Table s11. Prominet sub-lattice analysis: the five largest atom and coatom sub-lattices with their objects and attributes are listed for the YHS dataset with 100 clusters annotated by the GO biological process category (p < 0.005).

1	The largest prominent sub-lattice has 16 nodes having 5 clusters, 8, 16, 63, 70, and 72, with 118 genes and 14 GO terms.
	biosynthesis macromolecule biosynthesis macromolecule metabolism metabolism protein biosynthesis protein metabolism regulation of protein biosynthesis regulation of translation regulation of translational fidelity ribosomal small subunit assembly and maintenance ribosomal subunit assembly ribosome assembly ribosome biogenesis and assembly translation
2	The second largest sub-lattice has 13 nodes having 4 clusters, 7, 8, 16, and 63, with 79 genes and 10 GO terms.
	biosynthesis macromolecule biosynthesis macromolecule metabolism negative regulation of translation protein biosynthesis protein metabolism regulation of biosynthesis regulation of protein biosynthesis regulation of translation translation
3	The third largest sub-lattice has 13 nodes having 4 clusters, 8, 16, 63, and 84, with 72 genes and 9 GO terms.
	biosynthesis macromolecule biosynthesis macromolecule metabolism protein biosynthesis protein metabolism translation translational initiation
4	The fourth sub-lattice has 12 nodes having 2 clusters, 67, and 78, with 143 genes and 23 GO terms.
	SRP dependent cotranslational membrane targeting translocation alcohol biosynthesis alcohol metabolism carbohydrate metabolism catabolism citrate metabolism energy derivation by oxidation of organic compounds energy pathways gluconeogenesis glucose metabolism glutamate biosynthesis glutamate metabolism glutamine family amino acid biosynthesis glutamine family amino acid metabolism hexose biosynthesis hexose metabolism macromolecule metabolism main pathways of carbohydrate metabolism monosaccharide biosynthesis monosaccharide metabolism posttranslational protein folding protein catabolism protein folding response to stimulus response to stress trehalose catabolism tricarboxylic acid cycle tricarboxylic acid cycle intermediate metabolism vacuolar protein catabolism
5	The fifth sub-lattice has 11 nodes having 3 clusters, 31, 64, and 98, with 87 genes and 17 GO terms.
	35S primary transcript processing RNA metabolism RNA processing aromatic compound metabolism cell growth and/or maintenance cell organization and biogenesis cytoplasm organization and biogenesis host pathogen interaction nucleobase nucleoside nucleotide and nucleic acid metabolism processing of 20S pre rRNA rRNA metabolism rRNA modification rRNA processing ribosomal large subunit biogenesis ribosome biogenesis ribosome biogenesis and assembly transcription from Pol I promoter