mirDBA: microRNA discovery by similarity search to a database of RNA-seq profiles
miRRPdb v1.0: database of miRNA read profiles (release date: June 21, 2013) - download
The current version of the database has been prepared using short-reads mapped to 4,862 distinct microRNAs from 20 organisms. The short reads were downloaded from miRBase (ftp://mirbase.org/pub/mirbase/CURRENT/database_files/, dated: Jan 2, 2013 - RELEASE 19). All the mapped reads from each of the 20 organisms were preprocessed individually to obtain read profiles corresponding to distinct miRNAs (original article).
In total the database is comprised of 2,540 miRNA read profiles from 20 organisms
Organisma | # readsb | # miRNAc | # read profiles | |
alld | filterede | |||
Ame | 475,288 (1) | 159 | 109 | 96 |
Ath | 472,5021(8) | 275 | 303 | 173 |
Bfl | 37,217(1) | 113 | 71 | 34 |
Bmo | 2,021,309(3) | 384 | 264 | 194 |
Cbr | 17,442(1) | 115 | 81 | 25 |
Cel | 1,048,509(6) | 184 | 130 | 93 |
Cqu | 379,978(1) | 68 | 61 | 29 |
Cre | 1,082(1) | 28 | 19 | 11 |
Crm | 9,988(1) | 95 | 63 | 19 |
Cte | 50,659(1) | 118 | 72 | 8 |
Dme | 35,664,132(50) | 237 | 48 | 45 |
Hsa | 81,138,802(79) | 1,279 | 801 | 550 |
Mmu | 913,716,590(82) | 749 | 688 | 624 |
Nve | 2,711(1) | 34 | 17 | 2 |
Osa | 1,506,288(4) | 440 | 540 | 288 |
Ppc | 11,176(1) | 113 | 66 | 5 |
Ppt | 503,573(3) | 4224 | 285 | 148 |
Rco | 147(25) | 13 | 2 | 0 |
Spu | 6,458(1) | 38 | 25 | 7 |
Tca | 4,861,929(2) | 196 | 193 | 189 |
Total | 1,046,178,299 | 4,862 | 3,838 | 2,540 |
bnumber of mapped reads. Total number of GEO experiments are given in brackets. Some experiments are comprised of reads from multiple organisms,
ctotal number of distinct miRNAs with mapped reads.,
dtotal number of block groups or miRNAs retrieved after preprocessing,
eblock groups with >1 block and ≤200 nt in length.