Table II. GO categories significantly enriched in differentially regulated C. reinhardtii genes
GOAnnotationGO RaNo GO RbGO UcNo GO UdRegePfqg
GO:0006270 bphDNA replication initiation992606,633Down6.48 × 10−094.51 × 10−06
GO:0015995 bpChlorophyll biosynthetic process892706,633Down5.29 × 10−082.76 × 10−05
GO:0033014 bpTetrapyrrole biosynthetic process692906,633Down3.51 × 10−067.32 × 10−04
GO:0009765 bpPhotosynthesis, light harvesting22913146,619Down5.72 × 10−125.98 × 10−09
GO:0015979 bpPhotosynthesis2391206,633Down1.02 × 10−212.13 × 10−18
GO:0005576 cciExtracellular region11924146,619Down8.28 × 10−051.44 × 10−02
GO:0009522 ccPSI493106,633Down2.32 × 10−043.23 × 10−02
GO:0009538 ccPSI reaction center593006,633Down2.85 × 10−055.42 × 10−03
GO:0009654 ccOxygen-evolving complex692906,633Down3.51 × 10−067.32 × 10−04
GO:0019898 ccExtrinsic to membrane493106,633Down2.32 × 10−043.23 × 10−02
GO:0003755 mfjPeptidyl-prolyl cis-trans-isomerase activity21914326,601Down4.39 × 10−071.83 × 10−04
GO:0004600 mfCyclophilin19916306,603Down2.29 × 10−065.98 × 10−04
GO:0016851 mfMagnesium chelatase activity493106,633Down2.32 × 10−043.23 × 10−02
GO:0030051 mfFK506-sensitive peptidyl-prolyl cis-trans-isomerase19916306,603Down2.29 × 10−065.98 × 10−04
GO:0042027 mfCyclophilin-type peptidyl-prolyl cis-trans-isomerase activity19916306,603Down2.29 × 10−065.98 × 10−04
GO:0006006 bpGlc metabolic process594416,618Up1.65 × 10−043.83 × 10−02
GO:0006468 bpProtein amino acid phosphorylation1178325016,118Up2.37 × 10−062.47 × 10−03
GO:0006629 bpLipid metabolic process18931386,581Up9.92 × 10−052.59 × 10−02
GO:0004672 mfProtein kinase activity1138364796,140Up2.08 × 10−062.47 × 10−03
GO:0004713 mfProtein-Tyr kinase activity858643426,277Up8.04 × 10−064.20 × 10−03
GO:0004674 mfProtein Ser/Thr kinase activity928573916,228Up2.50 × 10−057.46 × 10−03
  • a GO R, Number of significantly up- or down-regulated (R) genes with the GO annotation in question.

  • b No GO R, Number of significantly up- or down-regulated genes without the GO annotation.

  • c GO U, Number of genes without significant expression change with the GO annotation.

  • d No GO U, Number of genes with no significant expression change that do not have the GO annotation.

  • e Reg, Direction of regulation (N deprived compared with N replete).

  • f Fisher’s exact test P value.

  • g The q value is calculated using the R package q value.

  • h bp, Biological process.

  • i cc, Cellular component.

  • j mf, Molecular function.