{"doi":"10.1371/journal.pone.0054699","title":"The 3D Organization of the Yeast Genome Correlates with Co-Expression and Reflects Functional Relations between Genes","abstract":null,"journal":"PLoS ONE","year":2013,"id":630716,"datarank":0.611630616585858,"base_score":4.07753744390572,"endowment":4.07753744390572,"self_citation_contribution":0.611630616585858,"citation_network_contribution":0.0,"self_endowment_contribution":0.611630616585858,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":58,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1634123,"name":"Andrzej S. Kudlicki","orcid":null,"position":1,"is_corresponding":false},{"id":1157327,"name":"Dirar Homouz","orcid":"0000-0002-8859-0265","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"The 3D Organization of the Yeast Genome Correlates with Co-Expression and Reflects Functional Relations between Genes","abstract":"The spatial organization of eukaryotic genomes is thought to play an important role in regulating gene expression. The recent advances in experimental methods including chromatin capture techniques, as well as the large amounts of accumulated gene expression data allow studying the relationship between spatial organization of the genome and co-expression of protein-coding genes. To analyse this genome-wide relationship at a single gene resolution, we combined the interchromosomal DNA contacts in the yeast genome measured by Duan et al. with a comprehensive collection of 1,496 gene expression datasets. We find significant enhancement of co-expression among genes with contact links. The co-expression is most prominent when two gene loci fall within 1,000 base pairs from the observed contact. We also demonstrate an enrichment of inter-chromosomal links between functionally related genes, which suggests that the non random nature of the genome organization serves to facilitate coordinated transcription in groups of genes.","is_dataset_classified":null,"base_score":4.07753744390572,"endowment":4.07753744390572,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"23382942","pmcid":"PMC3561378","openalex_id":"https://openalex.org/W1972336367","authors":[],"funders":[],"total_grants":0,"fwci":3.3019,"citation_percentile":0.9269863,"influential_citations":0,"citation_trend":[{"year":2013,"count":2},{"year":2014,"count":5},{"year":2015,"count":8},{"year":2016,"count":9},{"year":2017,"count":5},{"year":2018,"count":4},{"year":2019,"count":10},{"year":2020,"count":4},{"year":2021,"count":4},{"year":2022,"count":4},{"year":2023,"count":1},{"year":2026,"count":1}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0054699&type=printable","host_type":"journal"},{"url":"https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0054699&type=printable","host_type":"publisher"},{"url":"http://dx.plos.org/10.1371/journal.pone.0054699","host_type":"publisher"},{"url":"https://doi.org/10.1371/journal.pone.0054699","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/23382942","host_type":"repository"},{"url":"https://figshare.com/articles/dataset/The_3D_Organization_of_the_Yeast_Genome_Correlates_with_Co_Expression_and_Reflects_Functional_Relations_between_Genes__/155200","host_type":"repository"},{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.411.6485","host_type":""},{"url":"https://doaj.org/article/ac5cc6625e534b9185c79a818a516ead","host_type":"repository"},{"url":"http://europepmc.org/articles/PMC3561378","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3561378","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC3561378","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC3561378?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["Genomics and Chromatin Dynamics","Fungal and yeast genetics research","Genetic Mapping and Diversity in Plants and Animals"],"mesh_terms":["Epistasis, Genetic","Yeasts","Chromosomes, Fungal","Gene Expression Regulation, Fungal","Cluster Analysis","Genome, Fungal","Gene Expression Profiling","Gene Regulatory Networks","Genetic Loci"],"keywords":["Gene","Genome","Biology","Genetics","Gene expression","Chromatin","Regulation of gene expression","Genomic organization","Pair-rule gene","Computational biology","Regulator gene"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-05T21:59:56.315586Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}