. Author manuscript; available in PMC: 2018 Sep 1.

Published in final edited form as: Glia. 2017 Jun 15;65(9):1504–1520. doi: 10.1002/glia.23176

Table 2.

Microglial enriched genes that are positively correlated with MDI in pure developing microglia are also positively correlated with MDI in heterogeneous tissue from multiple gene expression studies where microglia contribute only a fraction of total mRNA.

Barres Brain RNA-seq		Fold-change P60/E18 (microglia RNAseq)	Correlation: (Pearson R) with MDI
Gene Symbol	Enrichment in Microglia vs. other CNS cells (Barres Brain RNAseq database)	Fold-change P60/E18 (microglia RNAseq)	In pure microglia	BRAIN DEVELOP GSE25219 n=1340	BRAIN SPAN n=524	ALZHEIMER S GSE5281 n=161	AUTISM GSE28521 n=51	Avg. R across datasets
csf1r	136.58	1.26	0.89^***	0.41^***	0.26^***	0.32^***	0.29^*	0.36
slc2a5	135.14	1.97	0.90^***	0.58^***	0.38^***	0.13	0.43^**	0.32
itgb2	114.17	1.4	0.91^***	0.42^***	0.17^***	−0.03	0.21	0.22
cx3cr1	74.98	1.47	0.88^***	0.26^***	−0.01	−0.1	−0.16	−0.02
inpp5d	72.97	1.47	0.90^***	0.67^***	0.52^***	0.47^***	0.50^***	0.52
capn3	69.46	2.09	0.92^***	0.78^***	0.60^***	0.17^*	0.56^***	0.46
hexb	67.74	1.27	0.93^***	0.63^***	−0.15^***	−0.32^***	−0.51^***	−0.32
mlxipl	51.74	2.17	0.85^***	0.70^***	0.41^***	−0.24^**	0.40^**	0.08
ly86	49.28	1.22	0.89^***	0.30^***	0.22^***	−0.02	0.07	0.21
itgb5	47.48	1.3	0.88^***	0.60^***	0.52^***	0.60^***	0.67^***	0.57
rgs10	45.87	1.4	0.84^***	0.02	0.27^***	0.11	−0.07	0.22
rab3il1	44.83	1.48	0.89^***	−0.10^***	0.04	0.24^**	0.73^***	0.3
cd84	36.76	1.38	0.90^***	0.53^***	0.25^***	0.31^***	0.31^*	0.36
sla	35.76	1.59	0.94^***	−0.65^***	−0.59^***	0.31^***	0.40^**	0.13
lair1	33.22	1.57	0.93^***	0.49^***	0.45^***	0.06	0.37^*	0.34
mafb	31.36	1.77	0.92^***	−0.34^***	−0.32^***	0.26^**	−0.58^***	−0.18
ier5	30.18	1.38	0.93^***	−0.38^***	−0.45^***	0.03	−0.57^***	−0.29
hk2	29.44	1.85	0.94^***	−0.36^***	−0.30^***	0.12	0.63^***	0.25
ptk2b	24.97	1.6	0.85^***	0.63^***	0.31^***	−0.63^***	0.11	−0.17
zfp36	23.13	1.42	0.93^***	0.42^***	0.22^***	0.43^***	0.50^***	0.4

Table shows the Pearson R values for the correlation with MDI of the top 20 microglial enriched genes that were most correlated with MDI in pure microglia. Looking at 4 datasets from heterogeneous tissue 58 out of 80 (4 datasets × 20 genes) gene measurements from heterogeneous tissue were positively correlated (red) with MDI (72.5%) compared to 5,254/12,500 (42%) for the remaining genes (Chi-square = 29.01, p<0.0001). Significant correlations are indicated with asterisks

p<0.05,

^**

p<0.01,

^***

p<0.005.