Table s5. Prominent 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 pathway information (p < 0.05).

[BC : BioCarta term, GM : GenMAPP term, KG : KEGG term, PG : PharmGKB term]

1	The largest prominent sub-lattice has 13 nodes having 3 clusters, 22, 26, and 43, with 20 genes and 16 pathways.
	BC_AKAP95_role_in_mitosis_and_chromosome_dynamics BC_Activation_of_Src_by_Protein_tyrosine_phosphatase_alpha BC_Apoptotic_DNA_fragmentation_and_tissue_homeostasis BC_Cell_Cycle_G1_S_Check_Point BC_Cell_Cycle_G2_M_Checkpoint BC_Cyclins_and_Cell_Cycle_Regulation BC_Estrogen_responsive_protein_Efp_controls_cell_cycle_and_breast_tumors_growth BC_How_Progesterone_Initiates_the_Oocyte_Maturation BC_Protein_Kinase_A_at_the_Centrosome BC_RB_Tumor_Suppressor_Checkpoint_Signaling_in_response_to_DNA_damage BC_Role_of_Ran_in_mitotic_spindle_regulation BC_Sonic_Hedgehog_SHH_Receptor_Ptc1_Regulates_cell_cycle BC_Sonic_Hedgehog_Shh_Pathway BC_Stathmin_and_breast_cancer_resistance_to_antimicrotubule_agents BC_cdc25_and_chk1_Regulatory_Pathway_in_response_to_DNA_damage GM_Cell_Cycle
2	The second largest sub-lattice has 10 nodes having 1 cluster, 63, with 18 genes and 29 pathways.
	BC_ATM_Signaling_Pathway BC_Angiotensin_II_mediated_activation_of_JNK_Pathway_via_Pyk2_dependent_signaling BC_BCR_Signaling_Pathway BC_Bioactive_Peptide_Induced_Signaling_Pathway BC_EGF_Signaling_Pathway BC_EPO_Signaling_Pathway BC_Erk1_Erk2_Mapk_Signaling_pathway BC_Fc_Epsilon_Receptor_I_Signaling_in_Mast_Cells BC_IGF_1_Signaling_Pathway BC_IL_2_signaling_pathway BC_Influence_of_Ras_and_Rho_proteins_on_G1_to_S_Transition BC_Inhibition_of_Cellular_Proliferation_by_Gleevec BC_Insulin_Signaling_Pathway BC_Integrin_Signaling_Pathway BC_Keratinocyte_Differentiation BC_Links_between_Pyk2_and_Map_Kinases BC_NFAT_and_Hypertrophy_of_the_heart_Transcription_in_the_broken_heart_ BC_Nerve_growth_factor_pathway_NGF_ BC_PDGF_Signaling_Pathway BC_Phosphorylation_of_MEK1_by_cdk5_p35_down_regulates_the_MAP_kinase_pathway_ BC_Role_of_EGF_Receptor_Transactivation_by_GPCRs_in_Cardiac_Hypertrophy BC_Role_of_MAL_in_Rho_Mediated_Activation_of_SRF BC_Signaling_Pathway_from_G_Protein_Families BC_Signaling_of_Hepatocyte_Growth_Factor_Receptor BC_Sprouty_regulation_of_tyrosine_kinase_signals BC_T_Cell_Receptor_Signaling_Pathway BC_Trka_Receptor_Signaling_Pathway BC_fMLP_induced_chemokine_gene_expression_in_HMC_1_cells BC_mCalpain_and_friends_in_Cell_motility
4	The fourth sub-lattice has 9 nodes having 2 clusters, 57, and 69, with 5 genes and 11 pathways.
	BC_ATM_Signaling_Pathway BC_Cell_Cycle_G1_S_Check_Point BC_Cell_Cycle_G2_M_Checkpoint BC_Cyclins_and_Cell_Cycle_Regulation BC_Effects_of_calcineurin_in_Keratinocyte_Differentiation BC_GATA3_participate_in_activating_the_Th2_cytokine_genes_expression BC_Hypoxia_and_p53_in_the_Cardiovascular_system BC_IL12_and_Stat4_Dependent_Signaling_Pathway_in_Th1_Development BC_Influence_of_Ras_and_Rho_proteins_on_G1_to_S_Transition KG_Alanine_and_aspartate_metabolism KG_Nitrogen_metabolism
3	The third largest sub-lattice has 9 nodes having 1 cluster, 11, with 15 genes and 24 pathways.
	BC_Angiotensin_II_mediated_activation_of_JNK_Pathway_via_Pyk2_dependent_signaling BC_BCR_Signaling_Pathway BC_Ceramide_Signaling_Pathway BC_EGF_Signaling_Pathway BC_FAS_signaling_pathway_CD95 BC_Fc_Epsilon_Receptor_I_Signaling_in_Mast_Cells BC_HIV_I_Nef_negative_effector_of_Fas_and_TNF BC_Inhibition_of_Cellular_Proliferation_by_Gleevec BC_Integrin_Signaling_Pathway BC_Keratinocyte_Differentiation BC_Links_between_Pyk2_and_Map_Kinases BC_MAPKinase_Signaling_Pathway BC_PDGF_Signaling_Pathway BC_Role_of_MAL_in_Rho_Mediated_Activation_of_SRF BC_Signal_transduction_through_IL1R BC_TNFR1_Signaling_Pathway BC_TNF_Stress_Related_Signaling BC_T_Cell_Receptor_Signaling_Pathway BC_The_4_1BB_dependent_immune_response BC_Toll_Like_Receptor_Pathway BC_p38_MAPK_Signaling_Pathway GM_Apoptosis GM_G13_Signaling_Pathway GM_MAPK_Cascade
5	The fifth sub-lattice has 8 nodes having 2 clusters, 69, and 93, with 16 genes and 23 pathways.
	BC_Actions_of_Nitric_Oxide_in_the_Heart BC_Activation_of_Csk_by_cAMP_dependent_Protein_Kinase_Inhibits_Signaling_through_the_T_Cell_Receptor BC_Activation_of_cAMP_dependent_protein_kinase_PKA BC_Attenuation_of_GPCR_Signaling BC_ChREBP_regulation_by_carbohydrates_and_cAMP BC_Cycling_of_Ran_in_nucleocytoplasmic_transport BC_Cystic_fibrosis_transmembrane_conductance_regulator_and_beta_2_adrenergic_receptor_pathway BC_GATA3_participate_in_activating_the_Th2_cytokine_genes_expression BC_How_Progesterone_Initiates_the_Oocyte_Maturation BC_Mechanism_of_Gene_Regulation_by_Peroxisome_Proliferators_via_PPARa_alpha BC_NFAT_and_Hypertrophy_of_the_heart_Transcription_in_the_broken_heart BC_Neuropeptides_VIP_and_PACAP_inhibit_the_apoptosis_of_activated_T_cells BC_Nitric_Oxide_Signaling_Pathway BC_Phospholipase_C_epsilon_pathway BC_Regulation_of_BAD_phosphorylation BC_Regulation_of_ck1_cdk5_by_type_1_glutamate_receptors BC_Repression_of_Pain_Sensation_by_the_Transcriptional_Regulator_DREAM BC_Signaling_Pathway_from_G_Protein_Families BC_Sonic_Hedgehog_Shh_Pathway BC_Stathmin_and_breast_cancer_resistance_to_antimicrotubule_agents BC_Transcription_Regulation_by_Methyltransferase_of_CARM1 BC_Transcription_factor_CREB_and_its_extracellular_signals BC_mCalpain_and_friends_in_Cell_motility