. 2019 Nov 25;9(12):340. doi: 10.3390/brainsci9120340

Table 8.

Literature-cited M1 or M2 microglial genes/proteins compared to RNAseq data. Green-font rows indicate significant change in expression that is directionally in agreement with literature citations. Yellow-font rows indicate significantly changed RNAseq genes that are closely related to literature-cited genes. ND = not detected. NS = not significant.

Symbol	Gene Name	M1/M2	Source	Brain Region	Average Log2 cpm Sal, METH	Fold Change	FDR
Ccl2 (MCP-1)	C-C motif chemokine ligand 2	M1	Zhou	STR	5.57, 6.34	2.15	0.17 (NS)
Ccl2 (MCP-1)	C-C motif chemokine ligand 2	M1	Zhou	PFC	5.66, 5.62	1.03	0.97 (NS)
Ccl5 (RANTES)	C-C motif chemokine ligand 5	M1	Chhor	STR	ND, ND	ND
Ccl5 (RANTES)	C-C motif chemokine ligand 5	M1	Chhor	PFC	ND, ND	ND
Ccr7	C-C Motif Chemokine Receptor 7	M1	Barakat	STR	ND, ND	ND
Ccr7	C-C Motif Chemokine Receptor 7	M1	Barakat	PFC	−4.59, −2.62	1.84	0.74 (NS)
Fcgr3a (Cd16)	Fc fragment of IgG, low affinity IIIa, receptor	M1	Barakat, Zhou	STR	8.12, 7.25	−1.78	8.5 × 10⁻⁸
Fcgr3a (Cd16)	Fc fragment of IgG, low affinity IIIa, receptor	M1	Barakat, Zhou	PFC	8.01, 7.01	−1.97	1.5 × 10⁻⁹
Fcer2 (Cd23)	Fc Fragment Of IgE Receptor II	M1	Barakat	STR	ND, ND	ND
Fcer2 (Cd23)	Fc Fragment Of IgE Receptor II	M1	Barakat	PFC	ND, ND	ND
Fcgr2a (Cd32)	Fc fragment of IgG, low affinity IIa, receptor	M1	Barakat, Zhou, Peng	STR	7.16, 7.79	1.58	9.6 × 10⁻⁷
Fcgr2a (Cd32)	Fc fragment of IgG, low affinity IIa, receptor	M1	Barakat, Zhou, Peng	PFC	7.25, 7.96	1.67	1.7 × 10⁻⁵
Cd40 (Tnfr)	Cd40 molecule	M1	Barakat	STR	6.08, 5.45	−1.46	0.13 (NS)
Cd40 (Tnfr)	Cd40 molecule	M1	Barakat	PFC	6.29, 5.30	−1.97	1.9 × 10⁻⁹
Cd80	Cd80 molecule	M1	Barakat	STR	3.24, 3.62	1.34	0.049
Cd80	Cd80 molecule	M1	Barakat	PFC	3.30, 3.68	1.32	0.14 (NS)
Cd86	Cd86 molecule	M1	Barakat, Zhou, Peng	STR	6.68, 6.47	−1.13	0.29 (NS)
Cd86	Cd86 molecule	M1	Barakat, Zhou, Peng	PFC	6.54, 6.57	1.11	0.41 (NS)
Cxcl1	C-X-C motif chemokine ligand 1	M1	Chhor	STR	−3.53, −0.28	6.3	0.01
Cxcl1	C-X-C motif chemokine ligand 1	M1	Chhor	PFC	−2.30, 0.40	5.09	0.001
Adgre1 (F4/80)	adhesion G protein-coupled receptor E1	M1	Barakat	STR	10.32, 10.05	−1.2	0.06 (NS)
Adgre1 (F4/80)	adhesion G protein-coupled receptor E1	M1	Barakat	PFC	10.47, 10.35	−1.1	0.47 (NS)
Il1a	interleukin 1 alpha	M1	Chhor	STR	6.84, 7.93	3.98	0.001
