The DOI matches its Crossref record; 15 of the 15 references it cites were found in a registry or an index.
PlantGSEA: a gene set enrichment analysis toolkit for plant community
Open accessAbstract
Gene Set Enrichment Analysis (GSEA) is a powerful method for interpreting biological meaning of a list of genes by computing the overlaps with various previously defined gene sets. As one of the most widely used annotations for defining gene sets, Gene Ontology (GO) system has been used in many enrichment analysis tools. EasyGO and agriGO, two GO enrichment analysis toolkits developed by our laboratory, have gained extensive usage and citations since their releases because of their effective performance and consistent maintenance. Responding to the increasing demands of more comprehensive analysis from the users, we developed a web server as an important component of our bioinformatics analysis toolkit, named PlantGSEA, which is based on GSEA method and mainly focuses on plant organisms. In PlantGSEA, 20 290 defined gene sets deriving from different resources were collected and used for GSEA analysis. The PlantGSEA currently supports gene locus IDs and Affymatrix microarray probe set IDs from four plant model species (Arabidopsis thaliana, Oryza sativa, Zea mays and Gossypium raimondii). The PlantGSEA is an efficient and user-friendly web server, and now it is publicly accessible at http://structuralbiology.cau.edu.cn/PlantGSEA.
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
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625
Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn923 · Cited by 14,108
Phytozome: a comparative platform for green plant genomics
Goodstein, D. M., Shu, S., Howson, R., Neupane, R., Hayes, R. D., Fazo, J., Mitros, T., Dirks, W., Hellsten, U., Putnam, N., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr944 · Cited by 5,420
agriGO: a GO analysis toolkit for the agricultural community
Du, Z., Zhou, X., Ling, Y., Zhang, Z., & Su, Z. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq310 · Cited by 2,396
Self-citationThe TIGR Rice Genome Annotation Resource: improvements and new features
Ouyang, S., Zhu, W., Hamilton, J., Lin, H., Campbell, M., Childs, K., Thibaud-Nissen, F., Malek, R. L., Lee, Y., Zheng, L., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkl976 · Cited by 1,268
The Arabidopsis Information Resource (TAIR): gene structure and function annotation
Swarbreck, D., Wilks, C., Lamesch, P., Berardini, T. Z., Garcia-Hernandez, M., Foerster, H., Li, D., Meyer, T., Muller, R., Ploetz, L., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm965 · Cited by 1,074
PlnTFDB: updated content and new features of the plant transcription factor database
Pérez-Rodríguez, P., Riaño-Pachón, D. M., Corrêa, L. G. G., Rensing, S. A., Kersten, B., & Mueller-Roeber, B. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp805 · Cited by 734
Zhang, Z., Yu, J., Li, D., Zhang, Z., Liu, F., Zhou, X., Wang, T., Ling, Y., & Su, Z. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp818 · Cited by 377
Self-citationThe Kyoto Encyclopedia of Genes and Genomes—KEGG
(2000) · Yeast · doi:10.1002/(sici)1097-0061(200004)17:1<48::aid-yea2>3.0.co;2-h · Cited by 278
Cited by
clusterProfiler 4.0: A universal enrichment tool for interpreting omics data
(2021) · doi:10.1016/j.xinn.2021.100141 · Cited by 12,455
ShinyGO: a graphical gene-set enrichment tool for animals and plants
Ge, S. X., Jung, D., & Yao, R. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btz931 · Cited by 5,270
agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update
Tian, T., Liu, Y., Yan, H., You, Q., Yi, X., Du, Z., Xu, W., & Su, Z. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx382 · Cited by 2,318
Self-citationRoot microbiota drive direct integration of phosphate stress and immunity
Castrillo, G., Teixeira, P. J. P. L., Paredes, S. H., Law, T. F., de Lorenzo, L., Feltcher, M. E., Finkel, O. M., Breakfield, N. W., Mieczkowski, P., Jones, C. D., et al. (2017) · Nature · doi:10.1038/nature21417 · Cited by 956
A phosphate starvation response-centered network regulates mycorrhizal symbiosis
Shi, J., Zhao, B., Zheng, S., Zhang, X., Wang, X., Dong, W., Xie, Q., Wang, G., Xiao, Y., Chen, F., et al. (2021) · Cell · doi:10.1016/j.cell.2021.09.030 · Cited by 384
Metadata
- Authors
- Yi, X., Du, Z., & Su, Z.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-04-30
- Volume
- 41
- Issue
- W1
- Pages
- W98-W103
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2001191731
- Cited by
- 276
- References
- 15
- FWCI
- 6.59
- 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: PlantGSEA: a gene set enrichment analysis toolkit for plant community. https://app.cochat.ai/papers/10.1093/nar/gkt281
- The paper
- Yi, X., Du, Z., & Su, Z. (2013). PlantGSEA: a gene set enrichment analysis toolkit for plant community. Nucleic Acids Research. https://doi.org/10.1093/nar/gkt281
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.
