The package depends on a remote database connection that may have been down. It's working as of 2023-10-26 15:09 PDT.
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
#> Bioconductor version '3.17' is out-of-date; the current release version '3.18'
#> is available with R version '4.3'; see https://bioconductor.org/install
BiocManager::install("multiMiR")
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#> CRAN: https://cran.rstudio.com/
#> Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.0 (2023-04-21)
#> Warning: package(s) not installed when version(s) same as or greater than current; use
#> `force = TRUE` to re-install: 'multiMiR'
#> Old packages: 'polspline', 'RMariaDB'
library(multiMiR)
#> Welcome to multiMiR.
#>
#> multiMiR database URL has been set to the
#> default value: http://multimir.org/
#>
#> Database Version: 2.3.0 Updated: 2020-04-15
db.ver <- multimir_dbInfoVersions()
db.ver
#> VERSION UPDATED RDA DBNAME
#> 1 2.3.0 2020-04-15 multimir_cutoffs_2.3.rda multimir2_3
#> 2 2.2.0 2017-08-08 multimir_cutoffs_2.2.rda multimir2_2
#> 3 2.1.0 2016-12-22 multimir_cutoffs_2.1.rda multimir2_1
#> 4 2.0.0 2015-05-01 multimir_cutoffs.rda multimir
#> SCHEMA PUBLIC TABLES
#> 1 multiMiR_DB_schema.sql 1 multiMiR_dbTables.txt
#> 2 multiMiR_DB_schema.sql 1 multiMiR_dbTables.txt
#> 3 multiMiR_DB_schema.sql 1 multiMiR_dbTables.txt
#> 4 multiMiR_DB_schema.sql 1 multiMiR_dbTables.txt
vers_table <- multimir_dbInfoVersions()
vers_table
#> VERSION UPDATED RDA DBNAME
#> 1 2.3.0 2020-04-15 multimir_cutoffs_2.3.rda multimir2_3
#> 2 2.2.0 2017-08-08 multimir_cutoffs_2.2.rda multimir2_2
#> 3 2.1.0 2016-12-22 multimir_cutoffs_2.1.rda multimir2_1
#> 4 2.0.0 2015-05-01 multimir_cutoffs.rda multimir
#> SCHEMA PUBLIC TABLES
#> 1 multiMiR_DB_schema.sql 1 multiMiR_dbTables.txt
#> 2 multiMiR_DB_schema.sql 1 multiMiR_dbTables.txt
#> 3 multiMiR_DB_schema.sql 1 multiMiR_dbTables.txt
#> 4 multiMiR_DB_schema.sql 1 multiMiR_dbTables.txt
multimir_dbSchema()
#>
#> --
#> -- Table structure for table `mirna`
#> --
#>
#> DROP TABLE IF EXISTS `mirna`;
#> CREATE TABLE `mirna` (
#> mature_mirna_uid INTEGER UNSIGNED AUTO_INCREMENT, -- mature miRNA unique ID
#> org VARCHAR(4) NOT NULL, -- organism abbreviation
#> mature_mirna_acc VARCHAR(20) default NULL, -- mature miRNA accession
#> mature_mirna_id VARCHAR(20) default NULL, -- mature miRNA ID/name
#> PRIMARY KEY (mature_mirna_uid),
#> KEY org (org),
#> KEY mature_mirna_acc (mature_mirna_acc),
#> KEY mature_mirna_id (mature_mirna_id)
#> );
#>
#> --
#> -- Table structure for table `target`
#> --
#>
#> DROP TABLE IF EXISTS `target`;
#> CREATE TABLE `target` (
#> target_uid INTEGER UNSIGNED AUTO_INCREMENT, -- target gene unique ID
#> org VARCHAR(4) NOT NULL, -- organism abbreviation
#> target_symbol VARCHAR(80) default NULL, -- target gene symbol
#> target_entrez VARCHAR(10) default NULL, -- target gene Entrez gene ID
#> target_ensembl VARCHAR(20) default NULL, -- target gene Ensembl gene ID
#> PRIMARY KEY (target_uid),
#> KEY org (org),
#> KEY target_symbol (target_symbol),
#> KEY target_entrez (target_entrez),
#> KEY target_ensembl (target_ensembl)
#> );
#>
