Lejeune et al. BMC Genomics 2012, 13:91 http://www.biomedcentral.com/1471-2164/13/91 Page 8 of 14 Table 1 Pathway analysis for 263 genes that enhanced 128Q-neuron dysfunction when knocked-down by RNAi Pathway Ascorbate and aldarate metabolism P value Gene 0.00000 B0218.8/clec-52, C01G6.1/aqp-2, C08B11.8, C12C8.2, C13B9.1, C36E8.3/pxd-1, C50D2.8, C52B9.1/cka-2, C52E4.1/cpr-1, C53B7.3, C54C8.9/nlp-39, D1025.4/nspc-20, D1086.3, F08B1.1/vhp-1, F29G6.2, F38E11.1/hsp- 12.3, F45C12.7/btb-6, F46H5.3, F49E12.1, F54B11.3/unc-84, F54F7.3, F56D6.2/clec-67, K07E3.3/dao-3, K08D8.3, K09C4.5, M02F4.7/clec-265, M03F4.7/calu-1, T07H3.3/math-38, T16H12.1, T23B3.2, T23H2.2/snt-4, W08D2.4/fat-3, Y38H6C.3/dct-14, ZC410.5, ZC416.6, ZK6.11 Starch and sucrose metabolism Tyrosine metabolism Amino sugar and nucleotide sugar metabolism Glycolysis Glycolysis/Gluconeogenesis Fatty acid biosynthesis Pentose phosphate pathway 0.00119 F57B10.7/tre-1, R05F9.6, T22F3.3, Y87G2A.8/gpi-1 0.00535 B0334.11/ooc-3, F46C3.1/pek-1, M110.5/dab-1 0.01885 F22B3.4, R05F9.6, Y87G2A.8/gpi-1 0.03209 T03F1.3/pgk-1, Y87G2A.8/gpi-1 0.03332 R05F9.6, T03F1.3/pgk-1, Y87G2A.8/gpi-1 0.03415 W09B6.1/pod-2 0.04375 R05F9.6, Y87G2A.8/gpi-1 Pathway analysis was based on hypergeomeric tests using pathways from Wormbook, KEGG and Panther. P < 0.05 was considered significant and results are shown by increasing P values. Table 2 Pathway analysis for 399 genes that reduced 128Q-neuron dysfunction when knocked-down by RNAi Pathway Ascorbate and aldarate metabolism P value Gene Sulfate assimilation Pyrimidine metabolism Pyridoxal phosphate salvage pathway Oxytocin receptor mediated signaling Interferon-gamma signaling Glycosphingolipid biosynthesis - ganglio series Cyanoamino acid metabolism Glycolysis/Gluconeogenesis Selenocompound metabolism Insulin_IGF pathway-protein kinase B signaling cascade 0.00000 B0281.5, B0286.3, B0478.1/jnk-1, C06B3.4/stdh-1, C08E3.4/fbxa-161, C08F8.5/fbxb-9, C09G1.1/pqn-11, C10C5.4, C10C5.5, C10G11.5/pnk-1, C17G10.5/lys-8, C17H12.8, C39D10.7, C45B11.3/dhs-18, C46E10.7/ srh-99, C54D10.3, D1054.10, D2045.6/cul-1, F07F6.1, F07F6.5/dct-5, F09B12.3, F17E5.1/lin-2, F28D1.5/ thn-2, F29G9.1, F31C3.6, F36F2.1, F38E11.2/hsp-12.6, F38H4.8/ech-2, F41B5.4/cyp-33C3, F42G10.1, F43G9.5, F44D12.8, F47C10.2/btb-21, F52H3.5, F53C3.5, F56D5.5, F56G4.3/pes-2.2, F57C9.4, F57H12.7/ mec-17, H04M03.1, H10D18.2/scl-12, K02B12.2, K02E11.5, K10B3.8/gpd-2, M01E11.2, M02D8.4, R03E9.1/ mdl-1, R05F9.10/sgt-1, R12B2.5/mdt-15, R12H7.2/asp-4, T03F6.1/qdpr-1, T17H7.1, T20B5.3/oga-1, T21C9.8/ttr-23, T22G5.2/lbp-7, T24B8.5, W02D3.1, W03D2.6, W05H9.1, Y106G6H.7/sec-8, Y106G6H.9, Y38H6C.1/dct-16, Y43C5B.2, Y47D3B.7/sbp-1, ZK1127.10, ZK1290.6/rnh-1.1, ZK384.2/scl-20, ZK520.4/ cul-2, ZK550.6, ZK637.8/unc-32, ZK829.6/tgt-1 0.00001 B0218.3/pmk-1, B0412.2/daf-7, B0478.1/jnk-1, C47G2.2/unc-130, C53D6.2/unc-129, F38A6.1/pha-4, F43C1.2/mpk-1, T23H2.5/rab-10, Y11D7A.4/rab-28 0.00113 B0304.1/hlh-1, B0478.1/jnk-1, B0547.1/csn-5, C04E7.2/sor-3, C07B5.5/nuc-1, C25D7.3/sdc-3, C34E10.7/ cnd-1, C37A2.4/cye-1, C47G2.2/unc-130, F14F3.1/vab-3, F38A6.1/pha-4, F56A8.7/unc-64, K01G5.2/hpl- 2, Y47D3A.6/tra-1, ZK520.4/cul-2 0.00176 B0218.3/pmk-1, B0478.1/jnk-1, F43C1.2/mpk-1, Y18D10A.5/gsk-3, Y38F1A.10/max-2 0.00236 B0478.1/jnk-1, B0547.1/csn-5, C44H4.6, F43C1.2/mpk-1, Y11D7A.4/rab-28, Y18D10A.5/gsk-3 0.00251 B0218.3/pmk-1, B0478.1/jnk-1, F43C1.2/mpk-1 0.00297 T14F9.3/hex-1, T26C5.3 0.00340 B0035.8/his-48, B0304.1/hlh-1, B0478.1/jnk-1, B0547.1/csn-5, C02B8.4/hlh-8, C04E7.2/sor-3, C07B5.5/ nuc-1, C09G9.7, C18A3.1, C25A1.11/aha-1, C25D7.3/sdc-3, C29F9.5, C34E10.7/cnd-1, C37A2.4/cye-1, C47G2.2/unc-130, F11A10.1/lex-1, F14F3.1/vab-3, F22D3.1/ceh-38, F22F1.1/hil-3, F38A6.1/pha-4, F45F2.4/his-7, F54C8.2/cpar-1, F56A8.7/unc-64, K01G5.2/hpl-2, K02B9.4/elt-3, R03E9.1/mdl-1, R05F9.10/ sgt-1, R07B1.1/vab-15, R13H8.1/daf-16, T05A6.1/cki-1, T19B10.11/mxl-1, T27F2.1/skp-1, W06E11.1, Y39B6A.2/pph-5, Y47D3A.6/tra-1, Y47D3B.7/sbp-1, Y49E10.1/rpt-6, Y57E12AL.5/mdt-6, ZC204.2, ZK131.7/his-13, ZK520.4/cul-2, ZK652.5/ceh-23 0.00365 AC3.7/ugt-1, C05C8.3/fkb-3, C06B3.4/stdh-1, C07B5.5/nuc-1, F11A5.12/stdh-2, F38E11.2/hsp-12.6, K10B3.8/gpd-2, R03E9.1/mdl-1, R12B2.5/mdt-15, R13H8.1/daf-16, T22G5.2/lbp-7, T28B8.2/ins-18 0.00365 AC3.7/ugt-1, C05C8.3/fkb-3, C06B3.4/stdh-1, C07B5.5/nuc-1, F11A5.12/stdh-2, F38E11.2/hsp-12.6, K10B3.8/gpd-2, R03E9.1/mdl-1, R12B2.5/mdt-15, R13H8.1/daf-16, T22G5.2/lbp-7, T28B8.2/ins-18 0.00404 C44H4.6, C47G2.2/unc-130, F38A6.1/pha-4, Y18D10A.5/gsk-3 Taurine/hypotaurine metabolism 0.00348 F56A8.7/unc-64, K02D10.5, T10H9.3, Y22F5A.3/ric-4 Salvage pyrimidine ribonucleotides 0.00417 F42G9.7/snt-2, K02D10.5, Y22F5A.3/ric-4 Tetrahydrofolate biosynthesis Apoptosis signaling 0.00417 B0218.3/pmk-1, B0478.1/jnk-1, F43C1.2/mpk-1 0.00503 B0218.3/pmk-1, B0478.1/jnk-1, F43C1.2/mpk-1, Y18D10A.5/gsk-3, Y38F1A.10/max-2 Glycosaminoglycan degradation 0.00520 K09E4.4, T14F9.3/hex-1