Table 3.
Wrongly identified nucleotide sequences summarized according to experimental technique and identity error type.
| Corpus | Technique | “Non-targeting” yet targeting proportion (%) | “Targeting” yet non-targeting proportion (%) | Targeting wrong gene/sequence proportion (%) | Total per corpus proportion (%) |
|---|---|---|---|---|---|
| SGK (n = 115 reagents in n = 75 articles) | PCRa | 0/45 (0) | 7/14 (50) | 45/57 (79) | 52/115 (45) |
| Gene knockdownb | 44/44 (100) | 7/14 (50) | 12/57 (21) | 63/115 (55) | |
| Otherc | 0/45 (0) | 0/14 (0) | 0/57 (0) | 0/115 (0) | |
| Total (Error type) | 44/44 (100) | 14/14 (100) | 57/57 (100) | 115/115 (100) | |
| miR-145 (n = 49 reagents in n = 31 articles) | PCR | 0/2 (0) | 8/9 (89) | 33/38 (87) | 41/49 (84) |
| Gene knockdown | 2/2 (100) | 1/9 (11) | 5/38 (13) | 8/49 (16) | |
| Other | 0/2 (0) | 0/9 (0) | 0/38 (0) | 0/49 (0) | |
| Total (Error type) | 2/2 (100) | 9/9 (100) | 38/38 (100) | 49/49 (100) | |
| C + G (n = 109 reagents in n = 51 articles) | PCR | 0/6 (0) | 23/24 (96) | 73/79 (93) | 96/109 (88) |
| Gene knockdown | 4/6 (67) | 1/24 (4) | 5/79 (6) | 10/109 (9) | |
| Other | 2/6 (33) | 0/24 (0) | 1/79 (1) | 3/109 (3) | |
| Total (Error type) | 6/6 (100) | 24/24 (100) | 79/79 (100) | 109/109 (100) | |
| Gene (n = 284 reagents in n = 128 articles) | PCR | 0/9 (0) | 35/42 (83) | 218/233 (94) | 253/284 (88) |
| Gene knockdown | 9/9 (100) | 7/42 (17) | 15/233 (6) | 31/284 (11) | |
| Other | 0/9 (0) | 0/42 (0) | 0/233 (0) | 0/284 (0) | |
| Total (Error type) | 9/9 (100) | 42/42 (100) | 233/233 (100) | 284/284 (100) | |
| Oncology Reports (n = 995 reagents in n = 436 articles) | PCR | 0/36 (0) | 296/335 (88) | 573/630 (91) | 869/995 (87) |
| Gene knockdown | 30/30 (100) | 37/335 (11) | 54/630 (8) | 121/995 (12) | |
| Other | 0/36 (0) | 2/335 (1) | 3/630 (1) | 5/995 (1) | |
| Total (Error type) | 30/30 (100) | 335/335 (100) | 630/630 (100) | 995/995 (100) | |
| Total (n = 1,535 reagents in n = 712 articles) | PCR | 0/89 (0) | 364/416 (87) | 937/1,030 (90) | 1,301/1,535 (84) |
| Gene knockdown | 87/89 (98) | 50/416 (12) | 89/1,030 (9) | 226/1,535 (15) | |
| Other | 2/89 (2) | 2/416 (1) | 4/1,030 (1) | 8/1,535 (1) | |
| Total (Error type) | 89/89 (100) | 416/416 (100) | 1,030/1,030 (100) | 1,535/1,535 (100) |
a
PCR = Human gene or genomic targeting primers for PCR, RT–PCR or methylation-specific PCR.
b
Gene knockdown = siRNA or shRNA.
c
Other = Claimed Ribozyme, TALEN, mimic sequences, and other oligonucleotide sequences.
Bold text indicates the most frequent error types per corpus.