Explore the Database

Quick-start entry points for targeted ASD workflows
Expression Studies

Explore miRNAs reported as differentially expressed in ASD case-control studies.

Browse Expression Studies
Genetic Alterations

Explore miRNAs implicated in ASD based on genetic and bioinformatics evidence.

Browse Genetic & Other Studies
Validated Targets

Query miRNA-target gene interactions from miRTarBase.

Query Target Genes
Functional Enrichment

Perform Gene Ontology & Pathway analyses of miRNA target genes.

Run Enrichment analysis

Database Overview

miR4ASD is an open-access, literature-based database that compiles human microRNAs (miRNAs) that were experimentally associated with Autism Spectrum Disorder (ASD). It includes manually curated data from peer-reviewed case-control studies, covering gene expression and genetic variant analysis. All miRNA names from different studies are standardized to miRBase (version 22.1). In addition, miR4ASD also includes information on experimentally validated miRNA-target gene interactions obtained from miRTarBase, information on ASD candidate genes from the SFARI gene database and an interactive functional enrichment tool that was implemented using the g:Profiler REST API.

Key Features of miR4ASD:

Integrated Data

Integrates gene expression and miRNA profiling data from ASD-control studies.

Tissue-Specific Patterns

Highlights tissue-specific miRNA expression patterns across different biological sample types.

Genetic Variants

Integrates evidence of genetic variants in miRNA genes, an underexplored area in ASD research.

Validated Target Genes

Incorporates information on experimentally validated miRNA targets from miRTarBase (version 10.0).

Functional Enrichment

Enables interactive Gene Ontology and Pathway enrichment analysis of miRNA target genes using g:Profiler.

ASD Risk Evidence

Includes SFARI Gene evidence categories, indicating the strength of evidence linking miRNA target genes to ASD risk.

Curation & Processing Workflow

Curation & Processing Workflow

Figure 1: Overview of the curation, standardization, and processing workflow implemented in the miR4ASD database.

Database Statistics & Visualizations

Curated visualizations and synthesis distributions across independent ASD cohorts and study categories.

Jump to:

Data Dictionary & Column Definitions

5 Table Specifications

Comprehensive guide explaining what each table header represents, the standardized data sources, and the precise definitions for all categorical values across miR4ASD.

This section provides information on human miRNAs identified in case-control expression studies of Autism Spectrum Disorder (ASD), including their expression patterns, sample types, and supporting evidence.

Column name Definition & Purpose Allowed Values & Formats
Precursor miRNA (hairpin) Name of the stem-loop precursor miRNA (hairpin), according to miRBase nomenclature (v22.1). It includes a hyperlink to the corresponding miRBase entry. e.g., hsa-let-7a-1, hsa-mir-146a, hsa-mir-155.
Mature miRNA Name of the functional, single-stranded mature miRNA derived from a precursor miRNA, according to miRBase nomenclature (v22.1). It includes a hyperlink to the corresponding miRBase entry. e.g., hsa-let-7a-5p, hsa-miR-146a-5p, hsa-miR-155-5p.
Expression change (ASD vs. controls) Direction of differential expression statistically reported in the ASD cohort versus neurotypical controls. Upregulated Increased expression in ASD.
Downregulated Decreased expression in ASD.
Sample Type Biological tissue, fluid, or cell type used for miRNA analysis. e.g., Blood, Saliva, post-mortem brain tissue (Brain), Lymphoblastoid Cell Lines (LCLs), Neural Stem Cells (NSCs), Olfactory Mucosal Stem Cells (OMSCs), Umbilical cord.
Overall evidence Classification of expression evidence based on the direction and consistency of miRNA dysregulation across independent ASD studies included in miR4ASD.
  • Consistent upregulation Reported in ≥ 2 independent studies, with all studies showing increased expression of the miRNA.
  • Consistent downregulation Reported in ≥ 2 independent studies, with all studies showing decreased expression of the miRNA.
  • Conflicting evidence Reported in ≥ 2 independent studies, with opposing directions of differential expression (both increased and decreased expression of the miRNA).
  • Single-study evidence Only one study reported altered miRNA expression in individuals with ASD, with no independent replication among the studies included in the database.
Evidence from other studies Additional evidence linking the miRNA to ASD from bioinformatics or genetic studies.
  • Bioinformatics Evidence from bioinformatics studies.
  • Genetics: SNP Evidence from genetic association studies evaluating Single Nucleotide Polymorphisms (SNPs) associated with ASD.
  • Genetics: SNV Evidence from sequencing studies reporting Single Nucleotide Variants (SNVs) involving miRNA genes.
  • Genetics: CNV Evidence from genetic studies reporting Copy Number Variants (CNVs) involving miRNA genes.
# up Number of independent peer-reviewed studies reporting upregulation of the miRNA in individuals with ASD compared with controls. Positive integer (≥1).
# down Number of independent peer-reviewed studies reporting downregulation of the miRNA in individuals with ASD compared with controls. Positive integer (≥1).
Total studies Sum of all independent expression studies evaluating this miRNA in ASD. Positive integer (≥1).

