Article Figures & Data
Figures
- Figure 1. Diagram describing the five literature corpora screened by S&B.
For each corpus (top row), the diagram shows the numbers of articles that were (i) screened by S&B (white), (ii) flagged by S&B with sequences manually verified (grey), and (iii) found to be problematic by describing at least one wrongly identified nucleotide sequence (dark grey). Total numbers of problematic articles and wrongly identified sequences are indicated below the diagram, corrected for duplicate articles between the corpora.
- Figure 2. Percentages of sequence identity error types in each corpus.
Percentages of wrongly identified nucleotide sequence reagents that correspond to the three identity error types (y-axis) in each corpus (x-axis). Percentages corresponding to each error type are indicated, rounded to the nearest single digit. The numbers of incorrect sequences in each corpus are shown below the x-axis.
- Figure 3. Percentages of wrongly identified nucleotide sequences that were either unique or repeated within each corpus.
Percentages of wrongly identified sequences that were identified at least twice in any single corpus (black) are shown above each image, rounded to the nearest single digit. All other wrongly identified sequences were unique in the indicated corpus (grey). Numbers of wrongly identified sequences identified in each corpus are shown below each image.
- Figure S1. Problematic Gene articles per year, according to country of origin and institutional affiliation type.
Total numbers of problematic articles for each country/group of countries are shown in the upper left corner of each panel. (A) Numbers of problematic Gene articles (y-axes) per publication year (x-axes) according to country of origin, shown above each graph. Countries are shown in alphabetical order, from top left. (B) Numbers of problematic Gene articles (y-axis) per publication year (x-axis) from China (right panel) or all other countries (left panel). Articles affiliated with hospitals or other institution types are shown in blue or grey, respectively. Numbers of problematic articles per year are shown below each stacked bar graph.
- Figure 4. Percentages of problematic Gene and Oncology Reports articles according to hospital affiliation status and country of origin.
Percentages of problematic Gene and Oncology Reports articles according to hospital affiliation status (y-axis) from either China or all other countries (x-axis). The journal and relevant date ranges of problematic articles are shown above each panel. Problematic articles that were (not) affiliated with hospitals are shown in blue (grey), respectively. Percentages shown have been rounded to the nearest single digit. Numbers of problematic articles from China or all other countries are indicated below the x-axis. For the comparisons shown in each panel, significantly higher proportions of problematic articles from China were affiliated with hospitals versus problematic articles from other countries (Fisher’s Exact test, P < 0.001).
- Figure S2. Problematic Oncology Reports articles per year, according to country of origin and institutional affiliation type.
Total numbers of problematic articles for each country/group of countries are shown in the upper left corner of each panel. (A) Numbers of problematic Oncology Reports articles (y-axes) per publication year (x-axes) according to country of origin, shown above each graph. Countries are shown in alphabetical order, from top left. (B) Numbers of problematic Oncology Reports articles (y-axis) per publication year (x-axis) from China (right panel) or all other countries (left panel). Articles affiliated with hospitals or other institution types are shown in blue or grey, respectively. Numbers of problematic articles per year are shown below each stacked bar graph.
- Figure 5. Percentages and numbers of problematic Gene and Oncology Reports articles per year.
Percentages of all Gene or Oncology Reports articles that were found to be problematic (y-axis) per publication year (x-axis). The journal and relevant publication year ranges are shown above each panel. Problematic articles from China or all other countries are shown in orange or grey, respectively. Percentages shown are rounded to one decimal place. Total numbers of problematic articles per year are shown below each graph.
- Figure 6. Summary of (RT-)PCR primer pairings that involved at least one wrongly identified primer.
For n = 851 primer pairs that were claimed to target particular genes/sequences (gene X) (left panel), one or both primers were predicted to be incorrect (right panel), either by targeting unrelated genes or sequences (gene Y or gene Z), or by having no predicted human target (no target). Numbers of primer pairs and affected articles are indicated below each incorrect primer pair category. Some problematic articles described more than one (category of) incorrect primer pairing. Left- or right-hand primers are not intended to indicate forward or reverse primer orientations.
- Figure 7. Numbers of past research articles that have studied human protein-coding genes in problematic articles.
