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Pregled bibliografske jedinice broj: 1094876

Patterns of diverse gene functions in genomic neighborhoods predict gene function and phenotype


Mihelčić, Matej; Šmuc, Tomislav; Supek, Fran
Patterns of diverse gene functions in genomic neighborhoods predict gene function and phenotype // Scientific reports, 9 (2019), 1; 1-16 doi:10.1038/s41598-019-55984-0 (međunarodna recenzija, članak, znanstveni)


CROSBI ID: 1094876 Za ispravke kontaktirajte CROSBI podršku putem web obrasca

Naslov
Patterns of diverse gene functions in genomic neighborhoods predict gene function and phenotype

Autori
Mihelčić, Matej ; Šmuc, Tomislav ; Supek, Fran

Izvornik
Scientific reports (2045-2322) 9 (2019), 1; 1-16

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
Gene function prediction ; bacteria ; fungi ; metazoan ; gene neighborhoods

Sažetak
Genes with similar roles in the cell cluster on chromosomes, thus benefiting from coordinated regulation. This allows gene function to be inferred by transferring annotations from genomic neighbors, following the guilt-by- association principle. We performed a systematic search for co-occurrence of >1000 gene functions in genomic neighborhoods across 1669 prokaryotic, 49 fungal and 80 metazoan genomes, revealing prevalent patterns that cannot be explained by clustering of functionally similar genes. It is a very common occurrence that pairs of dissimilar gene functions – corresponding to semantically distant Gene Ontology terms – are significantly co-located on chromosomes. These neighborhood associations are often as conserved across genomes as the known associations between similar functions, suggesting selective benefits from clustering of certain diverse functions, which may conceivably play complementary roles in the cell. We propose a simple encoding of chromosomal gene order, the neighborhood function profiles (NFP), which draws on diverse gene clustering patterns to predict gene function and phenotype. NFPs yield a 26–46% increase in predictive power over state-of-the-art approaches that propagate function across neighborhoods, thus providing hundreds of novel, high-confidence gene function inferences per genome. Furthermore, we demonstrate that copy number-neutral structural variation that shapes gene function distribution across chromosomes can predict phenotype of individuals from their genome sequence.

Izvorni jezik
Engleski

Znanstvena područja
Biologija, Računarstvo



POVEZANOST RADA


Projekti:
EK-KF-KK.01.1.1.01.009 - Napredne metode i tehnologije u znanosti o podatcima i kooperativnim sustavima (DATACROSS) (Lončarić, Sven; Ivan, Petrović, EK - KK.01.1.1.01) ( POIROT)
IP-2013-11-9623 - Postupci strojnog učenja za dubinsku analizu složenih struktura podataka (DescriptiveInduction) (Gamberger, Dragan, HRZZ - 2013-11) ( POIROT)

Ustanove:
Prirodoslovno-matematički fakultet, Matematički odjel, Zagreb,
Institut "Ruđer Bošković", Zagreb,
Prirodoslovno-matematički fakultet, Zagreb

Profili:

Avatar Url Tomislav Šmuc (autor)

Avatar Url Fran Supek (autor)

Avatar Url Matej Mihelčić (autor)

Citiraj ovu publikaciju

Mihelčić, Matej; Šmuc, Tomislav; Supek, Fran
Patterns of diverse gene functions in genomic neighborhoods predict gene function and phenotype // Scientific reports, 9 (2019), 1; 1-16 doi:10.1038/s41598-019-55984-0 (međunarodna recenzija, članak, znanstveni)
Mihelčić, M., Šmuc, T. & Supek, F. (2019) Patterns of diverse gene functions in genomic neighborhoods predict gene function and phenotype. Scientific reports, 9 (1), 1-16 doi:10.1038/s41598-019-55984-0.
@article{article, year = {2019}, pages = {1-16}, DOI = {10.1038/s41598-019-55984-0}, keywords = {Gene function prediction, bacteria, fungi, metazoan, gene neighborhoods}, journal = {Scientific reports}, doi = {10.1038/s41598-019-55984-0}, volume = {9}, number = {1}, issn = {2045-2322}, title = {Patterns of diverse gene functions in genomic neighborhoods predict gene function and phenotype}, keyword = {Gene function prediction, bacteria, fungi, metazoan, gene neighborhoods} }
@article{article, year = {2019}, pages = {1-16}, DOI = {10.1038/s41598-019-55984-0}, keywords = {Gene function prediction, bacteria, fungi, metazoan, gene neighborhoods}, journal = {Scientific reports}, doi = {10.1038/s41598-019-55984-0}, volume = {9}, number = {1}, issn = {2045-2322}, title = {Patterns of diverse gene functions in genomic neighborhoods predict gene function and phenotype}, keyword = {Gene function prediction, bacteria, fungi, metazoan, gene neighborhoods} }

Časopis indeksira:


  • Current Contents Connect (CCC)
  • Web of Science Core Collection (WoSCC)
    • Science Citation Index Expanded (SCI-EXP)
    • SCI-EXP, SSCI i/ili A&HCI
  • Scopus
  • MEDLINE


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