{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T04:47:12Z","timestamp":1760244432875,"version":"build-2065373602"},"reference-count":20,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2022,12,20]],"date-time":"2022-12-20T00:00:00Z","timestamp":1671494400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"\u201cOMICAS program: Optimizaci\u00f3n Multiescala In-silico de Cultivos Agr\u00edcolas Sostenibles (Infraestructura y validaci\u00f3n en Arroz y Ca\u00f1a de Az\u00facar)\u201d Scientific Ecosystem belonging to the Colombia Cient\u00edfica Program","award":["FP44842-217-2018"],"award-info":[{"award-number":["FP44842-217-2018"]}]},{"name":"Colombian Ministry of Education and the Colombian Ministry of Commerce, Industry and Turism","award":["FP44842-217-2018"],"award-info":[{"award-number":["FP44842-217-2018"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Data"],"abstract":"<jats:p>Sugarcane is a species of tall grass with high biomass and sucrose production, and the world\u2019s largest crop by production quantity. Its evolutionary environment adaptation and anthropogenic breeding response have resulted in a complex autopolyploid genome. Few efforts have been reported in the literature to document this organism\u2019s gene co-expression and annotation, and, when available, use different gene identifiers that cannot be easily associated across studies. This data descriptor paper presents a dataset that consolidates expression matrices of two Saccharum spontaneum AP85-441 genome versions and an algorithm implemented in Python to mechanically obtain this dataset. The data are processed from the allele-level information of the two sources, with BLASTn used bidirectionally to suggest feasible mappings between the two sets of alleles, and a graph-matching optimization algorithm to maximize global identity and uniqueness of genes. Association tables are used to consolidate the expression values from alleles to genes. The contributed expression matrices comprise 96 experiments and 109,050 and 35,516 from the two genome versions. They can represent significant computational cost reduction for further research on, e.g., sugarcane co-expression network generation, functional annotation prediction, and stress-specific gene identification.<\/jats:p>","DOI":"10.3390\/data8010001","type":"journal-article","created":{"date-parts":[[2022,12,20]],"date-time":"2022-12-20T01:36:02Z","timestamp":1671500162000},"page":"1","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Gene Expression Datasets for Two Versions of the Saccharum spontaneum AP85-441 Genome"],"prefix":"10.3390","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8060-6891","authenticated-orcid":false,"given":"Nicol\u00e1s","family":"L\u00f3pez-Rozo","sequence":"first","affiliation":[{"name":"Department of Electronics and Computer Science, Pontificia Universidad Javeriana, Cali 760031, Colombia"},{"name":"OMICAS Program, Pontificia Universidad Javeriana, Cali 760031, Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8525-5341","authenticated-orcid":false,"given":"Mauricio","family":"Ramirez-Castrillon","sequence":"additional","affiliation":[{"name":"OMICAS Program, Pontificia Universidad Javeriana, Cali 760031, Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7068-970X","authenticated-orcid":false,"given":"Miguel","family":"Romero","sequence":"additional","affiliation":[{"name":"Department of Electronics and Computer Science, Pontificia Universidad Javeriana, Cali 760031, Colombia"},{"name":"OMICAS Program, Pontificia Universidad Javeriana, Cali 760031, Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2393-6066","authenticated-orcid":false,"given":"Jorge","family":"Finke","sequence":"additional","affiliation":[{"name":"Department of Electronics and Computer Science, Pontificia Universidad Javeriana, Cali 760031, Colombia"},{"name":"OMICAS Program, Pontificia Universidad Javeriana, Cali 760031, Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4356-7704","authenticated-orcid":false,"given":"Camilo","family":"Rocha","sequence":"additional","affiliation":[{"name":"Department of Electronics and Computer Science, Pontificia Universidad Javeriana, Cali 760031, Colombia"},{"name":"OMICAS Program, Pontificia Universidad Javeriana, Cali 760031, Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,12,20]]},"reference":[{"key":"ref_1","first-page":"1","article-title":"Basic information on the sugarcane plant","volume":"9","author":"Henry","year":"2010","journal-title":"Genetics, Genomics and Breeding of Sugarcane"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"2420","DOI":"10.1105\/tpc.114.125583","article-title":"Comparative analysis of Miscanthus and Saccharum reveals a shared whole-genome duplication but different evolutionary fates","volume":"26","author":"Kim","year":"2014","journal-title":"Plant Cell"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1565","DOI":"10.1038\/s41588-018-0237-2","article-title":"Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.","volume":"50","author":"Zhang","year":"2018","journal-title":"Nat. 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