This section provides information on human miRNAs implicated in Autism Spectrum Disorder (ASD), based on evidence from genetic and bioinformatics studies.

Column name Definition & Purpose Allowed Values & Formats
Precursor miRNA (hairpin) Name of the stem-loop precursor miRNA (hairpin), according to miRBase nomenclature (v22.1). It includes a hyperlink to the corresponding miRBase entry. e.g., hsa-mir-34a, hsa-mir-106b, hsa-mir-211.
Mature miRNA Name of the functional, single-stranded mature miRNA derived from a precursor miRNA, according to miRBase nomenclature (v22.1). It includes a hyperlink to the corresponding miRBase entry. e.g., hsa-miR-34a-5p, miR-106b-5p, hsa-miR-211-5p.
Study Type Classification of studies according to the type of evidence supporting the association between the miRNA and ASD.
  • Genetics: Studies reporting genetic variants affecting miRNA genes in individuals with ASD.
  • Bioinformatics: Studies reporting ASD-associated miRNAs identified through computational approaches based on expression data.
Variant Type Type of genetic variation reported within miRNA genes in individuals with ASD.
  • CNV Evidence from genetic studies reporting Copy Number Variants (CNVs) affecting miRNA genes.
  • SNV Evidence from sequencing studies reporting Single Nucleotide Variants (SNVs) in miRNA genes.
  • SNP Evidence from genetic association studies evaluating Single Nucleotide Polymorphisms (SNPs) associated with ASD.
Evidence from expression studies Classification of expression evidence based on the direction and consistency of miRNA dysregulation across independent ASD studies included in miR4ASD.
  • Consistent upregulation Reported in ≥ 2 independent studies, with all studies showing increased expression of the miRNA.
  • Consistent downregulation Reported in ≥ 2 independent studies, with all studies showing decreased expression of the miRNA.
  • Conflicting evidence Reported in ≥ 2 independent studies, with opposing directions of differential expression (both increased and decreased expression of the miRNA).
  • Single-study evidence Only one study reported altered miRNA expression in individuals with ASD, with no independent replication among the studies included in the database.
  • None No expression evidence is reported in the studies included in the database.
Total expression studies Number of independent ASD expression studies included in the database reporting differential expression of the miRNA. Positive integer (≥1).
Description of expression evidence Detailed description of the expression evidence, including the direction of differential expression, number of independent studies, sample types analyzed, and mature miRNA-specific findings (e.g., -5p and -3p). Free text describing the available expression evidence, including mature miRNA-specific findings when applicable.

This section provides detailed information from the original studies included in miR4ASD. The information is accessible by clicking the "+" button associated with each miRNA entry in the Expression Studies and Genetic and Other Studies tabs.

