Table 1 Feature comparisons of five miRNA predicting tools
From: miREM: an expectation-maximization approach for prioritizing miRNAs associated with gene-set
miREM | CORNA | Geneset2miRNA | ChemiRs | Sylamer | |
|---|---|---|---|---|---|
Platform | Web-based | R package | Web-based | Web-based | Web-based |
standalone | |||||
Installation required | No | Yes | No | No | Optional |
GUI | Yes | No | Yes | Yes | Yes |
Software last update | 2017 | 2013 | 2009 | 2015 | Unspecified |
Organisms supported | Human, mouse | 22 species including | 6 species including | Human | 7 species including |
human and mouse | human and mouse | human and mouse | |||
Reference databases | Diana, | Miranda | mirDB, | Diana, | Unspecified |
Miranda, | Pictar, | Miranda, | |||
mirDB, | PITA, | mirDB, | |||
Pictar, | TargetScan | miRWalk, | |||
PITA, | RNA22, | ||||
RNA22, | RNAhybrid, | ||||
TargetScan | Pictar(4way), | ||||
Pictar(5way), | |||||
PITA, | |||||
TargetScan | |||||
Mirbase version | 21 (June 2014) | 10.0 (August 2007) | 11 (April 2008) | 21 (June 2014) | Unspecified |
Ability to specify | Yes | No | No | Yes | No |
database(s) | |||||
Database last updated | 2017 | 2007 | 2008 | 2015 | Unspecified |
Cross-database query | Yes | No | No | Yes | No |
Conserved/ nonconserved | Yes | No | No | No | No |
miRNA | |||||
distinction | |||||
Input format | List of DEG: | List of DEG: | List of DEG: | List of DEG: | Full gene list |
text file, | Ensembl | text file, | text file, | ranked by fold | |
Gene Symbol, | Gene Symbol, | Gene Symbol, | change | ||
RefSeq, | RefSeq Protein ID, | Ensembl | |||
Ensembl, | RefSeq Transcript ID, | ||||
UCSC | Ensembl, | ||||
UniGene, | |||||
Entrez Gene ID, | |||||
UniProt/Swiss-Prot, | |||||
Output formats | Tab-delimited file | R list | CSV | CSV | jnlp |
Scatterplot | |||||
Heatmap | |||||
Phylogenetic miRNA | |||||
classification | |||||
Show target gene list | Yes | No | Yes | No | No |
Algorithm | Hypergeometric | Hypergeometric | Hypergeometirc | Hypergeometirc | Hypergeometirc |
Expectation | Fisher’s exact test | ||||
Maximization | |||||
Chi-square | |||||
Detection of | Yes | No | No | No | No |
duplicated predictions |