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. GEO Series ID Treatment miRNA name Cell line GSE112859 OE miR-574-3p MGC-803 GSE112859 OE miR-574-5p MGC-803 GSE118315 KO miR-124-3p iNGN GSE124411 OE miR-150-5p LX-2 GSE124411 OE miR-150-5p QSQ-7701 GSE129076 OE miR-450a-5p A2780 GSE129076 OE miR-450a-5p SKOV-3 GSE148827 OE miR-1271-5p SH-SY5Y GSE154968 OE miR-21-3p HaCaT GSE160736 OE miR-642a-5p 22Rv1 GSE168484 OE miR-20b-5p Hep-G2 GSE169128 KO miR-3662 MDA-MB-231 GSE179399 KO miR-3662 LNCaP-clone-FGC GSE202135 OE miR-130a-3p N/A GSE202135 OE miR-130b-3p N/A GSE210778 OE miR-375-3p HUV-EC-C 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