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Table 2 Functional clustering of genes derived using the DAVID gene functional classification tool

From: Transcriptome profile analysis reflects rat liver and kidney damage following chronic ultra-low dose Roundup exposure

ES Term in DAVID n p value FE q-value
4.2 GO:0010558 ~ negative regulation of macromolecule biosynthetic process 40 3.7E-05 2.0 7.9E-3
GO:0031327 ~ negative regulation of cellular biosynthetic process 40 6.0E-05 2.0 1.1E-2
GO:0009890 ~ negative regulation of biosynthetic process 40 9.3E-05 1.9 1.6E-2
3.8 GO:0016279 ~ protein-lysine N-methyltransferase activity 7 5.0E-05 9.7 5.1E-3
GO:0016278 ~ lysine N-methyltransferase activity 7 5.0E-05 9.7 5.1E-3
GO:0018024 ~ histone-lysine N-methyltransferase activity 7 5.0E-05 9.7 5.1E-3
GO:0042054 ~ histone methyltransferase activity 7 3.0E-04 7.2 2.3E-2
GO:0008276 ~ protein methyltransferase activity 7 2.5E-03 5.0 7.7E-2
3.3 GO:0000377 ~ RNA splicing, via transesterification reactions with bulged adenosine as nucleophile 15 4.8E-04 3.0 6.0E-2
GO:0000375 ~ RNA splicing, via transesterification reactions 15 4.8E-04 3.0 6.0E-2
GO:0000398 ~ nuclear mRNA splicing, via spliceosome 15 4.8E-04 3.0 6.0E-2
3.3 IPR000504:RNA recognition motif, RNP-1 17 4.0E-04 2.8 3.1E-1
SM00360:RRM 17 5.1E-04 2.7 9.8E-2
IPR012677:Nucleotide-binding, alpha-beta plait 17 6.1E-04 2.7 2.5E-1
2.3 GO:0006099 ~ tricarboxylic acid cycle 6 1.7E-03 6.6 1.5E-1
GO:0046356 ~ acetyl-CoA catabolic process 6 2.1E-03 6.3 1.7E-1
GO:0009109 ~ coenzyme catabolic process 6 3.7E-03 5.6 2.3E-1
GO:0009060 ~ aerobic respiration 6 4.4E-03 5.4 2.5E-1
GO:0051187 ~ cofactor catabolic process 6 8.1E-03 4.7 3.4E-1
rno00020:Citrate cycle (TCA cycle) 6 9.2E-03 4.5 1.7E-1
GO:0006084 ~ acetyl-CoA metabolic process 6 1.9E-02 3.8 4.7E-1
2.2 GO:0030964 ~ NADH dehydrogenase complex 5 3.7E-03 7.5 7.1E-2
GO:0045271 ~ respiratory chain complex I 5 3.7E-03 7.5 7.1E-2
GO:0005747 ~ mitochondrial respiratory chain complex I 5 3.7E-03 7.5 7.1E-2
GO:0005746 ~ mitochondrial respiratory chain 5 4.3E-02 3.7 3.1E-1
2.1 GO:0016571 ~ histone methylation 6 1.4E-03 6.9 1.3E-1
GO:0008213 ~ protein amino acid alkylation 6 1.9E-02 3.8 4.7E-1
GO:0006479 ~ protein amino acid methylation 6 1.9E-02 3.8 4.7E-1
2.1 IPR001440:Tetratricopeptide TPR-1 9 4.5E-03 3.4 5.8E-1
IPR019734:Tetratricopeptide repeat 9 1.0E-02 2.9 7.2E-1
SM00028:TPR 9 1.2E-02 2.8 5.7E-1
  1. The rat genome was used as a background list to calculate the p-values of each term. A total of 868 genes were recognised. The p-values were calculated according to a modified Fisher’s exact test (EASE score). The q-values were calculated according to the Benjamini-Hochberg method. Cluster enrichment scores (ES) and fold enrichment (FE) rank overall importance (enrichment) of gene groups or the statistically most overrepresented (enriched) biological annotations. The highest classification stringency was used