The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Expression Atlas update—a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments
Open accessAbstract
Expression Atlas (http://www.ebi.ac.uk/gxa) is a value-added database providing information about gene, protein and splice variant expression in different cell types, organism parts, developmental stages, diseases and other biological and experimental conditions. The database consists of selected high-quality microarray and RNA-sequencing experiments from ArrayExpress that have been manually curated, annotated with Experimental Factor Ontology terms and processed using standardized microarray and RNA-sequencing analysis methods. The new version of Expression Atlas introduces the concept of 'baseline' expression, i.e. gene and splice variant abundance levels in healthy or untreated conditions, such as tissues or cell types. Differential gene expression data benefit from an in-depth curation of experimental intent, resulting in biologically meaningful 'contrasts', i.e. instances of differential pairwise comparisons between two sets of biological replicates. Other novel aspects of Expression Atlas are its strict quality control of raw experimental data, up-to-date RNA-sequencing analysis methods, expression data at the level of gene sets, as well as genes and a more powerful search interface designed to maximize the biological value provided to the user.
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
miRBase: integrating microRNA annotation and deep-sequencing data
Kozomara, A., & Griffiths-Jones, S. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1027 · Cited by 3,634
The Proteomics Identifications (PRIDE) database and associated tools: status in 2013
Vizcaíno, J. A., Côté, R. G., Csordas, A., Dianes, J. A., Fabregat, A., Foster, J. M., Griss, J., Alpi, E., Birim, M., Contell, J., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1262 · Cited by 1,918
NCBI GEO: archive for functional genomics data sets--10 years on
Barrett, T., Troup, D. B., Wilhite, S. E., Ledoux, P., Evangelista, C., Kim, I. F., Tomashevsky, M., Marshall, K. A., Phillippy, K. H., Sherman, P. M., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1184 · Cited by 1,124
Modeling sample variables with an Experimental Factor Ontology
Malone, J., Holloway, E., Adamusiak, T., Kapushesky, M., Zheng, J., Kolesnikov, N., Zhukova, A., Brazma, A., & Parkinson, H. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq099 · Cited by 568
Self-citationArrayExpress update—trends in database growth and links to data analysis tools
Rustici, G., Kolesnikov, N., Brandizi, M., Burdett, T., Dylag, M., Emam, I., Farne, A., Hastings, E., Ison, J., Keays, M., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1174 · Cited by 371
Self-citationKapushesky, M., Adamusiak, T., Burdett, T., Culhane, A., Farne, A., Filippov, A., Holloway, E., Klebanov, A., Kryvych, N., Kurbatova, N., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr913 · Cited by 164
Self-citation
Cited by
limma powers differential expression analyses for RNA-sequencing and microarray studies
Ritchie, M. E., Phipson, B., Wu, D., Hu, Y., Law, C. W., Shi, W., & Smyth, G. K. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv007 · Cited by 40,458
The Ensembl Variant Effect Predictor
McLaren, W., Gil, L., Hunt, S. E., Riat, H. S., Ritchie, G. R. S., Thormann, A., Flicek, P., & Cunningham, F. (2016) · Genome Biology · doi:10.1186/s13059-016-0974-4 · Cited by 8,099
Benchmark and integration of resources for the estimation of human transcription factor activities
Garcia-Alonso, L., Holland, C. H., Ibrahim, M. M., Turei, D., & Saez-Rodriguez, J. (2019) · Genome Research · doi:10.1101/gr.240663.118 · Cited by 1,122
The extracellular matrix: tools and insights for the "omics" era
Naba, A., Clauser, K. R., Ding, H., Whittaker, C. A., Carr, S. A., & Hynes, R. O. (2016) · Matrix Biology · doi:10.1016/j.matbio.2015.06.003 · Cited by 1,037
Distribution of miRNA expression across human tissues
Ludwig, N., Leidinger, P., Becker, K., Backes, C., Fehlmann, T., Pallasch, C., Rheinheimer, S., Meder, B., Stähler, C., Meese, E., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw116 · Cited by 968
Metadata
- Authors
- Petryszak, R., Burdett, T., Fiorelli, B., Fonseca, N. A., Gonzalez-Porta, M., Hastings, E., Huber, W., Jupp, S., Keays, M., Kryvych, N., McMurry, J., Marioni, J. C., Malone, J., Megy, K., Rustici, G., Tang, A. Y., Taubert, J., Williams, E., Mannion, O., Parkinson, H. E., & Brazma, A.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-12-04
- Volume
- 42
- Issue
- D1
- Pages
- D926-D932
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2058320302
- Cited by
- 344
- References
- 6
- FWCI
- 19.23
- 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: Expression Atlas update—a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments. https://app.cochat.ai/papers/10.1093/nar/gkt1270
- The paper
- Petryszak, R., Burdett, T., Fiorelli, B., Fonseca, N. A., Gonzalez-Porta, M., Hastings, E., Huber, W., Jupp, S., Keays, M., Kryvych, N., McMurry, J., Marioni, J. C., Malone, J., Megy, K., Rustici, G., Tang, A. Y., Taubert, J., Williams, E., Mannion, O., . . . Brazma, A. (2014). Expression Atlas update—a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments. Nucleic Acids Research. https://doi.org/10.1093/nar/gkt1270
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.
