Table 3.
Examples of genes differentially spliced in different cell types
| Gene | Coverage | dI | p value | FDR | |
|---|---|---|---|---|---|
| Astrocytes | Fyn | 771 | −0.27 | 1.15 E-176 | 1.95 E-174 |
| Prom1 | 251 | 0.86 | 1.12 E-133 | 4.59 E-131 | |
| Ncam1 | 3576 | 0.24 | 1.63 E-132 | 5.93 E-130 | |
| Ptprf | 480 | −0.58 | 1.03 E-120 | 2.98 E-118 | |
| Srgap3 | 308 | 0.69 | 1.99 E-84 | 1.44 E-82 | |
| Kif1a | 180 | 0.75 | 3.12 E-66 | 1.76 E-64 | |
| Ptk2 | 134 | −0.47 | 1.33 E-63 | 6.73 E-62 | |
| Cam2kg | 903 | −0.44 | 5.75 E-56 | 2.43 E-54 | |
| Mapk8 | 270 | −0.55 | 6.98 E-37 | 2.36 E-35 | |
| Pkm2 | 1112 | −0.23 | 2.85 E-25 | 6.58 E-24 | |
| Neurons | Agrn | 907 | −0.5 | <1 E-300 | <1 E-300 |
| App | 5181 | 0.2 | <1 E-300 | <1 E-300 | |
| Atp6v0a1 | 1815 | −0.66 | <1 E-300 | <1 E-300 | |
| Clta | 3032 | −0.81 | <1 E-300 | <1 E-300 | |
| Dync1i2 | 1618 | −0.82 | <1 E-300 | <1 E-300 | |
| Nfasc | 821 | −0.94 | <1 E-300 | <1 E-300 | |
| Rab6 | 3058 | 0.34 | <1 E-300 | <1 E-300 | |
| Mtss1 | 1244 | −0.6 | 5.19 E-216 | 7.02 E-214 | |
| Srgap3 | 834 | 0.62 | 1.69 E-132 | 1.52 E-130 | |
| Lrp8 | 328 | −0.75 | 3.23 E-119 | 2.51 E-117 | |
| Oligodendrocytes | Phldb1 | 2947 | −0.58 | <1 E-300 | <1 E-300 |
| Aplp2 | 1358 | 0.48 | <1 E-300 | <1 E-300 | |
| Capzb | 1350 | −0.58 | 5.97 E-263 | 3.54 E-260 | |
| Add1 | 1515 | −0.51 | 1.41 E-231 | 5.95 E-229 | |
| Mpzl1 | 1165 | 0.45 | 4.37 E-227 | 3.15 E-223 | |
| Cldnd1 | 1187 | −0.6 | 2.49 E-209 | 8.2 E-207 | |
| Enpp2 | 1550 | 0.23 | 1.63 E-209 | 2.35 E-191 | |
| H2afy | 320 | 0.43 | 1.31 E-35 | 5.11 E-34 | |
| Mtss1 | 181 | 0.44 | 1.58 E-24 | 4.54 E-23 | |
| Snap25 | 100 | 0.39 | 8.8 E-22 | 2.1 E-20 | |
| Microglia | Clstn1 | 588 | 0.91 | <1 E-300 | <1 E-300 |
| H13 | 1263 | 0.2 | 6.2 E-296 | 3.94 E-283 | |
| Sena4d | 768 | 0.6 | 1.19 E-282 | 6.79 E-280 | |
| App | 705 | −0.6 | 5.33 E-240 | 2.04 E-237 | |
| Add1 | 509 | 0.57 | 9.97 E-188 | 3.17 E-185 | |
| Lass5 | 408 | 0.65 | 2.49 E-174 | 7.12 E-172 | |
| Rapgef1 | 355 | 0.45 | 2.22 E-173 | 5.79 E-171 | |
| Fmnl1 | 493 | 0.44 | 1.32 E-158 | 3.15 E-156 | |
| Fez2 | 853 | 0.36 | 1.61 E-139 | 3.08 E-137 | |
| Fyn | 131 | 0.68 | 7.07 E-89 | 9.31 E-87 | |
| Endothelial | Adam15 | 893 | 0.7 | <1 E-300 | <1 E-300 |
| Mcf2l | 629 | 0.74 | <1 E-300 | <1 E-300 | |
| Palm | 942 | −0.65 | <1 E-300 | <1 E-300 | |
| Ablim1 | 1025 | 0.47 | <1 E-300 | <1 E-300 | |
| Mprip | 3292 | −0.51 | <1 E-300 | <1 E-300 | |
| Actn4 | 1805 | −0.31 | <1 E-300 | <1 E-300 | |
| Ktn1 | 809 | −0.7 | 3.84 E-226 | 1.02 E-223 | |
| Arhgef1 | 865 | 0.36 | 2.23 E-219 | 5.66 E-217 | |
| Eif4 h | 1199 | 0.46 | 1.14 E-197 | 2.29 E-195 | |
| Pkp4 | 577 | 0.63 | 1.68 E-195 | 3.26 E-193 |
The coverage, delta inclusion (dI), p value, and false discovery rate (FDR) are listed. To obtain dI values, we first calculated the ratio of inclusion junction tags to inclusion plus skipping junction tags in each cell type and then determined the differences of the ratios between cell types. dI essentially quantifies the magnitude of the difference between the splicing of the two groups being compared (1 or −1 represents maximum difference, whereas 0 represents no difference).