Column name Definition & Purpose Allowed Values & Formats
Study Reference to the original publication, displayed using the first author’s surname and publication year and linked to the corresponding publication. Author (year) format, with a hyperlink to the original publication (e.g., Mor (2015), Wu (2016), Toma (2015)).
Description Brief description of the study, including the main experimental approach, biological sample analyzed, and miRNA-related analysis performed. Free-text study description.
Sample Type Broad classification of the biological sample used for miRNA analysis. e.g., Brain, Blood, Saliva, Umbilical cord, Other.
Sample Subtype Specific biological material, cell type, or anatomical region analyzed within the corresponding sample type. Free text specifying the biological material, cell type, or anatomical region analyzed (e.g., plasma, serum, whole blood, LCLs, NSCs, specific post-mortem brain regions).
Methodology Experimental or analytical method used to generate or analyze the data reported in the study. e.g., RT-qPCR, Small RNA-seq, RNA-seq, miRNA microarray, WES, WGS, SNP array, aCGH.
Diagnostic Tools Diagnostic criteria and/or standardized assessment instruments used to establish or support ASD diagnosis in study participants. e.g. DSM-5, DSM-IV, DSM-IV-TR, ADI-R, ADOS, CARS, CARS, ABC, GARS, SRS.
ASD Samples Number of ASD samples analyzed in each study, with separate sample groups or analysis stages reported when applicable. Number of ASD samples (N ), reported as a single value or separately for distinct study groups, cohorts, analysis stages, or methodologies (e.g., ASD N = 31).
Control Samples Number of control samples analyzed in each study, with separate sample groups or analysis stages reported when applicable. Number of control samples (N ), reported as a single value or separately for distinct study groups, cohorts, analysis stages, or methodologies (e.g., Control N = 30).
Country Country where the study was conducted and/or population reported for the participants included in the study. e.g., USA, Brazil, China, Italy, Japan.

This section contains information on experimentally validated target genes of ASD-associated miRNAs, retrieved from miRTarBase version 10.0. It provides miRNA-target gene interactions and their supporting experimental evidence, enabling users to explore potential regulatory relationships. Additionally, it includes SFARI Gene evidence classifications, indicating the strength of evidence supporting the involvement of these target genes in ASD risk.

Column name Definition & Purpose Allowed Values & Formats
Precursor miRNA Name of the stem-loop precursor miRNA (hairpin), according to miRBase nomenclature (v22.1). It includes a hyperlink to the corresponding miRBase entry. e.g., hsa-mir-34a, hsa-mir-106b, hsa-mir-211.
Mature miRNA Name of the stem-loop precursor miRNA (hairpin), according to miRBase nomenclature (v22.1). It includes a hyperlink to the corresponding miRBase entry. e.g., hsa-mir-34a, hsa-mir-106b, hsa-mir-211.
Target Gene Official HGNC gene symbol of an experimentally validated target of the corresponding miRNA. It includes a hyperlink to the corresponding GeneCards entry. e.g., PTEN, SHANK3, MECP2, CHD8, AGO1, AGO4.
ASD Susceptibility (SFARI) Evidence category assigned to the target gene by SFARI Gene (Simons Foundation Autism Research Initiative), a database that curates genes implicated in ASD risk and classifies them according to the strength of evidence supporting their association with ASD.
  • 1SFARI Category 1 High Confidence: Genes with strong genetic evidence supporting their association with ASD, typically including at least three de novo likely gene-disrupting mutations.
  • 2SFARI Category 2 Strong Candidate: Genes supported by substantial genetic evidence, such as two de novo likely gene-disrupting mutations or compelling genome-wide association evidence.
  • 3SFARI Category 3 Suggestive Evidence: Genes with preliminary evidence of association with ASD, such as a single de novo likely gene-disrupting mutation or an unreplicated association.
  • SSFARI Syndromic Genes associated with increased ASD risk and additional clinical features characteristic of a genetic syndrome.
  • None Genes not listed in the SFARI Gene database.
Support Type Classification of miRNA-target interactions (MTIs) based on the experimental evidence reported in miRTarBase v10.0.
  • Functional MTI miRNA-target interaction is supported by strong experimental evidence (Reporter assay, qPCR or Western blot).
  • Weak Support miRNA-target interaction is supported by other type of experiments (e.g., pSILAC, microarray).
PubMed Reference Reference for the original publication reporting the miRNA-target interaction, with a hyperlink to the corresponding PubMed record. PubMed identifier (PMID, e.g.,24312487, 20144220, 23974008).
Experiments Experimental methods used to validate the miRNA-target interaction, as reported in miRTarBase v10.0. e.g., Luciferase reporter assay, Western blot, RT-qPCR, Microarray, HITS-CLIP, PAR-CLIP, ChIP-seq, pSILAC, Immunohistochemistry, Flow cytometry).

