Gene set enrichment analysis and Protein domain analysis in LTR retrotransposon captured genes.

<p>(<b>A</b>) Gene set enrichment analysis in sorghum. Blue and red columns indicate the percentages of this GO term in all LTR captured sorghum proteins and in total annotated proteins, respectively. The percentage is calculated as the frequency of the total numbers of each GO term in all LTR captured proteins with GO term assigned or in all annotated proteins with GO term assigned. “P”, “F” and “C” in (<b>A</b>) indicate GO three categories biological process, molecular function and cellular component, respectively. GO term annotation in (<b>A</b>) was shown below: 1, DNA integration; 2, reproductive cellular process; 3, DNA metabolic process; 4, RNA-dependent DNA replication; 5, DNA replication; 6, multicellular organism reproduction; 7, reproductive process in a multicellular organism; 8, chromatin assembly or disassembly; 9, chromatin organization; 10, RNA-directed DNA polymerase activity; 11, DNA polymerase activity; 12, aspartic-type endopeptidase activity; 13, aspartic-type peptidase activity; 14, nucleotidyltransferase activity; 15, ribonuclease H activity; 16, endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5′-phosphomonoesters; 17, chromatin binding; 18, endoribonuclease activity, producing 5′-phosphomonoesters; 19, nucleic acid binding; 20, endopeptidase activity; 21, peptidase activity; 22, hydrolase activity; 23, di-, tri-valent inorganic cation transmembrane transporter activity; 24, endoribonuclease activity; 25, nuclease activity; 26, endonuclease activity; 27, ribonuclease activity; 28, peptidase activity, acting on L-amino acid peptides; 29, zinc ion transmembrane transporter activity; 30, chromosomal part; 31, chromatin. (<b>B</b>) and (<b>C</b>) Pfam domain/motif analysis in rice and sorghum, respectively. Green and pink columns indicate the percentages of this domain in the LTR captured protein and in total proteins, respectively. Commonly detected over- or under- represented domains in rice and sorghum are highlighted with pink lines. Two stars indicate statistically significant differences at P value <0.01. PF00067, oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen; PF00069, protein phosphorylation; PF00076, nucleic acid binding; PF00122, nucleotide binding; PF00201, transferase activity, transferring hexosyl groups; PF00385, ‘chromo’ (CHRromatin Organisation MOdifier) domain; PF00400, WD domain, G-beta repeat; PF00560, protein binding; PF00642, nucleic acid binding; PF00806, RNA binding; PF00931, apoptosis; PF01190, Pollen proteins Ole e I like; PF01535, PPR repeat; PF05754, Domain of unknown function (DUF834); PF07714, protein phosphorylation; PF11835, Domain of unknown function (DUF3355.