Expression Data Collection
2 min
Expression data was obtained from Gene Expression Omnibus (GEO). Microarray datasets were extracted from GEO family SOFT files using in-house tools, and probe identifiers were mapped using platform annotation tables from the corresponding platform SOFT files. RNA-seq data was obtained (if made available by NCBI) as raw counts matrices mapped by NCBI’s pipeline (1x). Genes were translated to Ensembl ID using information from NCBI (as of 24 april 2024) and Ensembl (v113) (2x).
Datasets from single cell studies were identified and downloaded manually. Gene identifier translation was performed as explained in the Data Pre-Processingx section.
References
- NCBI-generated RNA-seq count data BETA - GEO - NCBI (2024) (available at https://www.ncbi.nlm.nih.gov/geo/info/rnaseqcounts.html).
- S. C. Dyer, O. Austine-Orimoloye, A. G. Azov, M. Barba, I. Barnes, V. P. Barrera-Enriquez, A. Becker, R. Bennett, M. Beracochea, A. Berry, J. Bhai, S. K. Bhurji, S. Boddu, P. R. Branco Lins, L. Brooks, S. B. Ramaraju, L. I. Campbell, M. C. Martinez, M. Charkhchi, L. A. Cortes, C. Davidson, S. Denni, K. Dodiya, S. Donaldson, B. El Houdaigui, T. El Naboulsi, O. Falola, R. Fatima, T. Genez, J. G. Martinez, T. Gurbich, M. Hardy, Z. Hollis, T. Hunt, M. Kay, V. Kaykala, D. Lemos, D. Lodha, N. Mathlouthi, G. A. Merino, R. Merritt, L. P. Mirabueno, A. Mushtaq, S. N. Hossain, J. G. Pérez-Silva, M. Perry, I. Piližota, D. Poppleton, I. Prosovetskaia, S. Raj, A. I. A. Salam, S. Saraf, N. Saraiva-Agostinho, S. Sinha, B. Sipos, V. Sitnik, E. Steed, M. M. Suner, L. Surapaneni, K. Sutinen, F. F. Tricomi, I. Tsang, D. Urbina-Gómez, A. Veidenberg, T. A. Walsh, N. L. Willhoft, J. Allen, J. Alvarez-Jarreta, M. Chakiachvili, J. Cheema, J. B. da Rocha, N. H. De Silva, S. Giorgetti, L. Haggerty, G. R. Ilsley, J. Keatley, J. E. Loveland, B. Moore, J. M. Mudge, G. Naamati, J. Tate, S. J. Trevanion, A. Winterbottom, B. Flint, A. Frankish, S. E. Hunt, R. D. Finn, M. A. Freeberg, P. W. Harrison, F. J. Martin, A. D. Yates, Ensembl 2025. Nucleic Acids Res 53, D948–D957 (2025). (available at https://academic.oup.com/nar/article/53/D1/D948/7916352).