-lncRNA dataset by strictness level
  • Recompute pairwise intersections when requested

Step 3: Filter the Network

  • Retain miRNA-mRNA pairs linked to the provided key genes
  • Retain miRNA-lncRNA pairs connected to the retained miRNAs
  • Apply the lncRNA frequency threshold
  • Stop with SKILL_INVALID_DATA if no lncRNA interactions remain after filtering, because the ceRNA layer has collapsed

Step 4: Build Outputs

  • Construct edge and node tables
  • Save CSV, PDF, and session information in the output directory root

Methods

combined

Uses the bundled precomputed overlap across three miRNA-mRNA resources for higher-confidence interactions.

Pairwise Intersections

starbase+mirdb, starbase+mirtarbase, and mirdb+mirtarbase recompute the overlap between two bundled databases. Pairwise intersections typically yield 20–40% fewer edges than combined mode because only interactions present in both selected databases are retained. Use pairwise modes when you need higher-confidence edges at the cost of reduced network coverage.

lncRNA Strictness

High, Median, and Low select different bundled starBase evidence levels for miRNA-lncRNA interactions.

Examples

Basic Combined Analysis

Rscript scripts/main.R \
  -i ./key_genes.txt \
  -o ./output \
  -m combined

Single Database Analysis

Rscript scripts/main.R \
  -i ./key_genes.txt \
  -o ./output_starbase \
  -m starbase \
  -l Median \
  -f 1

Error Handling

| Error | Cause | Solution | |-------|-------|----------| | SKILL_FILE_NOT_FOUND | Input file or database file is missing | Check the file path or bundled database directory | | SKILL_EMPTY_FILE | A required file exists but has no content | Replace or regenerate the file | | SKILL_EMPTY_DATA | A required reference table has no usable rows | Verify the input content and regenerate the file if needed | | SKILL_MISSING_COLUMNS | An input table lacks required columns | Verify the expected schema | | SKILL_INVALID_PARAMETER | An invalid CLI value was provided | Use one of the documented parameter values | | SKILL_INVALID_DATA | The input data cannot build a valid ceRNA network, or lncRNA filtering removes the ceRNA layer entirely | Verify the key genes and database files, then lower --lncrna_freq_thresh or choose a different dataset / strictness | | SKILL_DEPENDENCY_MISSING | A required package is not installed (igraph required for all modes including --help) | Install the missing package before running any command | | SKILL_TIMEOUT | The run exceeded the timeout limit | Increase --timeout_seconds | | SKILL_RUNTIME_ERROR | An unexpected runtime failure occurred | Re-run after checking the console error message |

IF error persists, READ: references/troubleshooting.md

Testing

Test with Sample Data

# Run with sample data (igraph must be installed first)
Rscript scripts/main.R \
  -i tests/data/gene.txt \
  -o tests/output/

Validation Commands

# Inspect edge output
wc -l tests/output/ceRNA_network_edges.csv

# Check plot exists
ls -la tests/output/ceRNA_network.pdf