#> --
#> -- Table structure for table `mirecords`
#> --
#>
#> DROP TABLE IF EXISTS `mirecords`;
#> CREATE TABLE `mirecords` (
#> mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
#> target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
#> target_site_number INT(10) default NULL, -- target site number
#> target_site_position INT(10) default NULL, -- target site position
#> experiment VARCHAR(160) default NULL, -- supporting experiment
#> support_type VARCHAR(40) default NULL, -- type of supporting experiment
#> pubmed_id VARCHAR(10) default NULL, -- PubMed ID
#> FOREIGN KEY (mature_mirna_uid)
#> REFERENCES mirna(mature_mirna_uid)
#> ON UPDATE CASCADE ON DELETE RESTRICT,
#> FOREIGN KEY (target_uid)
#> REFERENCES target(target_uid)
#> ON UPDATE CASCADE ON DELETE RESTRICT
#> );
#>
#> --
#> -- Table structure for table `mirtarbase`
#> --
#>
#> DROP TABLE IF EXISTS `mirtarbase`;
#> CREATE TABLE `mirtarbase` (
#> mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
#> target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
#> experiment VARCHAR(160) NOT NULL, -- supporting experiment
#> support_type VARCHAR(40) NOT NULL, -- type of supporting experiment
#> pubmed_id VARCHAR(10) default NULL, -- PubMed ID
#> FOREIGN KEY (mature_mirna_uid)
#> REFERENCES mirna(mature_mirna_uid)
#> ON UPDATE CASCADE ON DELETE RESTRICT,
#> FOREIGN KEY (target_uid)
#> REFERENCES target(target_uid)
#> ON UPDATE CASCADE ON DELETE RESTRICT
#> );
#>
#> --
#> -- Table structure for table `tarbase`
#> --
#>
#> DROP TABLE IF EXISTS `tarbase`;
#> CREATE TABLE `tarbase` (
#> mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
#> target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
#> experiment VARCHAR(160) NOT NULL, -- supporting experiment
#> support_type VARCHAR(40) NOT NULL, -- type of supporting experiment
#> pubmed_id VARCHAR(10) default NULL, -- PubMed ID
#> FOREIGN KEY (mature_mirna_uid)
#> REFERENCES mirna(mature_mirna_uid)
#> ON UPDATE CASCADE ON DELETE RESTRICT,
#> FOREIGN KEY (target_uid)
#> REFERENCES target(target_uid)
#> ON UPDATE CASCADE ON DELETE RESTRICT
#> );
#>
#> --
#> -- Table structure for table `miranda`
#> --
#>
#> DROP TABLE IF EXISTS `miranda`;
#> CREATE TABLE `miranda` (
#> mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
#> target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
#> conservation REAL NOT NULL, -- conservation score
#> mirsvr_score REAL NOT NULL, -- mirSVR downregulation score
#> FOREIGN KEY (mature_mirna_uid)
#> REFERENCES mirna(mature_mirna_uid)
#> ON UPDATE CASCADE ON DELETE RESTRICT,
#> FOREIGN KEY (target_uid)
#> REFERENCES target(target_uid)
#> ON UPDATE CASCADE ON DELETE RESTRICT,
#> KEY conservation (conservation),
#> KEY mirsvr_score (mirsvr_score)
#> );
#>
#> --
#> -- Table structure for table `targetscan`
#> --
#>
#> DROP TABLE IF EXISTS `targetscan`;
#> CREATE TABLE `targetscan` (
#> mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
#> target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
#> site_type INTEGER UNSIGNED NOT NULL, -- site type (see http://www.targetscan.org/faqs.html)
#> context_plus_score REAL NOT NULL, -- context+ score
