The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index
Open accessAbstract
ATTED-II (http://atted.jp) is a coexpression database for plant species to aid in the discovery of relationships of unknown genes within a species. As an advanced coexpression analysis method, multispecies comparisons have the potential to detect alterations in gene relationships within an evolutionary context. However, determining the validity of comparative coexpression studies is difficult without quantitative assessments of the quality of coexpression data. ATTED-II (version 9) provides 16 coexpression platforms for nine plant species, including seven species supported by both microarray- and RNA sequencing (RNAseq)-based coexpression data. Two independent sources of coexpression data enable the assessment of the reproducibility of coexpression. The latest coexpression data for Arabidopsis (Ath-m.c7-1 and Ath-r.c3-0) showed the highest reproducibility (Jaccard coefficient = 0.13) among previous coexpression data in ATTED-II. We also investigated the statistical basis of the mutual rank (MR) index as a coexpression measure by bootstrap sampling of experimental units. We found that the error distribution of the logit-transformed MR index showed normality with equal variances for each coexpression platform. Because the MR error was strongly correlated with the number of samples for the coexpression data, typical confidence intervals for the MR index can be estimated for any coexpression platform. These new, high-quality coexpression data can be analyzed with any tool in ATTED-II and combined with external resources to obtain insight into plant biology.
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
Adjusting batch effects in microarray expression data using empirical Bayes methods
Johnson, W. E., Li, C., & Rabinovic, A. (2007) · Biostatistics · doi:10.1093/biostatistics/kxj037 · Cited by 8,658
KEGG as a reference resource for gene and protein annotation
Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M., & Tanabe, M. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1070 · Cited by 7,387
A General Framework for Weighted Gene Co-Expression Network Analysis
Zhang, B., & Horvath, S. (2005) · Statistical Applications in Genetics and Molecular Biology · doi:10.2202/1544-6115.1128 · Cited by 5,684
Tackling the widespread and critical impact of batch effects in high-throughput data
Leek, J. T., Scharpf, R. B., Bravo, H. C., Simcha, D., Langmead, B., Johnson, W. E., Geman, D., Baggerly, K., & Irizarry, R. A. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2825 · Cited by 2,196
Guidance for RNA-seq co-expression network construction and analysis: safety in numbers
Ballouz, S., Verleyen, W., & Gillis, J. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv118 · Cited by 215 · cited 1×
“The function scores were correlated with the logarithmic number of samples for each species (PCC = 0.44), as reported previously (Ballouz et al. 2015).”
MethodInfluential
Cited by
High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types
Shulse, C. N., Cole, B. J., Ciobanu, D., Lin, J., Yoshinaga, Y., Gouran, M., Turco, G. M., Zhu, Y., O’Malley, R. C., Brady, S. M., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.04.054 · Cited by 432
Signaling Toward Reactive Oxygen Species-Scavenging Enzymes in Plants
Dvořák, P., Krasylenko, Y., Zeiner, A., Šamaj, J., & Takáč, T. (2021) · Frontiers in Plant Science · doi:10.3389/fpls.2020.618835 · Cited by 375
Genetic Contribution of Paleopolyploidy to Adaptive Evolution in Angiosperms
Wu, S., Han, B., & Jiao, Y. (2020) · Molecular Plant · doi:10.1016/j.molp.2019.10.012 · Cited by 334
Soubeyrand, E., Johnson, T. S., Latimer, S., Block, A., Kim, J., Colquhoun, T. A., Butelli, E., Martin, C., Wilson, M. A., & Basset, G. J. (2018) · The Plant Cell · doi:10.1105/tpc.18.00688 · Cited by 61
Metadata
- Authors
- Obayashi, T., Aoki, Y., Tadaka, S., Kagaya, Y., & Kinoshita, K.
- Venue
- Plant and Cell Physiology
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-12-04
- Volume
- 59
- Issue
- 1
- Pages
- e3-e3
- ISSN
- 0032-0781 (ISSN-L)
- 1471-9053
- OpenAlex
- W2775315818
- Cited by
- 252
- References
- 5
- FWCI
- 10.48
- Type
- journal article
- Language
- en
- Open access
- hybrid
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: ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index. https://app.cochat.ai/papers/10.1093/pcp/pcx191
- The paper
- Obayashi, T., Aoki, Y., Tadaka, S., Kagaya, Y., & Kinoshita, K. (2018). ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index. Plant and Cell Physiology. https://doi.org/10.1093/pcp/pcx191
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.
