FuNmiRBench datasets

FuNmiRBench is a benchmarking framework for evaluating functional microRNA (miRNA) target prediction methods using experimentally derived differential expression (DE) datasets. The benchmark compares predicted miRNA–target interactions against transcriptomic responses observed after miRNA overexpression (OE) or knockout (KO) experiments, enabling systematic assessment of functional target prediction performance across multiple prediction tools.

This Zenodo record contains the curated differential expression tables and standardized prediction outputs used in FuNmiRBench benchmarking experiments.

Differential Expression (DE) tables

This collection contains 16 standardized differential expression tables derived from miRNA overexpression (OE) and knockout (KO) experiments. Differential expression analyses were performed using DESeq2, and each table includes the following columns:

• gene_id
• logFC
• PValue
• FDR

The datasets span 13 GEO series and cover a diverse set of miRNA perturbation experiments across multiple cell lines. A summary of the included datasets is provided below.

Prediction files

Standardized prediction outputs generated from multiple miRNA target prediction tools. All predictor outputs were converted into a common tabular format to enable direct benchmarking and comparison within FuNmiRBench.

Each prediction file contains the following columns:

• Ensembl_ID
• Gene_Name
• miRNA_ID
• miRNA_Name
• Score

The prediction files are distributed as a compressed archive organized by prediction method, as shown below.

FuNmiRBench_standardized_predictions.zip

└── data
    └── predictions
        ├── microt_cnn
        │   └── microt_cnn_standardized.tsv.gz
        ├── miraw
        │   └── miraw_standardized.tsv.gz
        ├── mirbind2
        │   └── mirbind2_standardized.tsv.gz
        ├── mirdb_mirtarget
        │   └── mirdb_mirtarget_standardized.tsv.gz
        └── targetscan
            └── targetscan_standardized.tsv.gz