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Table 1 Summary of the organization of the transcriptional changes

From: Transcriptional program for nitrogen starvation-induced lipid accumulation in Chlamydomonas reinhardtii

Stage Time Trend Dynamics Waves, modules, transcripts Functional highlights (corrected p value)
Early 0–18 min Up Monotonic 2, 7, 105 Ammonium transport (1.7e−9) Potassium ion transmembrane transport (1.4e−5) Ion channel activity (2.8e−3) Ion transport (3.4e−3) Protein kinase activity (1.3e−2)
Transient 2, 7, 118
Down Monotonic 1, 1, 17 Ribosome biogenesis (6.3e−8) Transcription (3.7e−6) rRNA processing (2.9e−5) Pseudouridine synthesis (7.0e−5) Methyltransferase activity (9.0e−5)
Transient 1, 17, 202
Mid 18–60 min Up Monotonic 4, 24, 304 Mitochondrial pyruvate transport (1.0e−6) Glutamine biosynthetic process (3.0e−5) Lipid metabolic process (5.2e−5) Amine metabolic process (7.5e−5) Proteolysis (9.6e−3)
Transient 3, 7, 110
Down Monotonic 4, 44, 552 Purine nucleotide biosynthetic process (5.1e−5) Fatty acid beta-oxidation (4.9e−4) Pseudouridine synthesis (8.7e−4) Malate dehydrogenase activity (1.6e−3) Fatty acid biosynthetic process (1.9e−3)
Transient 4, 15, 237
Late 1–8 h Up Monotonic 3, 12, 177 DNA replication (8.6e−7) Microtubule cytoskeleton organization (1.1e−4) NADP binding (3.5e−3) Lipid metabolic process (1.8e−2) Nucleotide binding (2.4e−2)
Transient 2, 8, 139
Down Monotonic 3, 47, 489 Photosynthesis (7.7e−31) Protein folding (1.0e−13) Fructose-bisphosphate aldolase activity (8.4e−6) Cell redox homeostasis (4.9e−5) Fatty acid biosynthetic process (7.5e−3)
Transient 2, 5, 95
  1. Transcriptional transition is organized within three time stages according to their temporal schedules. Transcripts are organized into co-regulated modules, which in turn are compiled into transcriptional waves. Selected significantly enriched functional categories (GO terms) are shown