Additional file 10: Figure S6. of Stress-responsive pathways and small RNA changes distinguish variable developmental phenotypes caused by MSH1 loss

Comparison of transcriptome changes of several organelle mutants and chemical treatments, against biological processes enriched in msh1 -/- S2 variegated & dwarf plants. Samples are arranged from left to right according to assay type (microarray or RNA-seq) and number of shared enriched categories with msh1. For RNA-seq of public data sets, differentially expressed genes were called using DESeq2. To reduce the otherwise very large number of GO enriched categories, only mappings directly annotated by the source database were used (“GO DIRECT”). Only mutants or treatments with at least 4 enriched GO DIRECT categories in common with msh1 kept retained for analysis. Data were obtained from sources and studies listed in Additional file 7. (PDF 697 kb)