(A, B) Numbers (log base 10) of problematic articles (y-axis) versus past research articles (x-axis) for (A) primary protein-coding genes in problematic articles and (B) claimed protein-coding gene targets of wrongly identified reagents. Vertical dashed lines indicate the median number of research articles for protein-coding genes, with the associated interquartile range shown in grey. Subsets of protein-coding genes are highlighted in each panel.
- Figure S3. Human protein-coding genes in problematic articles appear frequently in PubMed.
(A, B) Numbers (log base 10) of PubMed articles (y-axis) for primary protein-coding genes in problematic articles (A) (green) or claimed protein-coding gene targets of wrongly identified reagents (B) (green), versus all other human protein-coding genes (A, B) (grey). Horizontal lines within box plots indicate median values, with box plots showing percentiles according to letter proportions, that is, ±25% percentile, ±(25 + 25/2)% percentile, ±(25 + 25/2 + 25/4)% percentile.
- Figure 8. Clinical trial citations and approximate potential to translate (APT) for problematic articles.
(A) Percentages of problematic articles that are cited at least once according to the NIH Open Citation Collection (y-axis), according to publication corpus (x-axis). Error bars indicate 95% confidence intervals of bootstrapped estimates of percentages. Numbers of problematic articles with at least one clinical citation are shown below the x-axis for each corpus. (B) Average APT for problematic articles (y-axis) according to publication corpus (x-axis). Error bars indicate bootstrapped 95% confidence intervals. Numbers of problematic articles for which the APT computed by iCite (88) are shown below the x-axis for each corpus.
Tables
- Table 1.
Descriptions of the targeted corpora screened by Seek & Blastn with manual verification of nucleotide sequence reagent identities.
Single gene knockdown (SGK) miR-145 Cisplatin + Gemcitabine (C + G) Corpus Problematic Corpus Problematic Corpus Problematic Number of articles (% of corpus) 174 (100%) 75 (43%) 50 (100%) 31 (62%) 100 (100%) 51 (50%) Number of journals 83 42 35 25 48 31 Publication year median (range) 2015 (2006–2019)a 2015 (2010–2019) 2017 (2009–2019) 2017 (2009–2019) 2017 (2008–2019) 2017 (2009–2019) Journal impact factor at publication year median (range) 2.204 (0.098–8.459) 1.778 (0.098–5.712) 3.34 (0.700–9.050) 3.23 (0.700–8.278) 3.571 (1.099–10.391) 3.041 (1.099–8.579) Number of sequences/article median (range) 6 (0–24) 6 (1–24) 11 (4–46) 10 (4–46) 11 (2–71) 12 (2–70) Number of incorrect sequences/article median (range) ND 1 (1–8) ND 1 (1–5) ND 2 (1–8) Articles from China proportion (%) 159/174 (91%) 73/75 (97%) 44/50 (88%) 31/31 (100%) 90/100 (90%) 50/51 (98%) Articles from China affiliated with hospitals proportion (%) 147/159 (92%) 68/73 (93%) 40/44 (91%) 28/31 (90%) 82/90 (91%) 48/50 (96%) Articles from all other countries affiliated with hospitals proportion (%) 6/15 (40%) 0/2 (0%) 0/6 (0%) 0/3 (0%) 1/10 (10%) 0/1 (0%) Articles with post-publication noticesb proportion (%) 20/174 (12%) 13/75 (17%) 1/50 (2%) 1/31 (3%) 1/100 (1%) 1/51 (2%) - Table 2.
Cancer types studied in the Single Gene Knockdown (SGK) corpus, where each cancer type corresponds to a single article.
