GOAtools

[…] change ≥1 (log2fc ≥1). degs were subsequently mapped to the database for pathway enrichment analysis []., in addition, the go and kegg enrichment analysis of degs were approved using the software goatools (https://github.com/tanghaibao/goatools) [, ] and kobas (http://kobas.cbi.pku.edu.cn/home.do) [] with the p-value< 0.05., the transcription factors in the transcriptome of c. officinalis […]

[…] domains in amino acid sequences were predicted using interpro scan version 5.17-56.0 (), which was also used to retrieve gene ontology (go) () terms. go terms were mapped to “go-slim” terms using goatools version 0.5.9 (available at https://libraries.io/github/tanghair/goatools)., putative effector prediction was carried out using the following pipeline: 1) signalp version 4.1 () was used […]

[…] metabolic pathways. a bonferroni-corrected p value of ≤0.05 was used for comparison with the whole-transcriptome background. kegg pathway and go functional enrichment analyses were performed with goatools (https://github.com/tanghaibao/goatools) and kobas (http://kobas.cbi.pku.edu.cn/home.do). the significantly enriched pathways among organs were analyzed according to wang et al. ., total rna […]

[…] (https://bioconductor.org/packages/release/bioc/html/edger.html). to study the functions of the differentially expressed genes, go functional enrichment and kegg pathway analysis were carried out by goatools (https://github.com/tanghaibao/goatools) and kobas (http://kobas.cbi.pku.edu.cn/home.do) respectively. gene expression changes higher than 2-fold with p-values less than 0.05 were regarded […]

[…] non-redundant (nr), swiss-prot, kyoto encyclopedia of genes and genome (kegg), and cluster of orthologous groups (cog) protein databases. go functional enrichment analyses were carried out using goatools and kobas (xie et al., ). degs were significantly enriched in go terms and metabolic pathways at bonferroni-corrected p-values of < 0.05., to validate of the reliability of transcriptome […]

[…] of zebrafish coding-gene was downloaded from gene ontology consortium (only biological process annotations were considered). while, go annotation of zebrafish lncrna was predicted using the goatools (version 0.6.4) [], which determines the go annotation of one gene in our network according to the go annotations of its immediate neighbor genes (p-value < 0.05)., the kegg annotation […]

[…] (go:0007165), metabolic process (go:0008152) and transmembrane transport (go:0055085).fig. 5, to investigate enrichment and purification (under-representation) of strs in go terms, we used goatools., [] (fig. , additional file : figure s2). we corrected for multiple testing. for some terms, both cod and haddock are enriched, whereas this is not the case in the other species. […]

[…] []. the p-values of degs were corrected by benjamini–hochberg fdr (false discovery rate) correction []. the over-representation of go terms and kegg pathways of degs were identified using the goatools (https://github.com/tanghaibao/goatools) and r go package [] respectively. the p-value of the enriched analyses was corrected by the fdr method., to verify the expression levels of tobacco […]

[…] to classify the degs. pathway analysis was performed using the kyoto encyclopedia of genes and genomes (kegg) database []. the enrichment analyses of go terms and kegg pathways were performed using goatools [] and kobas [] based on fisher’s exact test, respectively. multiple corrections including bonferroni, holm, sidak, and false discovery rate were used for correcting the p-value as described […]

[…] rate (fdr) was selected as the key index for screening degs. in this study, the fdr was <0.01, and the fold-change was ≥3., gene ontology (go) is a functional annotation of the degs. using the goatools software (https://github.com/tanghaibao/goatool) for feature enrichment, significant enrichment was observed when the fdr was <0.05. cog classification of degs from various groups […]