Meta-analysis of RNA Sequencing Data of Arabidopsis and Rice under Hypoxia

file1a,b: Metadata of the RNA-Seq experiments used for meta-analysis. (a) Arabidopsis, (b) rice. file2a,b: TPM values of the RNA-Seq experiments. (a) Arabidopsis, (b) rice. file3a,b: HN-ratio of the RNA-Seq experiments. (a) Arabidopsis, (b) rice. file4a,b: HN-score of the transcripts in each species. (a) Arabidopsis, (b) rice. The suffixes indicate At (<em>Arabidopsis thaliana</em>), Os (<em>Oryza sativa</em>), and Hs (<em>Homo sapiens</em>). file5a–d: HN-score of the hypoxia-inducible transcripts in each species. (a) Arabidopsis upregulated, (b) rice upregulated, (c) Arabidopsis downregulated, (d) rice downregulated. Columns with gene ontology (GO) names indicate annotation of the enrichment analysis in Metascape. 1 is having the annotation, and 0 is not having the annotation. file6a,b: HN-score of the genes related to general phenylpropanoid pathway. (a) Arabidopsis, (b) rice. file7: Gene set enrichment analysis of hypoxia-inducible genes in Arabidopsis when hypoxic treatments and submergence treatments were analyzed separately. file8: Gene set enrichment analysis of hypoxia-inducible upregulated genes with GO Molecular Functions (MF) or GO Cellular Components (CC). (a) Arabidopsis MF, (b) Arabidopsis CC, (c) rice MF, (d) rice CC. file9: Gene set enrichment analysis of hypoxia-inducible downregulated genes with GO Molecular Functions (MF) or GO Cellular Components (CC). (a) Arabidopsis MF, (b) Arabidopsis CC, (c) rice MF, (d) rice CC. file10: Protein–protein interaction network of the (a) commonly upregulated 40 genes and (b) commonly downregulated 19 genes analyzed by STRING. Differently colored lines represent seven types of evidence used in predicting the associations: Red, fusion evidence; Green, neighborhood evidence; Blue, cooccurrence evidence; Purple, experimental evidence; Yellow, textmining evidence; Light blue, database evidence; Black, coexpression evidence. file 11: Analysis of swapped pairs of biolocigal replicates.