Table 1.

Genes related to the innate immune response in Drosophila misregulated during neurodegeneration

Reference	Type of assay	Genes identified, total n	Genes related to immune responsea, n (%)	Genesb
Ferreiro et al. [24], 2012	spalt homozygous mutant vs. wild type at stages 16 and 17 of embryogenesis	482	48 (9.9)	CG10912, CG11842, CG13323, CG1358, CG14219, CG15784, CG16772, CG17107, CG18067, CG18179, CG18180, CG18301, CG30080, CG5778, CG5791, CG6639, CG7296, CG8562, CG9360, CG9468, CG9649, CG9989, Cpr49Ae, Ctr1B, deltaTry, Drsl5, Ect3, Hf, Hsp70Bc, IM1, IM10, IM14, IM2, IM23, IM3, IM4, Jon25Bi, Jon25Bii, Jon25Biii, Jon44E, Jon65Ai, Jon99Ci, Jon99Fi, Listericin, LysX, PebIII, Tg, Tsf1
Greene et al. [20], 2005	parkin homozygous mutant vs. heterozygous in 1-day-old adults	26	8 (30.8)	AttA, CG11459, CG12505, CG3604, Dpt, IM4, LysE, LysS
Kumimoto et al. [25], 2013	Expression of mutated human SOD1	124c	34 (27.4)	AttA, AttC, AttD, CecC, CG10912, CG13947, CG14500, CG15043, CG15263, CG15282, CG15829, CG18179, CG33109, CG4269, CG4757, CG9080, CG9463, CG9733, Def, DptB, Drs, Drsl3, Drsl4, fit, Jon65Ai, Jon99Fi, LysP, Mtk, Obp99b, PGRP-SB1, PGRP-SC1b, PGRP-SD, pirk, Prx2540-1
Nelson et al. [28], 2005	Overexpression of a polyQ repeat in the eye using GMR-GAL4	49	4 (8.2)	CG10641, crq, mus209, puc
Palgi et al. [23], 2012	Manf homozygous mutant embryos and larvae vs. wild type	1,243d	65 (5.2)	AGO2, AttA, cactin, Cec2, CecA1, CecA2, CecB, CG11159, CG13422, CG1887, CG9733, Drs, Drsl1, Drsl2, Drsl3, Drsl5, GNBP1, GNBP2, GNBP3, He, Hml, ik2, IM1, IM10, IM23, IM3, IM4, kay, key, LysX, lz, Mtk, os, PGRP-LA, PGRP-LB, PGRP-LC, PGRP-LF, PGRP-SA, PGRP-SD, Phk-3, pirk, Pli, pll, psh, Pvr, Rab11, Rala, Rel, Sp7, SPE, spirit, spz, Sr-CI, Sr-CII, Tep1, Tep3, Tep4, Tollo, TotA, TotC, TotX, Tsf3, upd3, vir-1, zfh1
Petersen et al. [11], 2012	Overexpression of human TBP protein with an expanded polyQ tract in the eye using GMR-GAL4	163	51 (31.3)	AttA, AttB, AttC, Cdc6, CecA1, CecA2, CecB, CecC, CG11459, CG13422, CG16978, CG17107, CG17760, CG33109, CG3699, CG4269, CG42807, CG6639, CG6788, CG7738, CG9616, CG9733, Cyp316a1, Cyp6g1, Def, Dpt, DptB, Drs, Drsl4, GADD45, grass, GstD5, IM10, IM23, Lsp1beta Lsp2, LysE, LysP, mthl2, Mtk, PGRP-SA, PGRP-SB1, PGRP-SC2, PGRPSD, pirk, Spn88Eb, Sr-CIV, Tep1, TotM, Tsf3, yellow-f
Ren et al. [22], 2011	Overexpression of human TBP protein with an expanded polyQ tract in the eye using GMR-GAL4	352	31 (8.8)	Cbs, CecB, CG10467, CG10514, CG10621, CG11891, CG11892, CG13641, CG15282, CG15784, CG16718, CG34370, CG3604, CG3699, CG42351, CG4269, CG4757, CG8129, Cyp28d1, deltaTry, kn, Lsp1beta mus209, PGRP-LC, PGRP-SD, Phk-3, Prat2, smp-30, Toll-6, Tsf1, Vago
Scherzer et al. [27], 2003	Overexpression of human a-synuclein in neurons using elav-GAL4	94	20 (21.3)	Acp1, CG10383, CG15065, CG4019, CG5778, CG7203, Cyp4e2, Cyp6g1, Glt, Got2, Irc, Obp99b, PGRP-SC1a, PGRP-SC1b, Prat2, Rfabg, Spat, Spn88Eb, Thor, vkg
Shieh and Bonini [21], 2011	Overexpression of CAG repeat in neurons using elav-GAL4	152	11 (7.2)	AttA, CG11413, CG13325, CG42351, CG5493, CG9119, CG9837, CG9935, Idgf3, IM2, Mtk
Vanden Broeck et al. [26], 2013	Loss of function and overexpression of TDP-43	100e	10 (10.0)	Acp1, CG15021, CG15293, CG18179, CG7778, Cpr49Ab, Cpr49Ae, Drsl2, Jon65Ai, Jon65aiv

^aPercentage of immune genes versus total number of genes is shown in parenthesis.

^bGenes in bold appear in more than one study. Underlined genes have human homologues.

^c124 genes upregulated at 5 or 45 days (from table 1 in Kumimoto et al. [25]).

^dOnly upregulated genes are considered.

^eThe 100 genes listed in figure 4 in Vanden Broeck et al. [26] (the top 50 down- and top 50 upregulated in both LOF and GOF conditions).