#> conserved_site ENUM('N','Y'), -- whether the target site is conserved
#> FOREIGN KEY (mature_mirna_uid)
#> REFERENCES mirna(mature_mirna_uid)
#> ON UPDATE CASCADE ON DELETE RESTRICT,
#> FOREIGN KEY (target_uid)
#> REFERENCES target(target_uid)
#> ON UPDATE CASCADE ON DELETE RESTRICT,
#> KEY context_plus_score (context_plus_score),
#> KEY conserved_site (conserved_site)
#> );
#>
#> --
#> -- Table structure for table `diana_microt`
#> --
#>
#> DROP TABLE IF EXISTS `diana_microt`;
#> CREATE TABLE `diana_microt` (
#> mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
#> target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
#> miTG_score REAL NOT NULL, -- miRNA target gene score
#> UTR3_hit INTEGER UNSIGNED NOT NULL, -- number of 3'-UTR binding sites
#> CDS_hit INTEGER UNSIGNED NOT NULL, -- number of CDS binding sites
#> FOREIGN KEY (mature_mirna_uid)
#> REFERENCES mirna(mature_mirna_uid)
#> ON UPDATE CASCADE ON DELETE RESTRICT,
#> FOREIGN KEY (target_uid)
#> REFERENCES target(target_uid)
#> ON UPDATE CASCADE ON DELETE RESTRICT,
#> KEY miTG_score (miTG_score)
#> );
#>
#> --
#> -- Table structure for table `elmmo`
#> --
#>
#> DROP TABLE IF EXISTS `elmmo`;
#> CREATE TABLE `elmmo` (
#> mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
#> target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
#> p REAL NOT NULL, -- "the posterior probability that the site is under evolutionnary selective pressure"
#> FOREIGN KEY (mature_mirna_uid)
#> REFERENCES mirna(mature_mirna_uid)
#> ON UPDATE CASCADE ON DELETE RESTRICT,
#> FOREIGN KEY (target_uid)
#> REFERENCES target(target_uid)
#> ON UPDATE CASCADE ON DELETE RESTRICT,
#> KEY p (p)
#> );
#>
#> --
#> -- Table structure for table `pita`
#> --
#>
#> DROP TABLE IF EXISTS `pita`;
#> CREATE TABLE `pita` (
#> mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
#> target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
#> ddG REAL NOT NULL, -- ddG = dGduplex (microRNA-target hybridization energy) - dGopen (energy required to make the target site accessible)
#> conservation REAL NOT NULL, -- site conservation (range 0~1)
#> FOREIGN KEY (mature_mirna_uid)
#> REFERENCES mirna(mature_mirna_uid)
#> ON UPDATE CASCADE ON DELETE RESTRICT,
#> FOREIGN KEY (target_uid)
#> REFERENCES target(target_uid)
#> ON UPDATE CASCADE ON DELETE RESTRICT,
#> KEY ddG (ddG),
#> KEY conservation (conservation)
#> );
#>
#> --
#> -- Table structure for table `microcosm`
#> --
#>
#> DROP TABLE IF EXISTS `microcosm`;
#> CREATE TABLE `microcosm` (
#> mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
#> target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
#> score REAL NOT NULL, -- miRanda score
#> FOREIGN KEY (mature_mirna_uid)
#> REFERENCES mirna(mature_mirna_uid)
#> ON UPDATE CASCADE ON DELETE RESTRICT,
#> FOREIGN KEY (target_uid)
#> REFERENCES target(target_uid)
#> ON UPDATE CASCADE ON DELETE RESTRICT,
#> KEY score (score)
#> );
#>
#> --
#> -- Table structure for table `pictar`
#> --
#>
#> DROP TABLE IF EXISTS `pictar`;
#> CREATE TABLE `pictar` (
#> mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
