Additional file 4 of Transcript profiling of plastid ferrochelatase two mutants reveals that chloroplast singlet oxygen signals lead to global changes in RNA profiles and are mediated by Plant U-Box 4

Additional file 4: Supplemental information, Tables S9 through S26. Table S9. Microautophagy (putative) genes analyzed in this study, Table S10. Differentially expressed genes that are unique or shared among fc2 and fc2 pub4, Table S11. Gene Ontology term enrichment of DEGs associated with fc2 pub4 in constant light conditions, Table S12. Gene Ontology term enrichment of DEGs associated with fc2 pub4 in cycling light conditions, Table S13. Differentially Expressed Gene Lists with relaxed cutoffs, Table S14. Identification of differentially expressed transcription factors, Table S15. Quantification of differentially expressed transcription factors among the pairwise comparisons, Table S16. Enrichment analysis of differentially expressed transcription factors, Table S17. Gene ontology term enrichment analysis of differentially expressed transcription factors, Table S18. Transcription factor enrichment analysis of differentially expressed genes, Table S19. Enrichment analysis of transcription factors whose targets are represented in differentially expressed gene lists, Table S20. Comparison of transcription factors (TFs) identified in differentially expressed TF (DETF) and TF enrichment analysis (TFEA), Table S21. The differentially expressed plastid protein-encoding genes identified in the RNA-seq dataset, Table S22. Gene Ontology term enrichment of differentially expressed plastid protein-encoding genes, Table S23. Salicylic acid-related genes analyzed in this study, Table S24. Assessing the salicylic acid transcriptional response in fc2 pub4 mutants, Table S25. Jasmonic acid-related genes analyzed in this study, Table S26. Analysis of the response of senescence-related genes to singlet oxygen stress.