Table 1.
The ALS genes predicted by DIANA-microT-CDS v5.0 to be targets of (A) the nine most frequently reported miRNAs from the studies, (B) nine deregulated miRNAs randomly selected from all ALS studies, and (C) nine randomly selected miRNAs not reported to be deregulated in the ALS studies.
| miRNAs | Number of Studies deregulated (out of 27) | Direction of deregulation (up, down or both) | ALS genes predicted by DIANA-T-CDS | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| (A) Most Frequently Reported miRNAs | hsa-miR-133a-3p | 9 | Both | TUBA4A | VAPB | MiRNA hits (8/9) Genes (15/37) Total (18) | ||||
| hsa-let-7a-5p | 7 | Both | ARHGEF28 | |||||||
| hsa-miR-127-3p | 6 | Both | ||||||||
| hsa-miR-155-5p | 6 | Both | TBK1 | UBQLN2 | ||||||
| hsa-miR-206-3p | 6 | Both | ATXN2 | MATR3 | ||||||
| hsa-miR-26a-5p | 6 | Both | ARHGEF28 | ERBB4 | MATR3 | |||||
| hsa-miR-455-3p | 6 | Both | TARDBP | |||||||
| hsa-miR-9-5p | 6 | Both | CHMP2B | CRYM | NEFH | TRPM7 | ||||
| hsa-miR-124-3p | 6 | Both | CHMP2B | SIGMAR1 | SQSTM1 | |||||
| (B) Random miRNAs from ALS studies | hsa-let-7b-5p | 5 | Down | ARHGEF28 | MiRNA hits (7/9) Genes (10/37) Total (16) | |||||
| hsa-let-7c-5p | 4 | Down | ARHGEF28 | |||||||
| hsa-miR-204-3p | 1 | Down | ERBB4 | VAPB | ||||||
| hsa-miR-766-3p | 2 | Both | DAO | DCTN1 | SIGMAR1 | VAPB | ||||
| hsa-miR-212-3p | 2 | Down | C9orf72 | ERBB4 | FIG4 | |||||
| hsa-miR-329-3p | 2 | Down | ||||||||
| hsa-miR-876-3p | 1 | Down | ERBB4 | MATR3 | TUBA4A | |||||
| hsa-miR-302a-5p | 1 | Down | ARHGEF28 | ERBB4 | ||||||
| hsa-miR-154-5p | 3 | Down | ||||||||
| (C) Random miRNAs absent from ALS studies | hsa-miR-3168-5p | TARDPB | MiRNA hits (5/9) Genes (8/37) Total (13) | |||||||
| hsa-miR-875-5p | ||||||||||
| hsa-miR-611-5p | ||||||||||
| hsa-miR-603-3p | ATXN2 | ERBB4 | MATR3 | OPTN | TARDBP | VAPB | ||||
| hsa-miR-500b-5p | DCTN1 | ERBB4 | ||||||||
| hsa-miR-325-5p | ||||||||||
| hsa-miR-764-5p | ||||||||||
| hsa-miR-665-3p | DCTN1 | |||||||||
| hsa-miR-4277-5p | DAO | TARDPB | VAPB | |||||||
Note that we report mature miRNAs; where specific miRNAs were not reported we considered dominant strands as reported on miRBase release 22.1: October 2018. For (A), all miRNAs deregulated in at least six studies were considered. For (B) nine miRNAs were randomly selected from those reported by <6 of the 27 studies. Further analysis regarding strand specificity was also performed on this group and on the nine miRNAs not found deregulated in the studies (C). MiRNAs in bold have confirmed interactions with the target experimentally, using miRTarBase v7.0 (23).