Il1a	interleukin 1 alpha	M1	Chhor	PFC	6.76, 7.50	2.16	0.03
Il1b	interleukin 1 beta	M1	Barakat, Chhor	STR	3.83, 5.97	4.82	1.2 × 10⁻⁵
Il1b	interleukin 1 beta	M1	Barakat, Chhor	PFC	3.85, 6.28	5.57	7.6 × 10⁻¹³
Il2	Interleukin 2	M1	Chhor	STR	ND, ND	ND
Il2	Interleukin 2	M1	Chhor	PFC	ND, ND	ND
Il6	interleukin 6	M1	Barakat, Chhor, Zhou	STR	3.05, 2.62	−1.26	0.35 (NS)
Il6	interleukin 6	M1	Barakat, Chhor, Zhou	PFC	3.13, 3.33	1.17	0.58 (NS)
Il12	interleukin 12	M1	Barakat, Chhor	STR	5.04, 4.52	−1.36	0.045
Il12	interleukin 12	M1	Barakat, Chhor	PFC	4.89, 4.47	−1.25	0.32 (NS)
Ifng	interferon gamma	M1	Chhor	STR	ND, ND	ND
Ifng	interferon gamma	M1	Chhor	PFC	ND, ND	ND
Nos2 (iNos)	nitric oxide synthase 2	M1	Barakat, Chhor	STR	ND, ND	ND
Nos2 (iNos)	nitric oxide synthase 2	M1	Barakat, Chhor	PFC	ND, ND	ND
Hla-d (Mhc II)*	major histocompatibility class II	M1	Barakat, Peng	STR	ND, ND	ND
Hla-d (Mhc II)*	major histocompatibility class II	M1	Barakat, Peng	PFC	ND, ND	ND
Tnf	tumor necrosis factor	M1	Barakat, Chhor, Zhou	STR	1.19, 0.89	−1.26	0.49 (NS)
Tnf	tumor necrosis factor	M1	Barakat, Chhor, Zhou	PFC	0.96, 0.46	−1.26	0.65 (NS)
Gene related to Tnf from RNAseq Data
Tnfsf9	tumor necrosis factor superfamily member 9			STR	0.33, 4.29	19.53	5.7 × 10⁻¹¹
Tnfsf9	tumor necrosis factor superfamily member 9			PFC	0.23, 3.63	11.45	2.5 × 10⁻⁸
Ptgs2 (COX2)	prostaglandin-endoperoxide synthase 2	M1/M2	Chhor	STR	−4.73, −0.62	47.3	0.002
Ptgs2 (COX2)	prostaglandin-endoperoxide synthase 2	M1/M2	Chhor	PFC	ND, ND	ND
Arg1	Arginase 1	M2	Cherry, Chhor	STR	ND, ND	ND
Arg1	Arginase 1	M2	Cherry, Chhor	PFC	ND, ND	ND
Ccl2 (MCP-1)	C-C motif chemokine ligand 2	M2	Chhor	STR	5.57, 6.34	2.15	0.17 (NS)
Ccl2 (MCP-1)	C-C motif chemokine ligand 2	M2	Chhor	PFC	5.66, 5.62	1.03	0.97 (NS)
Ccr2 (MCP-1-R)	C-C Motif Chemokine Receptor 2	M2	Chhor	STR	ND, ND	ND
Ccr2 (MCP-1-R)	C-C Motif Chemokine Receptor 2	M2	Chhor	PFC	ND, ND	ND
Cd163	CD163 molecule	M2	Barakat, Cherry	STR	ND, ND	ND
Cd163	CD163 molecule	M2	Barakat, Cherry	PFC	−2.16, 2.13	7.21	0.11 (NS)
Msr1 (Cd204)	macrophage scavenger receptor 1	M2	Barakat	STR	1.38, 2.58	2.55	3.4 × 10⁻⁴
Msr1 (Cd204)	macrophage scavenger receptor 1	M2	Barakat	PFC	1.06, 3.01	4.18	2.6 × 10⁻⁶
Cd209	CD209 molecule	M2	Barakat	STR	ND, ND	ND
Cd209	CD209 molecule	M2	Barakat	PFC	ND, ND	ND
Cd36	CD36 molecule	M2	Barakat	STR	−2.79, −2.13	1.12	0.88 (NS)
Cd36	CD36 molecule	M2	Barakat	PFC	−2.15, −0.79	1.91	0.42 (NS)
