From algae to crops: tracing gene regulatory elements in plant genomes with GOLEM
Identifikátory výsledku
Kód výsledku v IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F25%3A00143976" target="_blank" >RIV/00216224:14740/25:00143976 - isvavai.cz</a>
Výsledek na webu
<a href="https://www.efbiotechnology.org/g4g/=Green_for_Good_G4G_IV" target="_blank" >https://www.efbiotechnology.org/g4g/=Green_for_Good_G4G_IV</a>
DOI - Digital Object Identifier
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Alternativní jazyky
Jazyk výsledku
angličtina
Název v původním jazyce
From algae to crops: tracing gene regulatory elements in plant genomes with GOLEM
Popis výsledku v původním jazyce
The regulation of gene expression in plants relies heavily on cis-regulatory elements (CREs) within gene promoters, which control transcription initiation and gene activity across tissues and developmental stages. GOLEM (Gene regulatOry eLEMents; https://golem.ncbr.muni.cz) is a user-friendly tool developed developed to visualize the precise localization and distribution of CREs relative to transcription start sites (TSS) and translation start codons (ATG) across a wide range of plant genomes. Covering species from streptophyte algae, mosses, ferns, basal angiosperms, monocots, and dicots, including several crop plants, GOLEM integrates transcriptomic data to highlight motifs in genes with high expression in specific tissues, such as leaves and male reproductive structures. We demonstrate GOLEM's utility through the analysis of motifs involved in male gametophyte development, hormone responses, and conserved regulatory elements. GOLEM enables motif visualization in relation to gene transcript levels in leaves and reproductive tissues while also allowing comparison with genome-wide distributions independent of transcription levels. Furthermore, users can export lists of genes containing specific CREs at defined positions for further analysis.
Název v anglickém jazyce
From algae to crops: tracing gene regulatory elements in plant genomes with GOLEM
Popis výsledku anglicky
The regulation of gene expression in plants relies heavily on cis-regulatory elements (CREs) within gene promoters, which control transcription initiation and gene activity across tissues and developmental stages. GOLEM (Gene regulatOry eLEMents; https://golem.ncbr.muni.cz) is a user-friendly tool developed developed to visualize the precise localization and distribution of CREs relative to transcription start sites (TSS) and translation start codons (ATG) across a wide range of plant genomes. Covering species from streptophyte algae, mosses, ferns, basal angiosperms, monocots, and dicots, including several crop plants, GOLEM integrates transcriptomic data to highlight motifs in genes with high expression in specific tissues, such as leaves and male reproductive structures. We demonstrate GOLEM's utility through the analysis of motifs involved in male gametophyte development, hormone responses, and conserved regulatory elements. GOLEM enables motif visualization in relation to gene transcript levels in leaves and reproductive tissues while also allowing comparison with genome-wide distributions independent of transcription levels. Furthermore, users can export lists of genes containing specific CREs at defined positions for further analysis.
Klasifikace
Druh
O - Ostatní výsledky
CEP obor
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OECD FORD obor
10611 - Plant sciences, botany
Návaznosti výsledku
Projekt
<a href="/cs/project/EH22_008%2F0004581" target="_blank" >EH22_008/0004581: Nové poznatky pro plodiny nové generace</a><br>
Návaznosti
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Ostatní
Rok uplatnění
2025
Kód důvěrnosti údajů
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů