Table 1.

Overview of described tools available for miRNA analysis.

Category	Tool Name	Organism	Last Update	Summary Features	URL	References
miRNA sequences and annotation	miRBase	271 species, including humans	2019	Central primary repository for the storage of miRNA annotation and sequence data Nomenclature may differ according to the version of miRBase utilized, especially in the case of tools incorporating data from miRBase	https://www.mirbase.org/	[32,33,34,35]
	Rfam	9 species, including humans	2022	Allows users to submit a novel RNA family to ensure up-to-date annotations Synchronization of the majority of miRNA families across miRBase, Rfam and RNAcentral is currently in progress.	https://rfam.xfam.org/	[36,37]
	RNAcentral	>800,00 species, including humans	2022	A public resource capturing information on all non-coding RNAs, including miRNAs Comprehensive and actively updated	https://rnacentral.org/	[38,39]
Target Discovery	miRTarBase	37 species, including humans	2021	One of the largest databases of experimentally validated MTIs Regulators of miRNAs are included in the database	https://mirtarbase.cuhk.edu.cn/	[40,41,42,43,44,45]
	TargetScan	13 species, including humans	2018	Can distinguish between different isoforms of a particular gene target during scoring TargetScan conducts its own classification of miRNA families, based on the identical seed region, so the nomenclature can differ between databases such as miRBase	https://www.targetscan.org/vert_72/	[46,47,48,49]
	DIANA-TarBase	18 species, including humans	2017	Places focus on experimentally validated MTIs across 18 species Over 1 million entries, consisting of 670,000 unique, experimentally supported MTIs Tedious interface layout when investigating reference links and MTIs	https://dianalab.e-ce.uth.gr/html/diana/web/index.php?r=tarbasev8	[50,51]
	miRDB	5 species, including humans	2019	Allows for custom prediction through the submission of user-provided miRNA or gene target sequences	http://mirdb.org/	[52,53]
Human disease-related	HMDD	Humans	2019	User-friendly interface offering clear explanatory notes and references for users HMDD is only limited to collating data surrounding humans only and ignores model organisms such mice and rats	http://www.cuilab.cn/hmdd	[54,55,56,57]
	OncomiR	Humans	2017	Clear walkthrough page with guidance for users, with all features clearly defined Users are able to explore for data capturing almost 10,000 patients across 30 cancer types	http://www.oncomir.org/	[58]
	dbDEMC	3 species, including humans	2021	Offers analysis on additional species other than humans (mice and rats) Currently, 40 cancer types and 149 cancer subtypes are captured	https://www.biosino.org/dbDEMC/index	[59,60]
Pathway-related	DIANA-miRPath	7 species, including humans	2015	Unique reverse search module allowing for the identification of miRNAs enriched within a particular pathway Offers analysis extended to a further list of species (humans, mice, rats, dogs, flies, worms and chickens) Of the remaining tools described under this category, DIANA-miRPath represents the oldest updated tool	https://dianalab.e-ce.uth.gr/html/mirpathv3/index.php?r=mirpath	[61]
	miRPathDB	2 species, including humans	2018	Clear user-friendly layout, with clear explanatory notes and an available guide Places focus on two species: humans and mice	https://mpd.bioinf.uni-sb.de/	[62,63]
	miTALOS	2 species, including humans	2016	First resource to offer a tissue-specific filter Three major pathways are integrated: KEGG, Wiki Pathways and Reactome	http://mips.helmholtz-muenchen.de/mitalos/#/search	[64,65]
SNP effect prediction	PolymiRTS	2 species, including humans	2014	Provides an advantage through the analysis of mouse data Last known update of PolymiRTS was in 2014.	https://compbio.uthsc.edu/miRSNP//	[66,67,68]
	miRNASNP	Humans	2020	Compared to PolymiRTS, it contains fewer available features on the web interface for users MiRNASNP is kept continuously up to date	http://bioinfo.life.hust.edu.cn/miRNASNP/#!/	[69,70,71]