This section allows users to perform functional enrichment analyses by selecting ASD-associated miRNAs and/or their target genes. Gene Ontology (GO) and pathway enrichment analyses are executed through the g:Profiler REST API, and the results are displayed on the miR4ASD website, highlighting enriched biological processes and pathways associated with the selected target genes.

Column name Definition & Purpose Allowed Values & Formats
Source Curated biological pathway or gene ontology database queried. GO:BP Biological Process
GO:MF Molecular Function
GO:CC Cellular Component
KEGG Biological Pathways
REAC Reactome Pathways
HP Human Phenotype Ontology
WP WikiPathways
Term ID Official ontology or pathway database identifier hyperlinking to the external source repository. e.g. GO:0007268, KEGG:04724, REAC:R-HSA-112316, HP:0000729
Term Name Human-readable biological process, functional cascade, or clinical phenotype description. e.g. chemical synaptic transmission, Glutamatergic synapse, Autistic behavior
Adjusted P-Value Corrected statistical significance value for hypergeometric overrepresentation. Corrected via g:SCS (default), Benjamini-Hochberg FDR, or Bonferroni ($p_{\text{adj}} < 0.05$).
Overlap (k/N) Ratio of user submitted target genes in term ($k$) relative to total submitted query size ($N$). e.g. 25 / 120 target genes intersecting the enriched term.
Term Size Total number of annotated human protein-coding genes belonging to this functional term. Positive integer (e.g. 210, 450, 1,280).
Intersecting Target Genes List of user query target genes found in the term with clickable GeneCards links and SFARI autism risk confidence tiers. Clickable GeneCards links with symbol tokens (1 Cat 1, 2 Cat 2, 3 Cat 3, S Syndromic, 2S Dual Status).
Significance Score Bar Chart Metric Ranking metric used in Top 15 enrichment visualization charts: $-\log_{10}(p_{\text{adj}})$. Higher values denote stronger statistical enrichment and lower false discovery rates.

Experimental Methodologies

10 Profiling Technologies

Reference table explaining the laboratory platforms, high-throughput sequencing technologies, and molecular assays used for microRNA expression profiling and genetic variant detection in miR4ASD.

Method Abbreviation Method Name Study Type Description
Gene expression microarray Gene expression microarray Expression Hybridization-based technology using predefined probes to measure the relative expression levels of mRNA transcripts/genes across multiple targets simultaneously.
miRNA microarray MicroRNA expression microarray Expression Hybridization-based technology using predefined probes specifically designed to detect and measure the relative expression levels of multiple mature miRNAs.
RT-qPCR Reverse transcription-quantitative PCR Expression PCR-based method in which RNA is reverse-transcribed into cDNA and specific miRNAs or transcripts are quantified through real-time amplification. Includes individual, multiplex, and array-based RT-qPCR assays such as TLDA/TaqMan miRNA arrays.
RNA-seq RNA sequencing Expression High-throughput sequencing of RNA-derived libraries used for transcriptome-wide characterization and quantification of RNA expression, particularly mRNA and other longer RNA transcripts.
Small RNA-seq Small RNA sequencing Expression High-throughput sequencing using libraries enriched for small RNA molecules, enabling detection and quantification of miRNAs and other small non-coding RNAs.
NanoString NanoString nCounter Expression Direct digital RNA detection and counting using sequence-specific barcoded probes, without enzymatic amplification.
SNP array Single nucleotide polymorphism array Genetics DNA hybridization-based technology using predefined probes to genotype large numbers of SNPs across the genome. Probe intensity and allelic signals can also be used to identify copy-number variants and regions of homozygosity.
WES Whole exome sequencing Genetics High-throughput DNA sequencing targeting primarily the protein-coding regions (exons) of the genome, enabling detection of SNVs and small insertions/deletions and, depending on the analytical pipeline, other variant types.
WGS Whole genome sequencing Genetics High-throughput sequencing of genomic DNA across coding and non-coding regions, enabling comprehensive detection of SNVs, insertions/deletions, and, depending on the analytical pipeline, structural and copy-number variants.
aCGH Array comparative genomic hybridization Genetics DNA hybridization-based technology comparing test and reference DNA across genomic probes to identify copy-number gains and losses, including genomic deletions and duplications.

Clinical Diagnostic Tools & Assessment Instruments

9 Diagnostic Instruments

Reference guide specifying the diagnostic criteria and/or standardized assessment instruments used to establish or support ASD diagnosis in study participants.

Diagnostic Tool / Abbreviation Full Name & Description
DSM-5 Diagnostic and Statistical Manual of Mental Disorders 5th Edition
DSM-IV Diagnostic and Statistical Manual of Mental Disorders 4th Edition
DSM-IV-TR Diagnostic and Statistical Manual of Mental Disorders 4th Edition Text Revision
ADI-R Autism Diagnostic Interview-Revised
ADOS Autism Diagnostic Observation Schedule
CARS Childhood Autism Rating Scale
ABC Autism Behavior Scale
GARS Gilliam Autism Rating Scale
SRS Social Responsiveness Scale

How to cite miR4ASD

If you use miR4ASD in your research, please cite the following publication:

Marques AR, Martiniano H, Vilela J, Vicente AM. miR4ASD: A Database of Human microRNAs Associated with Autism Spectrum Disorder. Current Issues in Molecular Biology. 2026; 48(10):1044.

View publication (DOI)

If your work uses information or analyses obtained from external resources integrated into miR4ASD, please also cite the corresponding original resources:

miRBase miRTarBase g:Profiler
Select candidate miRNAs using the checkboxes below to analyze their target genes and perform functional enrichment analysis.
Selections sync globally across all tabs
Expression Studies Filters
No Filters Active
Precursor miRNA
(hairpin)		 Mature
miRNA		 Expression change
(ASD vs. controls)		 Sample Type Overall evidence Evidence from
other studies		 # up # down Total
studies
Select candidate miRNAs using the checkboxes below to analyze their target genes and perform functional enrichment analysis.
Selections sync globally across all tabs
Genetic & Other Studies Filters
No Filters Active
Precursor miRNA
(hairpin)		 Mature
miRNA		 Study Type Variant Type Evidence from
expression studies		 Total expression
studies		 Description of
expression evidence
Explore experimentally validated miRNA-target interactions, the experimental methods supporting these interactions, and SFARI Gene evidence for target gene involvement in ASD.
miRTarBase 10.0
17,150 Target Interactions (2,995 Target Genes)
Select miRNA-target interactions using the checkboxes below to perform functional enrichment analysis on the corresponding target genes.
SFARI Tiers: 1Cat 1 2Cat 2 3Cat 3 SSyndromic 2SDual Status
Selected miRNAs: 0
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No miRNAs selected yet. Use the checkboxes in the Expression or Genetic Studies tables, or paste miRNA IDs above.
Target Genes Filters
No Filters Active Gene search & annotation filters
Precursor miRNA Mature
miRNA		 Target Gene Gene Description ASD Susceptibility (SFARI) Support Type PubMed Reference Experiments
Discover enriched biological pathways, Gene Ontology terms (GO:BP, GO:MF, GO:CC), and disease phenotypes (KEGG, Reactome, HP) for your selected miRNA targets, powered by the g:Profiler REST API.
Selected miRNAs: 0
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No miRNAs selected yet. Use the checkboxes in the Expression or Genetic Studies tables, or paste miRNA IDs above.

Functional Enrichment Analysis

Target Genes of Analyzed miRNAs: Awaiting miRNA selection from tables
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miRTarBase 10.0
Resolved Target Genes:
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No target genes selected. Select microRNAs from the Expression or Genetic Studies tables to populate their validated target genes, or enter custom gene symbols above.
Run Overrepresentation Analysis:
Querying g:Profiler REST API...

Computing overrepresentation statistics across biological pathways and ontologies.

Enrichment Analysis Notice
An error occurred while querying g:Profiler.
Enriched Terms

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p_adj < 0.05
Top Pathway Source

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Most Significant Term
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SFARI Genes Covered

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In Enriched Terms
Top 15 Enriched Biological Pathways & Ontologies
Ranked by Significance (−log₁₀ p-adj)
Enriched Terms & Intersecting Target Genes
Open in g:Profiler Web Portal
Source Term ID Term Name Adjusted P-Value Overlap (k/N) Term Size Intersecting Target Genes