The DOI matches its Crossref record; 47 of the 47 references it cites were found in a registry or an index.
miRSystem: An Integrated System for Characterizing Enriched Functions and Pathways of MicroRNA Targets
Open accessAbstract
BACKGROUND: Many prediction tools for microRNA (miRNA) targets have been developed, but inconsistent predictions were observed across multiple algorithms, which can make further analysis difficult. Moreover, the nomenclature of human miRNAs changes rapidly. To address these issues, we developed a web-based system, miRSystem, for converting queried miRNAs to the latest annotation and predicting the function of miRNA by integrating miRNA target gene prediction and function/pathway analyses. RESULTS: First, queried miRNA IDs were converted to the latest annotated version to prevent potential conflicts resulting from multiple aliases. Next, by combining seven algorithms and two validated databases, potential gene targets of miRNAs and their functions were predicted based on the consistency across independent algorithms and observed/expected ratios. Lastly, five pathway databases were included to characterize the enriched pathways of target genes through bootstrap approaches. Based on the enriched pathways of target genes, the functions of queried miRNAs could be predicted. CONCLUSIONS: MiRSystem is a user-friendly tool for predicting the target genes and their associated pathways for many miRNAs simultaneously. The web server and the documentation are freely available at http://mirsystem.cgm.ntu.edu.tw/.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
Edgar, R. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.207 · Cited by 13,288
Lewis, B. P., Burge, C. B., & Bartel, D. P. (2005) · Cell · doi:10.1016/j.cell.2004.12.035 · Cited by 11,855
Most mammalian mRNAs are conserved targets of microRNAs
Friedman, R. C., Farh, K. K.-H., Burge, C. B., & Bartel, D. P. (2009) · Genome Research · doi:10.1101/gr.082701.108 · Cited by 8,462
KEGG for linking genomes to life and the environment
Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm882 · Cited by 6,782
Origins and Mechanisms of miRNAs and siRNAs
Carthew, R. W., & Sontheimer, E. J. (2009) · Cell · doi:10.1016/j.cell.2009.01.035 · Cited by 5,018
Combinatorial microRNA target predictions
Krek, A., Grün, D., Poy, M. N., Wolf, R., Rosenberg, L., Epstein, E. J., MacMenamin, P., da Piedade, I., Gunsalus, K. C., Stoffel, M., et al. (2005) · Nature Genetics · doi:10.1038/ng1536 · Cited by 4,603
John, B., Enright, A. J., Aravin, A., Tuschl, T., Sander, C., & Marks, D. S. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020363 · Cited by 3,796
MicroRNA Targeting Specificity in Mammals: Determinants beyond Seed Pairing
Grimson, A., Farh, K. K.-H., Johnston, W. K., Garrett-Engele, P., Lim, L. P., & Bartel, D. P. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.06.017 · Cited by 3,766
MicroRNA targets in Drosophila
Enright, A. J., John, B., Gaul, U., Tuschl, T., Sander, C., & Marks, D. S. (2003) · Genome Biology · doi:10.1186/gb-2003-5-1-r1 · Cited by 3,597
The microRNA.org resource: targets and expression
Betel, D., Wilson, M., Gabow, A., Marks, D. S., & Sander, C. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm995 · Cited by 2,503
Cited by
Ru, Y., Kechris, K. J., Tabakoff, B., Hoffman, P., Radcliffe, R. A., Bowler, R., Mahaffey, S., Rossi, S., Calin, G. A., Bemis, L., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku631 · Cited by 800
A network-biology perspective of microRNA function and dysfunction in cancer
Bracken, C. P., Scott, H. S., & Goodall, G. J. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.134 · Cited by 668
mirDIP 4.1—integrative database of human microRNA target predictions
Tokar, T., Pastrello, C., Rossos, A. E. M., Abovsky, M., Hauschild, A.-C., Tsay, M., Lu, R., & Jurisica, I. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx1144 · Cited by 572
Reis, M., Mavin, E., Nicholson, L., Green, K., Dickinson, A. M., & Wang, X.-N. (2018) · Frontiers in Immunology · doi:10.3389/fimmu.2018.02538 · Cited by 286
MirGeneDB 2.0: the metazoan microRNA complement
Fromm, B., Domanska, D., Høye, E., Ovchinnikov, V., Kang, W., Aparicio-Puerta, E., Johansen, M., Flatmark, K., Mathelier, A., Hovig, E., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkz885 · Cited by 261
Metadata
- Authors
- Lu, T.-P., Lee, C.-Y., Tsai, M.-H., Chiu, Y.-C., Hsiao, C. K., Lai, L.-C., & Chuang, E. Y.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2012-08-01
- Volume
- 7
- Issue
- 8
- Pages
- e42390
- ISSN
- 1932-6203 (ISSN-L)
- OpenAlex
- W2003816656
- Cited by
- 354
- References
- 47
- FWCI
- 5.09
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: miRSystem: An Integrated System for Characterizing Enriched Functions and Pathways of MicroRNA Targets. https://app.cochat.ai/papers/10.1371/journal.pone.0042390
- The paper
- Lu, T.-P., Lee, C.-Y., Tsai, M.-H., Chiu, Y.-C., Hsiao, C. K., Lai, L.-C., & Chuang, E. Y. (2012). miRSystem: An Integrated System for Characterizing Enriched Functions and Pathways of MicroRNA Targets. PLoS ONE. https://doi.org/10.1371/journal.pone.0042390
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
