GENIUS: web server to predict local gene networks and key genes for biological functions

Puelma, Tomas; Araus, Viviana; Canales, Javier; Vidal, Elena A.; Cabello, Juan M.; Soto, Álvaro; Gutiérrez, Rodrigo A.

doi:10.1093/bioinformatics/btw702

Cited by 2 publications

(2 citation statements)

References 15 publications

(17 reference statements)

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“…We deployed GENIUS (GEne Networks Inference Using Signatures) tool to predict local gene networks and key genes for biological functions [56]. The network was constructed using supervised machine learning method to find expression signatures.…”

Section: Methodsmentioning

confidence: 99%

Cisplatin treatment of testicular cancer patients introduces long-term changes in the epigenome

et al. 2019

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BackgroundCisplatin-based chemotherapy (CBCT) is part of standard treatment of several cancers. In testicular cancer (TC) survivors, an increased risk of developing metabolic syndrome (MetS) is observed. In this epigenome-wide association study, we investigated if CBCT relates to epigenetic changes (DNA methylation) and if epigenetic changes render individuals susceptible for developing MetS later in life. We analyzed methylation profiles, using the MethylationEPIC BeadChip, in samples collected ~ 16 years after treatment from 279 Norwegian TC survivors with known MetS status. Among the CBCT treated (n = 176) and non-treated (n = 103), 61 and 34 developed MetS, respectively. We used two linear regression models to identify if (i) CBCT results in epigenetic changes and (ii) epigenetic changes play a role in development of MetS. Then we investigated if these changes in (i) and (ii) links to genes, functional networks, and pathways related to MetS symptoms.ResultsWe identified 35 sites that were differentially methylated when comparing CBCT treated and untreated TC survivors. The PTK6–RAS–MAPk pathway was significantly enriched with these sites and infers a gene network of 13 genes with CACNA1D (involved in insulin release) as a network hub. We found nominal MetS-associations and a functional gene network with ABCG1 and NCF2 as network hubs.ConclusionOur results suggest that CBCT has long-term effects on the epigenome. We could not directly link the CBCT effects to the risk of developing MetS. Nevertheless, since we identified differential methylation occurring in genes associated with conditions pertaining to MetS, we hypothesize that epigenomic changes may also play a role in the development of MetS in TC survivors. Further studies are needed to validate this hypothesis.

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Section: Methodsmentioning

confidence: 99%

Cisplatin treatment of testicular cancer patients introduces long-term changes in the epigenome

et al. 2019

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“…Different methods (webservers) of gene prediction and alignment have been developed. These include, GENOMESCAN (Yeh et al, 2001), AUGUSTUS (Stanke et al, 2004), Open Reading Frame Finder (Wheeler et al, 2003), GENIUS (Puelma et al, 2017), GENEMARK (Lomsadze et al, 2018), GENESCAN (Burge, 1998), Unipro UGENE (Okonechnikoy et al, 2012), CLC workbench (www.qiagenbioinformatics.com/products/clc-mainworkbench) among others. Further, plant based bioinformatics tools and databases have been developed, for instance SOL genomics Network (for Solanaceous plants) (Mueller et al, 2005) and Phytozome (for land plants and algae) (Goodstein et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

In silico prediction and segregation analysis of putative virus defense genes based on SSR markers in sweet potato F1 progenies of cultivars New Kawogo and Resisto

Ssamula

Okiror

Avrahami-Moyal

et al. 2019

Afr. J. Biotechnol.

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In sweet potato, an anti-virus defense mechanism termed reversion has been postulated to lead to virus freedom from once infected plants. The objectives of this study were to identify anti-virus defense genes and evaluate their segregation in progenies. Reference genes from different plant species were used to assemble transcript sequences of each sweet potato defense gene in silico. Sequences were used for evaluate phylogenetic relationships with similar genes from different plant species, mining respective defense genes and thereafter developing simple sequence repeats (SSRs) for segregation analysis. Eight potential defense genes were identified: RNA dependent RNA polymerases 1, 2, 5, and 6; Argonaute 1, and Dicer-like 1, 2, and 4. Identified genes were differentially related to those of other plants and were observed on different chromosomes. The defense genes contained mono-, di-, tri-, tetra, penta-, and hexa-nucleotide repeat motifs. The SSR markers within progenies were segregated in disomic, co-segregation, nullisomic, monosomic, and trisomic modes. These findings indicate the possibility of deriving and utilizing SSRs using published genomic information. Furthermore, and given that the SSR markers were derived from known genes on defined chromosomes, this work will contribute to future molecular breeding and development of resistance gene analogs in this economically important crop.

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GENIUS: web server to predict local gene networks and key genes for biological functions

Cited by 2 publications

References 15 publications

Cisplatin treatment of testicular cancer patients introduces long-term changes in the epigenome

Cisplatin treatment of testicular cancer patients introduces long-term changes in the epigenome

In silico prediction and segregation analysis of putative virus defense genes based on SSR markers in sweet potato F1 progenies of cultivars New Kawogo and Resisto

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