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Table S1 List of genes upregulated (≥ twofold) after 30 min hypoxia (1% and 4% O2)

Table S2 List of genes upregulated after 2 h hypoxia (1% and 4% O2)

Table S3 List of genes downregulated after 30 min hypoxia (1% and 4% O2)

Table S4 List of genes downregulated after 2 h hypoxia (1% and 4% O2)

Table S5 6-Mer over-represented motif in the promoter of genes in Table  S1

Table S6 6-Mer over-represented motif in the promoter of genes in Table  S2

Table S7 6-Mer over-represented motif in the promoter of genes in Table  S3

Table S8 6-Mer over-represented motif in the promoter of genes in Table  S4

Table S9 Known DNA elements bound by transcription factors (TFs) in the promoter dataset (Tables  S1–S4)

Table S10 DNA binding element of the differentially expressed transcription factors (TFs) under hypoxia and its occurrence in the promoter regions of low oxygen responsive genes (Tables  S1, S2)

Table S11 Expression of the putative targets of differentially expressed microRNA primary transcripts (pri-miRNAs) in the TF dataset and previous microarray analyses

Table S12 Relative mRNA level of transcription factors (TFs) genes and microRNA primary transcripts (pri-miRNAs) in Arabidopsis roots under different hypoxic conditions

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