#> target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
#> score REAL NOT NULL, -- score
#> FOREIGN KEY (mature_mirna_uid)
#> REFERENCES mirna(mature_mirna_uid)
#> ON UPDATE CASCADE ON DELETE RESTRICT,
#> FOREIGN KEY (target_uid)
#> REFERENCES target(target_uid)
#> ON UPDATE CASCADE ON DELETE RESTRICT,
#> KEY score (score)
#> );
#>
#> --
#> -- Table structure for table `mirdb`
#> --
#>
#> DROP TABLE IF EXISTS `mirdb`;
#> CREATE TABLE `mirdb` (
#> mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
#> target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
#> score REAL NOT NULL, -- score
#> FOREIGN KEY (mature_mirna_uid)
#> REFERENCES mirna(mature_mirna_uid)
#> ON UPDATE CASCADE ON DELETE RESTRICT,
#> FOREIGN KEY (target_uid)
#> REFERENCES target(target_uid)
#> ON UPDATE CASCADE ON DELETE RESTRICT,
#> KEY score (score)
#> );
#>
#> --
#> -- Table structure for table `mir2disease`
#> --
#>
#> DROP TABLE IF EXISTS `mir2disease`;
#> CREATE TABLE `mir2disease` (
#> mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
#> disease VARCHAR(100) NOT NULL, -- disease
#> mirna_regulation VARCHAR(20) NOT NULL, -- how miRNA is regulated in the disease (up-regulated, down-regulated or normal)
#> experiment VARCHAR(40) NOT NULL, -- supporting experiment
#> year INTEGER UNSIGNED NOT NULL, -- year of the paper
#> title TEXT NOT NULL, -- title of the paper
#> FOREIGN KEY (mature_mirna_uid)
#> REFERENCES mirna(mature_mirna_uid)
#> ON UPDATE CASCADE ON DELETE RESTRICT,
#> KEY disease (disease)
#> );
#>
#> --
#> -- Table structure for table `pharmaco_mir`
#> --
#>
#> DROP TABLE IF EXISTS `pharmaco_mir`;
#> CREATE TABLE `pharmaco_mir` (
#> mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
#> target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
#> drug VARCHAR(40) NOT NULL, -- disease
#> pubmed_id VARCHAR(10) NOT NULL, -- PubMed ID
#> FOREIGN KEY (mature_mirna_uid)
#> REFERENCES mirna(mature_mirna_uid)
#> ON UPDATE CASCADE ON DELETE RESTRICT,
#> FOREIGN KEY (target_uid)
#> REFERENCES target(target_uid)
#> ON UPDATE CASCADE ON DELETE RESTRICT,
#> KEY drug (drug)
#> );
#>
#> --
#> -- Table structure for table `phenomir`
#> --
#>
#> DROP TABLE IF EXISTS `phenomir`;
#> CREATE TABLE `phenomir` (
#> mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
#> pre_mirna_acc VARCHAR(20) default NULL, -- precursor miRNA accession
#> pre_mirna_id VARCHAR(20) default NULL, -- precursor miRNA ID
#> disease VARCHAR(60) NOT NULL, -- disease
#> disease_class VARCHAR(20) NOT NULL, -- disease class
#> mirna_expression VARCHAR(30) NOT NULL, -- how miRNA is expressed in the disease
#> study VARCHAR(40) NOT NULL, -- type of study (in cells, patients, etc)
#> experiment VARCHAR(40) NOT NULL, -- supporting experiment
#> pubmed_id VARCHAR(10) NOT NULL, -- PubMed ID
#> FOREIGN KEY (mature_mirna_uid)
#> REFERENCES mirna(mature_mirna_uid)
#> ON UPDATE CASCADE ON DELETE RESTRICT,
#> KEY disease (disease),
#> KEY disease_class (disease_class)
#> );
#>
#> --
#> -- Table structure for table `metadata`
#> --
#>
#> DROP TABLE IF EXISTS `metadata`;
#> CREATE TABLE metadata (
#> name VARCHAR(80) PRIMARY KEY,
#> value VARCHAR(255)
#> );