Gene Previously reported SGK articles New SGK articles ADAM8 Livera Breast, Breast, Colorectal, Gastric, Liver, Lung, Pancreatic ANXA1 N/A Breast, Breast, Breast, Esophageal, Leukemia, Liver, Lung, Prostate EAG1 Liposarcoma, Osteosarcoma Brain, Osteosarcoma, Osteosarcoma, Ovarian, Sarcoma GPR137 Bladder, Brain, Colorectalb, Pancreatic Brain, Gastric, Leukemia, Liver, Osteosarcoma, Ovarian, Prostate ICT1 Brain Breast, Gastric, Leukemia, Lung, Lymphoma, Prostate KLF8 Osteosarcoma Bladder, Brain, Brain, Brain, Breast, Colorectal, Colorectal, Gastric, Gastric, Gastric, Gastric, Liver, Liver, Nasopharyngeal, Oral, Ovarian, Pancreatic, Renal MACC1 Ovarian Bladder, Brain, Cervical, Cervical, Colorectal, Colorectal, Esophageal, Esophageal, Gallbladder, Gastric, Liver, Liver, Lung, Oral, Oral, Nasopharyngeal, Ovarian, Ovarian, Skin MYO6 Brain, Colorectal, Liver, Lung Breast, Gastric, Oral, Prostate NOB1 Brain, Breast, Colorectal, Liver, Osteosarcoma, Ovarian, Prostate Laryngeal, Lung, Lung, Oral, Osteosarcoma, Renal, Thyroid, Thyroid PP4R1 Breast, Liver Lung PP5 Colorectal, Ovarian Bladder, Brain, Leukemia, Liver, Osteosarcoma, Pancreatic, Prostate PPM1D Bladder, Lung Brain, Brain, Breast, Breast, Liver, Pancreatic RPS15A Brain, Lung Brain, Gastric, Leukemia, Liver, Lung, Osteosarcoma, Renal, Thyroid TCTN1 Brain, Brain, Pancreatic Brain, Colorectal, Gastric, Thyroid TPD52L2 Brain, Breast, Gastric, Liver, Oral Brain USP39 Liver, Thyroid Breast, Colorectal, Colorectal, Gastric, Liver, Liver, Lung, Oral, Osteosarcoma, Renal, Skin ZFX Brain, Breast Brain, Brain, Gallbladder, Laryngeal, Leukemia, Lung, Lung, Oral, Oral, Osteosarcoma, Pancreatic, Prostate, Renal - 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) - Table 4.
Summary of features of Gene and Oncology Reports journals and problematic articles.
Feature Gene Oncology Reports Publication years screened by Seek & Blastn 2007–2018 2014–2018 Journal impact factor (range during years screened) 2.082–2.871 2.301–3.041 Flagged/screened articles proportion (%) 742/7,399 (10%) 1,709/3,778 (45%) Problematic/flagged articles proportion (%) 128/742 (17%) 436/1,709 (26%) Incorrect sequences/problematic article median (range) 2 (1–36) 2 (1–15) Problematic articles from China proportion (%) 69/128 (54%) 393/436 (90%) Problematic articles from all other countries proportion (%) 59/128 (46%) 43/436 (10%) Problematic articles from China affiliated with hospitals proportion (%) 54/69 (78%) 342/393 (87%) Problematic articles from all other countries affiliated with hospitals proportion (%) 5/59 (9%) 5/43 (12%) Retracted or corrected problematic articles proportion (%) 2/128 (2%) 2/436 (0.5%)
Supplemental Data 1.
Single gene knockdown (SGK) corpus. All SGK articles screened by S&B and problematic SGK articles are shown in separate tabs. Primary human genes refer to the first-mentioned gene in the publication title or abstract.[LSA-2021-01203_Supplemental_Data_1.xlsx]
Supplemental Data 2.
miR-145 corpus. All miR-145 articles flagged by S&B screening and problematic miR-145 articles are shown in separate tabs. Primary human genes refer to the first-mentioned gene(s) in the publication title or abstract.[LSA-2021-01203_Supplemental_Data_2.xlsx]
Supplemental Data 3.
Cisplatin + gemcitabine (C + G) corpus. All C + G articles flagged by S&B screening and problematic C + G articles are shown in separate tabs. Primary human genes refer to the first-mentioned gene(s) in the publication title or abstract.[LSA-2021-01203_Supplemental_Data_3.xlsx]
Supplemental Data 4.
Problematic Gene articles. Primary human genes refer to the first-mentioned gene(s) in the publication title or abstract.[LSA-2021-01203_Supplemental_Data_4.xlsx]
Supplemental Data 5.
Problematic Oncology Reports corpus. Primary human genes refer to the first-mentioned gene(s) in the publication title or abstract.[LSA-2021-01203_Supplemental_Data_5.xlsx]
Supplemental Data 6.
Journals and publishers that have published problematic articles. Journals and publishers of problematic single gene knockdown, miR-145, and C + G articles and all problematic articles are shown in separate tabs.[LSA-2021-01203_Supplemental_Data_6.xlsx]
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