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Table 1 Overview of the differential expression patterns based on gene function categoriesa

From: Loss of malic enzymes leads to metabolic imbalance and altered levels of trehalose and putrescine in the bacterium Sinorhizobium meliloti

Gene category No. of genes significantly regulatedb (increased/decreased)
Glucose vs succinate (wt)c dme vs wt (succinate)d tme vs wt (succinate)e dme vs wt (glucose)f tme vs wt (glucose)g
Amino acid metabolism 3/0 17/0 4/0 3/2 2/0
Cofactor and vitamin metabolism 3/0 12/0 1/0 0/0 0/0
Fatty acid, ester, and phospholipid 1/1 4/0 2/0 0/0 1/0
Carbohydrate metabolism 13/3 13/0 2/0 0/0 0/0
Purine, pyrimidine, and nucleotide 0/1 1/0 3/0 1/0 1/1
Regulatory function 7/0 3/0 2/3 3/1 1/1
DNA replication and repair 1/1 4/0 1/1 0/0 0/1
Transport system 16/5 54/0 9/0 3/5 3/5
Energy metabolism 2/2 17/0 8/0 0/3 2/3
Other categories 4/3 7/3 3/2 2/2 5/0
Hypothetical protein 14/31 47/16 21/8 11/4 12/8
Total (6269) 64/47 179/19 56/14 23/17 27/19
  1. aThe complete list of differentially regulated genes can be found in Additional file 1: Tables S3–S6
  2. bGenes significantly regulated have a fold change of ≥ 3 and a P-value (Student’s t test) of ≤ 0.05
  3. cComparing S. meliloti wild type grown in glucose and succinate
  4. dComparing dme mutant & wild type grown in succinate (includes smb20178 and smb2080 Additional file 1: Table S2)
  5. eComparing tme mutant and wild type grown in succinate
  6. fComparing dme mutant and wild type grown in glucose
  7. gComparing tme mutant and wild type grown in glucose