Credits

auto-Enrich was developed in the context of a graduate Master’s thesis project in the University of Porto. Please cite the following when using the Pipeline:

• Ribeiro, JMS. (2025). auto-Enrich: a pipeline streamlined enrichment analysis [Master’s thesis, University of Porto]. Repositório Aberto. https://repositorio-aberto.up.pt/bitstream/10216/169254/2/738334.pdf

Author Contributions

• J.M.S. Ribeiro¹ – Development of pipeline and thesis work

• C.P. Vieira¹,² – Supervision, conceptual support

• J. Vieira¹,² – Supervision, conceptual support

• H. López Fernández³,⁴ – Technical guidance

¹ Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal

² Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135 Porto, Portugal

³ Department of Computer Science, CINBIO, Universidade de Vigo, ESEI – Escuela Superior de Ingeniería Informática, 32004 Ourense, Spain

⁴ SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36213 Vigo, Spain

References

• g:Profiler: Raudvere, U., et al. (2019). g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update). Nucleic Acids Research, 47(W1), W191–W198.

• PANTHER: Mi, H., et al. (2021). PANTHER version 16: a revised family classification, tree-based tools and extensive API. Nucleic Acids Research, 49(D1), D394–D403.

• GSEA (Gene Set Enrichment Analysis): Subramanian, A., et al. (2005). Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. PNAS, 102(43), 15545–15550.

• MSigDB (Molecular Signatures Database): Liberzon, A., et al. (2015). The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Systems, 1(6), 417–425.

• Gene Ontology (GO): Ashburner, M., et al. (2000). Gene Ontology: tool for the unification of biology. Nature Genetics, 25(1), 25–29.

• Reactome Pathway Database: Jassal, B., et al. (2020). The Reactome pathway knowledgebase. Nucleic Acids Research, 48(D1), D498–D503.

• UniProt: Bateman, A., Martin, M. J., Orchard, S., et al. (2025). UniProt: the Universal Protein Knowledgebase. Nucleic Acids Research, 53(D1), D190–D199.