Table 4 Integrated overview of DEGs GO terms and KEGG pathways with DAMs, consolidated as jointly altered pathways. Numbers in parentheses denote the count of differentially expressed genes.
Comparison | Correlation networks comprising DEGs and DAMs | Joint pathway | ||
|---|---|---|---|---|
DEGs - GO terms (matched) | DEGs - KEGG enrichment pathways (matched) | DAMs | ||
SI vs. Apex | Tricarboxylic acid cycle (12), aerobic respiration (12), glyoxylate cycle (3) | Carbon metabolism (90), Citrate cycle (TCA cycle) (21) | Succinic.acid, Aconitic.acid.cis., Malic.acid.2.methyl. Fumaric acid, Isocitric acid | TCA/Respiration |
SI vs. Apex | carbohydrate metabolic process (241), cell wall organization or biogenesis (102), carbohydrate catabolic process (62) | Starch and sucrose metabolism (55) | Erythronic.acid, Threonic.acid, Fucose | Carbohydrates/Cell wall |
SI vs. Apex | No significant enrichment | No significant enrichment | Phenylalanine | Phenylpropanoid/Lignin |
SI vs. Apex | cutin biosynthetic process (8), cutin-based cuticle development (6) | Fatty acid metabolism (30), Fatty acid biosynthesis (18) | No differentiation in stage | Fatty acids/Lipids |
SII vs. SI | Glyoxylate cycle (2), glyoxylate metabolic process (2) | No significant enrichment | Succinic.acid | TCA/Respiration |
SII vs. SI | Trehalose biosynthetic process (7), carbohydrate metabolic process (69), cell wall organization (22) | Starch and sucrose metabolism (21) | Lyxonic.acid, Threonic.acid, Gluconic.acid | Carbohydrates/Cell wall |
SII vs. SI | No significant enrichment | Phenylpropanoid biosynthesis (15) | No differentiation in stage | Phenylpropanoid/Lignin |
SII vs. SI | No significant enrichment | Linoleic acid metabolism (6), alpha-Linolenic acid metabolism (8) | No differentiation in stage | Fatty acids/Lipids |
SIII vs. SII | tricarboxylic acid cycle(13) | Citrate cycle (TCA cycle)(19), Carbon metabolism (48), Glyoxylate and dicarboxylate metabolism (15) | No differentiation in stage | TCA/Respiration |
SIII vs. SII | carbohydrate metabolic process (165), cell wall modification (25), pectin catabolic process (52) | Pentose and glucuronate interconversions (38), Starch and sucrose metabolism (36), Amino sugar and nucleotide sugar metabolism (25) | Gluconic.acid, Glyceric.acid, Lyxonic.acid | Carbohydrates/Cell wall |
SIII vs. SII | lignin catabolic process (6), lignin biosynthetic process (9) | No significant enrichment | Tyramine | Phenylpropanoid/Lignin |
SIII vs. SII | fatty acid oxidation (7), fatty acid beta-oxidation (6), fatty acid catabolic process(6) | Cutin, suberine and wax biosynthesis (10), alpha-Linolenic acid metabolism (13), Fatty acid degradation (11) | No differentiation in stage | Fatty acids/Lipids |
SIV vs. SIII | No significant enrichment | No significant enrichment | Succinic.acid, Aconitic.acid.cis. | TCA/Respiration |
SIV vs. SIII | carbohydrate metabolic process (28), plant-type cell wall biogenesis (6), plant-type secondary cell wall biogenesis (4) | No significant enrichment | Threonic.acid, Erythronic.acid, Glucopyranose | Carbohydrates/Cell wall |
SIV vs SIII | lignin catabolic process (4) | Phenylpropanoid biosynthesis (9) | Tyramine | Phenylpropanoid/Lignin |
