TABLE 2.
Overview of differential expression patterns based on gene functional categories
| Gene category (no. of genes) | No. of genes differentially expresseda (increased/decreased)
|
|||
|---|---|---|---|---|
| Bacteroid vs TY | Bacteroid vs MMO | MMO vs TY | Naringenin addition vs no addition | |
| Amino acid biosynthesis (132) | 15/19 | 15/20 | 14/6 | 1/0 |
| Cofactor, prosthetic group, and carrier biosynthesis (159) | 22/34 | 18/22 | 21/14 | 0/2 |
| Cell envelope (174) | 17/54 | 15/48 | 29/9 | 0/4 |
| Cellular process (200) | 17/45 | 45/23 | 13/58 | 0/0 |
| Central intermediary metabolism (161) | 71/18 | 62/16 | 25/16 | 1/0 |
| Energy metabolism (303) | 49/45 | 53/28 | 24/51 | 0/0 |
| Fatty acid, phospholipid, and sterol metabolism (136) | 14/35 | 15/20 | 16/13 | 0/0 |
| Purine, pyrimidine, nucleoside, and nucleotide (66) | 2/13 | 3/11 | 7/8 | 0/0 |
| Regulatory function (384) | 31/70 | 26/61 | 29/21 | 0/1 |
| DNA replication, recombination, and repair (79) | 7/1 | 4/17 | 5/2 | 0/0 |
| Transcription (49) | 8/5 | 6/4 | 5/2 | 1/0 |
| Signal transduction (39) | 1/9 | 2/7 | 2/4 | 0/0 |
| Translation (227) | 22/60 | 24/29 | 20/27 | 0/0 |
| Transport and binding protein (714) | 49/186 | 66/114 | 59/82 | 1/4 |
| Other categories (765) | 87/143 | 75/90 | 59/75 | 13/2 |
| Hypothetical protein (954) | 145/144 | 122/153 | 115/79 | 1/1 |
| Unknown protein (175) | 25/28 | 22/30 | 23/10 | 0/0 |
| Total (4,717) | 582/919 | 573/693 | 466/477 | 18/14 |
a
A differentially expressed gene has a log2 signal with a P value of ≤0.05 (Student's t test) and a |WAD| of ≥0.5.