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Table 2 Composition and scoring of Alzheimer’s disease molecular sub-networks generated by IPA

From: Knowledge-based compact disease models identify new molecular players contributing to early-stage Alzheimer’s disease

ID Molecules in network Score Focus molecules Top functions
1 ADCY,Ap1,AP2A2,ATPIF1,BLVRA,CCKBR,CIRBP,Clathrin,CLTA,CRYM,DUSP8,ERK1/2,FSH, GABBR2,Girk,GNAS,GNB5,GNG3,GPRASP2, GTPASE,LGALS8,Lh,PAK1,PPIA,PPIB,RGS4,RGS6,RGS7,Sapk,SYN2,THY1,TNPO1 49 23 Neurological Disease, Reproductive System Development and Function, Cell Death
2 14-3-3,ACTB,ACTG1,Actin,ACTR1A,aldo,Alpha tubulin,ATP5C1,ATP5G1,ATP6V1D (includes EG:299159),ATP6V1E1,ATP6V1E2,Beta Tubulin,Cofilin,Dynein,EIF3K,ELAVL4,F Actin, GAPDH, H + −transporting two-sector ATPase, Hsp90,NFkB(complex),PFDN5,SMARCC1,SNCA,SORBS1,STMN2,TUBA1B,TUBA1C,TUBB3,TUBB,TUBB2C,Tubulin,Vacuolar H + ATPase,ZBTB20 47 22 Cellular Assembly and Organization, Cellular Function and Maintenance, Immunological Disease
3 26sProteasome,Akt,ATP8A2,BAG6,CD3,COPS4, COX5B (includes EG:100002384),DNAJB12, DNAJC6,DNAJC8,ERK,GABRG2,Hsp70,HSP,HSPA8,HSPB3,Ikb,Insulin,Jnk,Laminin,LSM14B,Mapk,NDFIP2,P38MAPK,Pka,PPME1,PSMD4, PTP4A2,SNRPN,Sos,SYT1 (includes EG:20979), TCR,UBE2N,Ubiquitin, YWHAZ 31 16 Cellular Compromise, Cell-To-Cell Signaling and Interaction, Cellular Growth and Proliferation
4 ADORA2A,ATP,ATP6V1H,CACNA1E,CACNA2D3,CACNB2,DYNC1I1,EIF1,EIF5B,FOS,GPR1 (includes EG:100004124),IDS,KDM5B,KIFAP3, KLF15,L-glutamic acid,LANCL1,MAP2K7,MAPK3, MYC,MZT1,PNO1,PPP1R7,RAD51C,REEP1,RPL15,SLC17A7,SLC17A,SRSF2,TGFB1 (includes EG:21803),TIMM23,TMEM97,TUBGCP2,TUBGCP3,XRCC3 29 17 Hematological System Development and Function, Hematopoiesis, Tissue Development
5 AGRP,APC,ARHGEF9,CHCHD3,CHCHD6,CYB5D1,EIF3C/EIF3CL,IDH3G,LAMA3,MC4R,MRPS7,MRPS22,NAV1,NAV2,NFIA,POLH,PRDM5,PSMA1,PSMB2,PSMB3,PSMB6,RPL5,RPL6,RPL17,RPL19,RPL30,RPL31,RPL10A,RPLP0,RPLP2,RUNX2,SLC35E1,UBC,UBL7,USP3 21 12 Connective Tissue Development and Function, Tissue Morphology, Genetic Disorder
6 ACACB,ATP5A1,ATP5C1,ATP5D,BBX,BCL2L1,CDC16,CUEDC1,CUL3 (includes EG:26554), DHX30,E2F4,FAM162A,GSK3A,HINT1,IL4 (includes EG:16189),KCNAB2,LAMP2,mir-451,NACC1,NFIC,OTUD7B,PEBP1,PRKCQ,PSEN1,RELA,RTN1 (includes EG:104001),SLC11A2, SMAD3,SYT13,TMEM85,TNFSF10,TPT1 (includes EG:100043703),TTK,TUBA3C/TUBA3D, ZNF83 21 12 Nucleic Acid Metabolism, Small Molecule Biochemistry, Cellular Compromise
7 FAM63A,NAA38 2 1  
8 GNB2L1,SLC9A6 2 1 Cell Cycle, Connective Tissue Development and Function, Developmental isorder
9 DDX19B,GADD45G,RWDD2B 2 1 Tissue Development, Cell Cycle, DNA Replication, Recombination, and Repair
  1. Molecules in network comprise both experimentally discovered molecules and known/predicted close interaction partners. The Score is a measure of clustering coefficient between the sub-network components. Focus Molecules are the differentially expressed gene products with experimental evidence of the linkage to disease pathogenesis and are denoted by capital letters, while small letters designate inferred interactions.