Table s3. Prominet sub-lattice analysis: the five largest atom and coatom sub-lattices with their objects and attributes are listed for the HCDC dataset with 100 clusters annotated by the GO biolocal process category (p < 0.01).

1	The largest prominent sub-lattice has 21 nodes having 2 clusters, 24, and 46, with 17 genes and 22 GO terms.
	DNA dependent DNA replication DNA metabolism DNA repair DNA replication DNA replication and chromosome cycle G1 phase of mitotic cell cycle cell cycle cell cycle checkpoint cell proliferation cellular physiological process negative regulation of metabolism negative regulation of nucleobase nucleoside nucleotide and nucleic acid metabolism nucleobase nucleoside nucleotide and nucleic acid metabolism regulation of DNA metabolism regulation of DNA replication regulation of cell cycle regulation of metabolism regulation of nucleobase nucleoside nucleotide and nucleic acid metabolism regulation of physiological process response to DNA damage stimulus response to endogenous stimulus response to stress
2	The second largest sub-lattice has 17 nodes having 4 clusters, 28, 46, 50, and 60, with 62 genes and 17 GO terms.
	DNA dependent DNA replication DNA metabolism DNA replication DNA replication and chromosome cycle DNA replication initiation cell cycle cell proliferation nucleobase nucleoside nucleotide and nucleic acid metabolism regulation of biological process regulation of cell cycle regulation of metabolism regulation of nucleobase nucleoside nucleotide and nucleic acid metabolism regulation of physiological process regulation of transcription regulation of transcription DNA dependent transcription transcription DNA dependent
3	The third largest sub-lattice has 14 nodes having 2 clusters, 13, and 84, with 27 genes and 21 GO terms.
	anti apoptosis apoptosis calcium ion homeostasis cell death chemotaxis death humoral immune response programmed cell death regulation of apoptosis regulation of cellular process regulation of programmed cell death response to bacteria response to external biotic stimulus response to pathogen response to pathogenic bacteria response to pest pathogen or parasite response to stress taxis viral genome replication viral infectious cycle viral life cycle
4	The fourth sub-lattice has 14 nodes having 2 clusters, 46, and 74, with 18 genes and 14 GO terms.
	DNA dependent DNA replication DNA metabolism DNA packaging DNA repair DNA replication DNA replication and chromosome cycle cell cycle cell proliferation cellular physiological process establishment and/or maintenance of chromatin architecture nucleobase nucleoside nucleotide and nucleic acid metabolism regulation of DNA metabolism response to DNA damage stimulus response to endogenous stimulus
5	The fifth sub-lattice has 13 nodes having 2 clusters, 9, and 26, with 33 genes and 10 GO terms.
	M phase M phase of mitotic cell cycle cell cycle cell proliferation cellular physiological process mitosis mitotic cell cycle nuclear division protein modification regulation of cell cycle