Table s1. Prominet sub-lattice analysis: the five largest atom and coatom sub-lattices with their objects and attributes are listed for the ABGM 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 43 nodes having 2 cluster, 71, and 73, with 37 genes and 51 pathways.
	BC_Angiotensin_II_mediated_activation_of_JNK_Pathway_via_Pyk2_dependent_signaling BC_BCR_Signaling_Pathway BC_Bioactive_Peptide_Induced_Signaling_Pathway BC_CCR3_signaling_in_Eosinophils BC_CXCR4_Signaling_Pathway BC_Cadmium_induces_DNA_synthesis_and_proliferation_in_macrophages BC_Calcium_Signaling_by_HBx_of_Hepatitis_B_virus BC_EGF_Signaling_Pathway BC_EPO_Signaling_Pathway BC_Erk1_Erk2_Mapk_Signaling_pathway BC_Erk_and_PI_3_Kinase_Are_Necessary_for_Collagen_Binding_in_Corneal_Epithelia BC_Fc_Epsilon_Receptor_I_Signaling_in_Mast_Cells BC_Growth_Hormone_Signaling_Pathway BC_How_Progesterone_Initiates_the_Oocyte_Maturation BC_IGF_1_Signaling_Pathway BC_IL_2_Receptor_Beta_Chain_in_T_cell_Activation BC_IL_2_signaling_pathway BC_IL_3_signaling_pathway BC_IL_6_signaling_pathway BC_Influence_of_Ras_and_Rho_proteins_on_G1_to_S_Transition BC_Inhibition_of_Cellular_Proliferation_by_Gleevec BC_Inhibition_of_Matrix_Metalloproteinases BC_Insulin_Signaling_Pathway BC_Integrin_Signaling_Pathway BC_Keratinocyte_Differentiation BC_Links_between_Pyk2_and_Map_Kinases BC_MAPKinase_Signaling_Pathway BC_METS_affect_on_Macrophage_Differentiation BC_Multiple_antiapoptotic_pathways_from_IGF_1R_signaling_lead_to_BAD_phosphorylation BC_NFAT_and_Hypertrophy_of_the_heart_Transcription_in_the_broken_heart BC_Nerve_growth_factor_pathway_NGF BC_PDGF_Signaling_Pathway BC_Ras_Signaling_Pathway BC_Regulation_of_transcriptional_activity_by_PML BC_Role_of_EGF_Receptor_Transactivation_by_GPCRs_in_Cardiac_Hypertrophy BC_Role_of_ERBB2_in_Signal_Transduction_and_Oncology BC_Role_of_Erk5_in_Neuronal_Survival BC_Role_of_MAL_in_Rho_Mediated_Activation_of_SRF BC_Roles_of_arrestin_dependent_Recruitment_of_Src_Kinases_in_GPCR_Signaling BC_Signaling_Pathway_from_G_Protein_Families BC_Signaling_of_Hepatocyte_Growth_Factor_Receptor BC_Sprouty_regulation_of_tyrosine_kinase_signals BC_TPO_Signaling_Pathway BC_T_Cell_Receptor_Signaling_Pathway BC_The_IGF_1_Receptor_and_Longevity BC_Transcription_factor_CREB_and_its_extracellular_signals BC_Trefoil_Factors_Initiate_Mucosal_Healing BC_Trka_Receptor_Signaling_Pathway BC_fMLP_induced_chemokine_gene_expression_in_HMC_1_cells BC_mCalpain_and_friends_in_Cell_motility BC_p38_MAPK_Signaling_Pathway
2	The second largest sub-lattice has 38 nodes having 2 clusters, 71, and 95, with 41 genes and 38 pathways.
	BC_Agrin_in_Postsynaptic_Differentiation BC_Angiotensin_II_mediated_activation_of_JNK_Pathway_via_Pyk2_dependent_signaling BC_Bioactive_Peptide_Induced_Signaling_Pathway BC_CCR3_signaling_in_Eosinophils BC_CXCR4_Signaling_Pathway BC_Cadmium_induces_DNA_synthesis_and_proliferation_in_macrophages BC_Ceramide_Signaling_Pathway BC_Erk1_Erk2_Mapk_Signaling_pathway BC_Erk_and_PI_3_Kinase_Are_Necessary_for_Collagen_Binding_in_Corneal_Epithelia BC_Fc_Epsilon_Receptor_I_Signaling_in_Mast_Cells BC_Growth_Hormone_Signaling_Pathway BC_How_Progesterone_Initiates_the_Oocyte_Maturation BC_Human_Cytomegalovirus_and_Map_Kinase_Pathways BC_IL_2_Receptor_Beta_Chain_in_T_cell_Activation BC_Influence_of_Ras_and_Rho_proteins_on_G1_to_S_Transition BC_Integrin_Signaling_Pathway BC_Keratinocyte_Differentiation BC_Links_between_Pyk2_and_Map_Kinases BC_MAPKinase_Signaling_Pathway BC_Multiple_antiapoptotic_pathways_from_IGF_1R_signaling_lead_to_BAD_phosphorylation BC_NFAT_and_Hypertrophy_of_the_heart_Transcription_in_the_broken_heart BC_Oxidative_Stress_Induced_Gene_Expression_Via_Nrf2 BC_PTEN_dependent_cell_cycle_arrest_and_apoptosis BC_Phospholipids_as_signalling_intermediaries BC_Phosphorylation_of_MEK1_by_cdk5_p35_down_regulates_the_MAP_kinase_pathway BC_Regulation_of_Splicing_through_Sam68 BC_Regulation_of_eIF4e_and_p70_S6_Kinase BC_Role_of_ERBB2_in_Signal_Transduction_and_Oncology BC_Role_of_Erk5_in_Neuronal_Survival BC_Role_of_MAL_in_Rho_Mediated_Activation_of_SRF BC_Role_of_arrestins_in_the_activation_and_targeting_of_MAP_kinases BC_Roles_of_arrestin_dependent_Recruitment_of_Src_Kinases_in_GPCR_Signaling BC_Signaling_of_Hepatocyte_Growth_Factor_Receptor BC_Sprouty_regulation_of_tyrosine_kinase_signals BC_Stat3_Signaling_Pathway BC_Transcription_factor_CREB_and_its_extracellular_signals BC_Trefoil_Factors_Initiate_Mucosal_Healing BC_fMLP_induced_chemokine_gene_expression_in_HMC_1_cells