Cd68	Cd68 molecule	M2	Barakat	STR	6.83, 6.68	−1.11	0.38 (NS)
Cd68	Cd68 molecule	M2	Barakat	PFC	6.70, 6.49	−1.14	0.28 (NS)
Cxcr3	C-X-C motif chemokine receptor 3	M2	Chhor	STR	2.49, 1.61	−1.53	0.21 (NS)
Cxcr3	C-X-C motif chemokine receptor 3	M2	Chhor	PFC	2.79, 2.15	−1.54	0.01
Clec7a (Dectin 1)	C-type lectin domain family 7, member A	M2	Barakat, Cherry	STR	2.34, 2.59	1.38	0.35 (NS)
Clec7a (Dectin 1)	C-type lectin domain family 7, member A	M2	Barakat, Cherry	PFC	1.22, 2.75	3.02	0.006
Retnlb (Fizz1)	Resistin Like Beta	M2	Barakat, Cherry, Chhor	STR	ND, ND	ND
Retnlb (Fizz1)	Resistin Like Beta	M2	Barakat, Cherry, Chhor	PFC	ND, ND	ND
Lgals3 (Gal-3)	galectin 3	M2	Chhor	STR	0.79, 3.06	6.2	3.0 × 10⁻⁴
Lgals3 (Gal-3)	galectin 3	M2	Chhor	PFC	0.13, 2.49	6.7	6.8 × 10⁻⁴
Csf3 (G-CSF)	Colony Stimulating Factor 3	M2	Chhor	STR	ND, ND	ND
Csf3 (G-CSF)	Colony Stimulating Factor 3	M2	Chhor	PFC	ND, ND	ND
Csf2 (GM-CSF)	Colony Stimulating Factor 2	M2	Chhor	STR	ND, ND	ND
Csf2 (GM-CSF)	Colony Stimulating Factor 2	M2	Chhor	PFC	ND, ND	ND
Gene related to Csf3 from RNAseq Data
Csf1 (M-CSF)	Colony Stimulating Factor 1			STR	1.54, 4.91	12.52	7.6 × 10⁻⁹
Csf1 (M-CSF)	Colony Stimulating Factor 1			PFC	1.71, 4.14	7.1	7.3 × 10⁻⁷
Igf1	insulin-like growth factor 1	M2	Chhor	STR	4.81, 5.26	1.41	0.01
Igf1	insulin-like growth factor 1	M2	Chhor	PFC	4.87, 5.57	1.65	0.004
Il1rn (Il1ra)	interleukin 1 receptor antagonist	M2	Chhor	STR	−0.40, 1.39	4.04	0.002
Il1rn (Il1ra)	interleukin 1 receptor antagonist	M2	Chhor	PFC	−0.29, 1.19	3.43	0.4 (NS)
Genes related to Il1rn from RNAseq Data
Il1rl1 (receptor for IL33 with Il1RAP)	interleukin 1 receptor-like 1			STR	6.31, 5.82	−1.39	0.01
Il1rl1 (receptor for IL33 with Il1RAP)	interleukin 1 receptor-like 1			PFC	6.26, 5.87	−1.3	0.08 (NS)
Il1rap	interleukin 1 receptor accessory protein			STR	3.49, 3.94	1.36	0.004
Il1rap	interleukin 1 receptor accessory protein			PFC	3.29, 3.55	1.19	0.29 (NS)
Il1r2 (IL1b decoy receptor)	interleukin 1 receptor type 2			STR	−1.75, 3.59	39.1	1.9 × 10⁻¹⁰
Il1r2 (IL1b decoy receptor)	interleukin 1 receptor type 2			PFC	−3.37, 4.48	131.46	2.0 × 10⁻¹⁰
Il4	Interleukin 4	M2	Barakat, Chhor	STR	ND, ND	ND
Il4	Interleukin 4	M2	Barakat, Chhor	PFC	ND, ND	ND
Il4r	Interleukin 4 Receptor	M2	Chhor	STR	8.12, 8.41	1.25	0.21 (NS)
Il4r	Interleukin 4 Receptor	M2	Chhor	PFC	8.11, 8.39	1.23	0.16 (NS)