#>
#> --
#> -- Table structure for table `map_metadata`
#> --
#>
#> DROP TABLE IF EXISTS `map_metadata`;
#> CREATE TABLE map_metadata (
#> map_name VARCHAR(80) PRIMARY KEY,
#> source_name VARCHAR(80) NOT NULL,
#> source_version VARCHAR(20),
#> source_date VARCHAR(20),
#> source_url VARCHAR(255) NOT NULL
#> );
#>
#> --
#> -- Table structure for table `map_counts`
#> --
#>
#> DROP TABLE IF EXISTS `map_counts`;
#> CREATE TABLE map_counts (
#> map_name VARCHAR(80) PRIMARY KEY,
#> human_count INTEGER UNSIGNED NOT NULL,
#> mouse_count INTEGER UNSIGNED NOT NULL,
#> total_count INTEGER UNSIGNED NOT NULL
#> );
db.info <- multimir_dbInfo()
db.info
#> map_name source_name source_version source_date
#> 1 diana_microt DIANA-microT 5 Sept, 2013
#> 2 elmmo EIMMo 5 Jan, 2011
#> 3 microcosm MicroCosm 5 Sept, 2009
#> 4 mir2disease miR2Disease Mar 14, 2011
#> 5 miranda miRanda Aug, 2010
#> 6 mirdb miRDB 6 June, 2019
#> 7 mirecords miRecords 4 Apr 27, 2013
#> 8 mirtarbase miRTarBase 7.0 Sept, 2017
#> 9 pharmaco_mir Pharmaco-miR (Verified Sets)
#> 10 phenomir PhenomiR 2 Feb 15, 2011
#> 11 pictar PicTar 2 Dec 21, 2012
#> 12 pita PITA 6 Aug 31, 2008
#> 13 tarbase TarBase 8 2018
#> 14 targetscan TargetScan 7.2 March, 2018
#> source_url
#> 1 http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=microT_CDS/index
#> 2 http://www.mirz.unibas.ch/miRNAtargetPredictionBulk.php
#> 3 http://www.ebi.ac.uk/enright-srv/microcosm/cgi-bin/targets/v5/download.pl
#> 4 http://www.mir2disease.org
#> 5 http://www.microrna.org/microrna/getDownloads.do
#> 6 http://mirdb.org
#> 7 http://mirecords.biolead.org/download.php
#> 8 http://mirtarbase.mbc.nctu.edu.tw/php/download.php
#> 9 http://www.pharmaco-mir.org/home/download_VERSE_db
#> 10 http://mips.helmholtz-muenchen.de/phenomir/
#> 11 http://dorina.mdc-berlin.de
#> 12 http://genie.weizmann.ac.il/pubs/mir07/mir07_data.html
#> 13 http://carolina.imis.athena-innovation.gr/diana_tools/web/index.php?r=tarbasev8%2Findex
#> 14 http://www.targetscan.org/cgi-bin/targetscan/data_download.cgi?db=vert_61
predicted_tables()
#> [1] "diana_microt" "elmmo" "microcosm" "miranda" "mirdb"
#> [6] "pictar" "pita" "targetscan"
validated_tables()
#> [1] "mirecords" "mirtarbase" "tarbase"
diseasedrug_tables()
#> [1] "mir2disease" "pharmaco_mir" "phenomir"
reverse_table_lookup("targetscan")
#> [1] "predicted"
db.count <- multimir_dbCount()
db.count
#> map_name human_count mouse_count rat_count total_count
#> 1 diana_microt 7664602 3747171 0 11411773
#> 2 elmmo 3959112 1449133 547191 5955436
#> 3 microcosm 762987 534735 353378 1651100
#> 4 mir2disease 2875 0 0 2875
#> 5 miranda 5429955 2379881 247368 8057204
#> 6 mirdb 1990425 1091263 199250 3280938
#> 7 mirecords 2425 449 171 3045
#> 8 mirtarbase 544588 50673 652 595913
#> 9 pharmaco_mir 308 5 0 313
#> 10 phenomir 15138 491 0 15629
#> 11 pictar 404066 302236 0 706302
#> 12 pita 7710936 5163153 0 12874089
#> 13 tarbase 433048 209831 1307 644186
#> 14 targetscan 13906497 10442093 0 24348590
apply(db.count[,-1], 2, sum)
#> human_count mouse_count rat_count total_count
#> 42826962 25371114 1349317 69547393
Created on 2023-10-26 with reprex v2.0.2