3	The third largest sub-lattice has 26 nodes having 1 cluster, 65, with 21 genes and 35 pathways.
	BC_Activation_of_PKC_through_G_protein_coupled_receptor BC_Activation_of_Src_by_Protein_tyrosine_phosphatase_alpha BC_Angiotensin_II_mediated_activation_of_JNK_Pathway_via_Pyk2_dependent_signaling BC_Apoptotic_Signaling_in_Response_to_DNA_Damage BC_Attenuation_of_GPCR_Signaling BC_BCR_Signaling_Pathway BC_Bioactive_Peptide_Induced_Signaling_Pathway BC_CBL_mediated_ligand_induced_downregulation_of_EGF_receptors BC_CCR3_signaling_in_Eosinophils BC_CXCR4_Signaling_Pathway BC_Cadmium_induces_DNA_synthesis_and_proliferation_in_macrophages BC_EGF_Signaling_Pathway BC_Effects_of_calcineurin_in_Keratinocyte_Differentiation BC_Fc_Epsilon_Receptor_I_Signaling_in_Mast_Cells BC_Growth_Hormone_Signaling_Pathway BC_Ion_Channel_and_Phorbal_Esters_Signaling_Pathway BC_Keratinocyte_Differentiation BC_Links_between_Pyk2_and_Map_Kinases BC_Nitric_Oxide_Signaling_Pathway BC_Oxidative_Stress_Induced_Gene_Expression_Via_Nrf2 BC_PDGF_Signaling_Pathway BC_Pertussis_toxin_insensitive_CCR5_Signaling_in_Macrophage BC_Phospholipase_C_Signaling_Pathway BC_Phospholipase_C_d1_in_phospholipid_associated_cell_signaling BC_Phospholipids_as_signalling_intermediaries BC_Regulation_of_eIF4e_and_p70_S6_Kinase BC_Role_of_EGF_Receptor_Transactivation_by_GPCRs_in_Cardiac_Hypertrophy BC_Role_of_MEF2D_in_T_cell_Apoptosis BC_Signaling_Pathway_from_G_Protein_Families BC_TPO_Signaling_Pathway BC_T_Cell_Receptor_Signaling_Pathway BC_Thrombin_signaling_and_protease_activated_receptors BC_Transcription_factor_CREB_and_its_extracellular_signals BC_Trka_Receptor_Signaling_Pathway BC_g_Secretase_mediated_ErbB4_Signaling_Pathway
4	The fourth sub-lattice has 19 nodes having 2 clusters, 18, and 71, with 41 genes and 21 pathways.
	BC_Agrin_in_Postsynaptic_Differentiation BC_Angiotensin_II_mediated_activation_of_JNK_Pathway_via_Pyk2_dependent_signaling BC_BCR_Signaling_Pathway BC_Fc_Epsilon_Receptor_I_Signaling_in_Mast_Cells BC_Influence_of_Ras_and_Rho_proteins_on_G1_to_S_Transition BC_Links_between_Pyk2_and_Map_Kinases BC_Phosphoinositides_and_their_downstream_targets BC_Phospholipase_C_Signaling_Pathway BC_Phospholipids_as_signalling_intermediaries BC_Rac_1_cell_motility_signaling_pathway BC_Ras_Independent_pathway_in_NK_cell_mediated_cytotoxicity BC_Ras_Signaling_Pathway BC_Role_of_MAL_in_Rho_Mediated_Activation_of_SRF BC_Role_of_PI3K_subunit_p85_in_regulation_of_Actin_Organization_and_Cell_Migration BC_T_Cell_Receptor_Signaling_Pathway BC_Transcription_factor_CREB_and_its_extracellular_signals BC_Tumor_Suppressor_Arf_Inhibits_Ribosomal_Biogenesis BC_Y_branching_of_actin_filaments BC_fMLP_induced_chemokine_gene_expression_in_HMC_1_cells BC_p38_MAPK_Signaling_Pathway BC_uCalpain_and_friends_in_Cell_spread
5	The fifth sub-lattice has 16 nodes having 2 clusters, 42, and 71, with 42 genes and 13 pathways.
	BC_Angiotensin_II_mediated_activation_of_JNK_Pathway_via_Pyk2_dependent_signaling BC_Bioactive_Peptide_Induced_Signaling_Pathway BC_Erk1_Erk2_Mapk_Signaling_pathway BC_Human_Cytomegalovirus_and_Map_Kinase_Pathways BC_Integrin_Signaling_Pathway BC_Links_between_Pyk2_and_Map_Kinases BC_Phosphorylation_of_MEK1_by_cdk5_p35_down_regulates_the_MAP_kinase_pathway BC_Role_of_MAL_in_Rho_Mediated_Activation_of_SRF BC_Role_of_arrestins_in_the_activation_and_targeting_of_MAP_kinases BC_Roles_of_arrestin_dependent_Recruitment_of_Src_Kinases_in_GPCR_Signaling BC_Signaling_of_Hepatocyte_Growth_Factor_Receptor BC_The_IGF_1_Receptor_and_Longevity BC_fMLP_induced_chemokine_gene_expression_in_HMC_1_cells