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Guidelines for the design, analysis and interpretation of ‘omics’ data: focus on human endometrium
Open accessAbstract
BACKGROUND: 'Omics' high-throughput analyses, including genomics, epigenomics, transcriptomics, proteomics and metabolomics, are widely applied in human endometrial studies. Analysis of endometrial transcriptome patterns in physiological and pathophysiological conditions has been to date the most commonly applied 'omics' technique in human endometrium. As the technologies improve, proteomics holds the next big promise for this field. The 'omics' technologies have undoubtedly advanced our knowledge of human endometrium in relation to fertility and different diseases. Nevertheless, the challenges arising from the vast amount of data generated and the broad variation of 'omics' profiling according to different environments and stimuli make it difficult to assess the validity, reproducibility and interpretation of such 'omics' data. With the expansion of 'omics' analyses in the study of the endometrium, there is a growing need to develop guidelines for the design of studies, and the analysis and interpretation of 'omics' data. METHODS: Systematic review of the literature in PubMed, and references from relevant articles were investigated up to March 2013. RESULTS: The current review aims to provide guidelines for future 'omics' studies on human endometrium, together with a summary of the status and trends, promise and shortcomings in the high-throughput technologies. In addition, the approaches presented here can be adapted to other areas of high-throughput 'omics' studies. CONCLUSION: A highly rigorous approach to future studies, based on the guidelines provided here, is a prerequisite for obtaining data on biological systems which can be shared among researchers worldwide and will ultimately be of clinical benefit.
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“Many centres worldwide have been collecting blood or other body fluids such as peritoneal fluid, endometrial fluid, and menstrual fluid, as well as tissue samples—in particular ectopic and eutopic endometrium—from women with and without endometriosis, for a variety of research purposes [145–147].”
From Update on biomarkers for the detection of endometriosis (2015) · cites this paper as [145]
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Boldu-Fernández, S., Lliberos, C., Simón, C., & Mas, A. (2025) · Cells · doi:10.3390/cells14030156 · Cited by 18
Self-citationRicard‐Blum, S., & Miele, A. E. (2019) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2019.12.009 · Cited by 15
Embryo secretome in predicting embryo quality and IVF treatment outcome
Toporcerová, S., Badovská, Z., Kriváková, E., Mikulová, V., Mareková, M., Altmäe, S., & Rabajdová, M. (2025) · Reproductive BioMedicine Online · doi:10.1016/j.rbmo.2025.104825 · Cited by 15
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Self-citationSilveira, C. O., Rezende, C. P., Ferreira, M. C. F., Puerto, H. L. D., & dos Reis, F. M. (2016) · Reproductive Sciences · doi:10.1177/1933719116667490 · Cited by 14
Liang, X., He, J., He, L., Lin, Y., Li, Y., Cai, K., Wei, J. J., Lu, Y., & Chen, Z. (2023) · Reproductive BioMedicine Online · doi:10.1016/j.rbmo.2023.03.015 · Cited by 13
Badie, A., Saliminejad, K., Salahshourifar, I., & Khorshid, H. R. K. (2019) · Gynecological Endocrinology · doi:10.1080/09513590.2019.1631790 · Cited by 12
Gatius, S., Jové, M., Megino‐Luque, C., Albertí‐Valls, M., Yeramian, A., Bonifaci, N., Piñol, M., Santacana, M., Pradas, I., Llobet‐Navàs, D., et al. (2022) · Cancers · doi:10.3390/cancers14122842 · Cited by 11
Reproductomics: Exploring the Applications and Advancements of Computational Tools
Sengupta, P., Dutta, S., Liew, F. F., Samrot, A. V., Dasgupta, S., Rajput, M., Sláma, P., Kolesárová, A., & Roychoudhury, S. (2024) · Physiological Research · doi:10.33549/physiolres.935389 · Cited by 10
Small, S. L. (2024) · Ageing Research Reviews · doi:10.1016/j.arr.2024.102632 · Cited by 10
The endometrial transcriptome of infertile women with and without implantation failure
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Hu, S., Sun, Z., Li, B., Zhao, H., Wang, Y., Yao, G., Li, X., Bian, X., Li, T. C., Vankelecom, H. E. J., et al. (2023) · Endocrinology · doi:10.1210/endocr/bqad012 · Cited by 9
The endometrial proteomic profile around the time of embryo implantation†
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OMICs Studies and Endometriosis Biomarker Identification
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DNA Repair Gene XRCC1 and XRCC4 Variations and Risk of Endometriosis: An Association Study
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Uterine Transcriptome: Understanding Physiology and Disease Processes
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Metadata
- Authors
- Altmäe, S., Esteban, F. J., Stavreus-Evers, A., Simón, C., Giudice, L., Lessey, B. A., Horcajadas, J. A., Macklon, N. S., D'Hooghe, T., Campoy, C., Fauser, B. C., Salamonsen, L. A., & Salumets, A.
- Affiliations
- Universidad de Granada (ES)
- Universidad de Jaén (ES)
- Uppsala University (SE)
- Valencian Infertility Institute (ES)
- University of California, San Francisco (US)
- Prisma Health (US)
- Fundacion Agencia Aragonesa para la Investigacion y el Desarrollo (ES)
- Princess Anne Hospital (GB)
- University Medical Center Utrecht (NL)
- Competence Centre on Health Technologies (Estonia) (EE)
- ORCID
- Venue
- Human Reproduction Update
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-09-29
- Volume
- 20
- Issue
- 1
- Pages
- 12-28
- ISSN
- 1355-4786 (ISSN-L)
- 1460-2369
- PMC
- PMC3845681
- OpenAlex
- W2143750395
- Cited by
- 151
- References
- 201
- Citations by year
- 2026: 4 · 2025: 7 · 2024: 15 · 2023: 12 · 2022: 10 · 2021: 9 · 2020: 14 · 2019: 16 · 2018: 14 · 2017: 16 · 2016: 12 · 2015: 16 · 2014: 6
- FWCI
- 1.07
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- other-oa
- Locations
- Human Reproduction Update (publishedVersion, other-oa)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Institutional Repository of the University of Granada (University of Granada) (submittedVersion, other-oa)
- Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion)
- ePrints Soton (University of Southampton) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- European Commission (329812)
- State Government of Victoria
- Ettevõtluse Arendamise Sihtasutus (EU324509, EU30020)
- National Institutes of Health
- National Health and Medical Research Council (494802, 1002028)
- National Institute of Child Health and Human Development
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01HD067721)
- Eurostars
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- human endometrium, omics data, data analysis and interpretation, transcriptomics, proteomics, metabolomics, epigenomics, high-throughput technologies, reproducibility, endometrial disease
- MeSH terms
- Endometrium, Female, Humans, Embryo Implantation, Guidelines as Topic, Genomics, Systems Biology, Metabolomics, High-Throughput Nucleotide Sequencing
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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.
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