Il10	Interleukin10	M2	Barakat, Chhor	STR	ND, ND	ND
Il10	Interleukin10	M2	Barakat, Chhor	PFC	ND, ND	ND
Genes related to Il10 from RNAseq Data
Il10ra	interleukin 10 receptor subunit alpha			STR	8.35, 7.75	−1.52	2.0 × 10⁻⁴
Il10ra	interleukin 10 receptor subunit alpha			PFC	8.34, 8.07	−1.23	0.06 (NS)
Il10rb	interleukin 10 receptor subunit beta			STR	7.98, 7.53	−1.34	6.0 × 10⁻⁴
Il10rb	interleukin 10 receptor subunit beta			PFC	7.94, 7.62	−1.22	0.04
Il13	Interleukin13	M2	Barakat	STR	ND, ND	ND
Il13	Interleukin13	M2	Barakat	PFC	ND, ND	ND
Gene related to Il13 from RNAseq Data
Il13ra1	interleukin 13 receptor subunit alpha 1			STR	3.77, 4.01	1.18	0.19 (NS)
Il13ra1	interleukin 13 receptor subunit alpha 1			PFC	3.77, 4.48	1.6	1.7 × 10⁻³
Clec10a (Cd301)	C-type lectin domain family 10, member A	M2	Cherry	STR	−0.89, −0.36	−1.19	0.75 (NS)
Clec10a (Cd301)	C-type lectin domain family 10, member A	M2	Cherry	PFC	1.78, 3.67	4.08	0.08 (NS)
Mrc1 (Cd206)	mannose receptor, C type 1	M2	Barakat Cherry, Chorr, Zhou, Peng	STR	−0.86, 0.66	2.72	0.009
Mrc1 (Cd206)	mannose receptor, C type 1	M2	Barakat Cherry, Chorr, Zhou, Peng	PFC	0.83, 3.77	6.39	0.04
Socs3	suppressor of cytokine signaling 3	M2	Chhor	STR	5.31, 5.49	1.04	0.91 (NS)
Socs3	suppressor of cytokine signaling 3	M2	Chhor	PFC	5.71, 6.13	1.34	0.29 (NS)
SphK1	Sphingosine Kinase 1	M2	Chhor	STR	ND, ND	ND
SphK1	Sphingosine Kinase 1	M2	Chhor	PFC	ND, ND	ND
SphK2	sphingosine kinase 2	M2	Chhor	STR	5.90, 6.02	1.1	0.37 (NS)
SphK2	sphingosine kinase 2	M2	Chhor	PFC	6.05, 6.23	1.14	0.30 (NS)
TGFb, subtypes below		M2	Barakat, Chhor
TGFb1	transforming growth factor, beta 1			STR	6.14, 6.14	−1.09	0.62 (NS)
TGFb1	transforming growth factor, beta 1			PFC	6.34, 6.40	1	1.00 (NS)
TGFb2	transforming growth factor, beta 2			STR	−1.15, −1.34	−1.14	0.80 (NS)
TGFb2	transforming growth factor, beta 2			PFC	ND, ND	ND
TGFb3	transforming growth factor, beta 3			STR	−0.63, −1.79	−1.27	0.72 (NS)
TGFb3	transforming growth factor, beta 3			PFC	−0.93, −1.46	−1.24	0.77 (NS)
Trem2	triggering receptor expressed on myeloid cells 2	M2	Cherry	STR	10.50, 9.06	−2.58	1.30 × 10⁻⁸
Trem2	triggering receptor expressed on myeloid cells 2	M2	Cherry	PFC	10.59, 8.88	−3.18	6.1 × 10⁻¹⁴
Chi3l3 (Ym1)	chitinase 3 like 3	M2	Barakat, Cherry, Chhor	STR	ND, ND	ND
Chi3l3 (Ym1)	chitinase 3 like 3	M2	Barakat, Cherry, Chhor	PFC	ND, ND	ND