# Microglial composition index — OSDR brain datasets (OMROS LAB, 2026-09-23) OMROS LAB · Omar Rafael Pérez Gallardo · ORCID 0009-0008-8328-6978 · built 2026-09-23 from public NASA OSDR GeneLab processed files (rRNA-removed normalized counts + sample tables). Per-animal indices (mean log2(norm+1) of each marker set): - homeostatic microglia H: P2ry12 Tmem119 Sall1 Fcrls Olfml3 Gpr34 Hexb Siglech Cx3cr1 Csf1r - peripheral / border-associated macrophage P: Ms4a7 Lyz2 Mrc1 F13a1 Pf4 Lyve1 Cd163 Ms4a6c Clec12a Ccr2 - single-timepoint inflammatory I: Il1b Tnf Cd68 Nlrp3 Casp1 Aif1 Tyrobp Trem2 - composition index C = P - H Stats: Hedges g and Welch t per dataset; tissues from the same mission averaged in z before Stouffer across the 4 independent missions (RR-3, RR-23, RR-10, RRRM-2). Technical replicates dropped. Permutation: flight/ground labels shuffled within dataset, 2,000 draws. Files: microglia_composition_by_dataset.csv, microglia_composition_per_sample.csv, composition.py, robust.py ## Per dataset | osd | mission | tissue | n_exp | n_ctl | g_homeostatic | p_homeostatic | g_peripheral | p_peripheral | g_composition | p_composition | g_inflammatory | p_inflammatory | r_comp_vs_infl | |:--------|:----------|:--------------------|--------:|--------:|----------------:|----------------:|---------------:|---------------:|----------------:|----------------:|-----------------:|-----------------:|-----------------:| | OSD-352 | RR-3 | brain | 3 | 3 | 0.25 | 0.72 | -0.6 | 0.412 | -0.76 | 0.312 | -0.41 | 0.598 | 0.8 | | OSD-525 | RR-23 | cerebellum | 8 | 8 | -0.64 | 0.198 | -1.59 | 0.00466 | -1.25 | 0.0198 | -1.39 | 0.012 | 0.29 | | OSD-563 | RR-10 | cerebellum | 5 | 5 | 0.27 | 0.653 | 0.04 | 0.939 | -0.21 | 0.725 | 0.29 | 0.62 | -0.49 | | OSD-564 | RR-10 | hippocampus | 5 | 5 | 1.48 | 0.037 | -1.47 | 0.0435 | -2.08 | 0.00763 | -0.72 | 0.247 | 0.71 | | OSD-612 | RR-10 | cerebral hemisphere | 4 | 5 | 1.11 | 0.0945 | 0.06 | 0.929 | -1 | 0.121 | 1.05 | 0.105 | -0.84 | | OSD-561 | RRRM-2 | cerebellum | 14 | 12 | 0.27 | 0.492 | -0.52 | 0.176 | -0.62 | 0.112 | -0.19 | 0.61 | 0.3 | | OSD-562 | RRRM-2 | hippocampus | 15 | 12 | -0.18 | 0.622 | -0.07 | 0.854 | 0.08 | 0.837 | -0.24 | 0.502 | -0.05 | | OSD-613 | RRRM-2 | cerebral hemisphere | 9 | 9 | -0.53 | 0.257 | -0.49 | 0.292 | -0.28 | 0.546 | -0.86 | 0.085 | 0.42 | | OSD-374 | proton | hippocampus | 4 | 4 | -0.23 | 0.727 | -0.01 | 0.987 | 0.01 | 0.982 | -0.43 | 0.52 | -0.65 | | OSD-611 | Si-28 | hippocampus | 7 | 3 | -0.09 | 0.893 | 0.31 | 0.517 | 0.29 | 0.556 | 0.37 | 0.623 | 0.58 | | OSD-202 | Co-57 LDR | brain | 12 | 10 | 0.06 | 0.891 | 0.44 | 0.293 | 0.52 | 0.212 | 0.36 | 0.425 | -0.05 | ## Per animal | osd | mission | tissue | sample | group | condition | homeostatic | peripheral | inflammatory | composition_P_minus_H | |:--------|:----------|:--------------------|:---------------------------------------|:--------|:--------------------------------------------------------------|--------------:|-------------:|---------------:|------------------------:| | OSD-352 | RR-3 | brain | RR3_BRN_FLT_F1 | exposed | Space.Flight | 10.2727 | 4.438 | 6.4618 | -5.8347 | | OSD-352 | RR-3 | brain | RR3_BRN_FLT_F2 | exposed | Space.Flight | 10.1263 | 3.6408 | 6.452 | -6.4856 | | OSD-352 | RR-3 | brain | RR3_BRN_FLT_F7 | exposed | Space.Flight | 10.3841 | 4.8107 | 6.5143 | -5.5734 | | OSD-352 | RR-3 | brain | RR3_BRN_GC_G7 | control | Ground.Control | 10.3301 | 5.276 | 6.9499 | -5.0541 | | OSD-352 | RR-3 | brain | RR3_BRN_GC_G8 | control | Ground.Control | 10.1229 | 4.7849 | 6.7476 | -5.338 | | OSD-352 | RR-3 | brain | RR3_BRN_GC_G9 | control | Ground.Control | 10.2192 | 4.139 | 6.1681 | -6.0803 | | OSD-525 | RR-23 | cerebellum | RR23_Cb_FLT_F2 | exposed | Space.Flight | 8.6519 | 5.7922 | 5.5716 | -2.8597 | | OSD-525 | RR-23 | cerebellum | RR23_Cb_FLT_F3 | exposed | Space.Flight | 8.8115 | 6.2986 | 5.5898 | -2.5129 | | OSD-525 | RR-23 | cerebellum | RR23_Cb_FLT_F4 | exposed | Space.Flight | 8.4355 | 6.1683 | 5.0264 | -2.2672 | | OSD-525 | RR-23 | cerebellum | RR23_Cb_FLT_F5 | exposed | Space.Flight | 8.4731 | 6.1172 | 5.3799 | -2.3559 | | OSD-525 | RR-23 | cerebellum | RR23_Cb_FLT_F6 | exposed | Space.Flight | 8.6233 | 6.7099 | 5.4158 | -1.9133 | | OSD-525 | RR-23 | cerebellum | RR23_Cb_FLT_F7 | exposed | Space.Flight | 8.6496 | 6.5913 | 5.195 | -2.0583 | | OSD-525 | RR-23 | cerebellum | RR23_Cb_FLT_F8 | exposed | Space.Flight | 8.6781 | 6.113 | 5.3488 | -2.5652 | | OSD-525 | RR-23 | cerebellum | RR23_Cb_FLT_F9 | exposed | Space.Flight | 8.3508 | 5.8644 | 5.2543 | -2.4864 | | OSD-525 | RR-23 | cerebellum | RR23_Cb_GC_G2 | control | Ground.Control | 8.7192 | 7.0859 | 5.8409 | -1.6333 | | OSD-525 | RR-23 | cerebellum | RR23_Cb_GC_G3 | control | Ground.Control | 8.6325 | 6.5619 | 5.5003 | -2.0706 | | OSD-525 | RR-23 | cerebellum | RR23_Cb_GC_G4 | control | Ground.Control | 8.4534 | 6.949 | 6.0588 | -1.5044 | | OSD-525 | RR-23 | cerebellum | RR23_Cb_GC_G5 | control | Ground.Control | 8.7992 | 6.2801 | 6.0298 | -2.5191 | | OSD-525 | RR-23 | cerebellum | RR23_Cb_GC_G6 | control | Ground.Control | 8.872 | 7.1767 | 5.3487 | -1.6954 | | OSD-525 | RR-23 | cerebellum | RR23_Cb_GC_G7 | control | Ground.Control | 8.4718 | 6.8223 | 5.7265 | -1.6495 | | OSD-525 | RR-23 | cerebellum | RR23_Cb_GC_G8 | control | Ground.Control | 8.8068 | 6.9752 | 5.5389 | -1.8317 | | OSD-525 | RR-23 | cerebellum | RR23_Cb_GC_G9 | control | Ground.Control | 8.7487 | 6.3008 | 5.4588 | -2.448 | | OSD-563 | RR-10 | cerebellum | RR10_Cb_FLT_WT_F1 | exposed | Space.Flight | 10.5443 | 6.9442 | 7.1025 | -3.6001 | | OSD-563 | RR-10 | cerebellum | RR10_Cb_FLT_WT_F3 | exposed | Space.Flight | 9.4212 | 7.3212 | 6.319 | -2.1 | | OSD-563 | RR-10 | cerebellum | RR10_Cb_FLT_WT_F5 | exposed | Space.Flight | 9.752 | 6.3481 | 6.7413 | -3.4039 | | OSD-563 | RR-10 | cerebellum | RR10_Cb_FLT_WT_F7 | exposed | Space.Flight | 8.8721 | 6.9213 | 5.8966 | -1.9508 | | OSD-563 | RR-10 | cerebellum | RR10_Cb_FLT_WT_F9 | exposed | Space.Flight | 8.9551 | 6.3123 | 5.4078 | -2.6428 | | OSD-563 | RR-10 | cerebellum | RR10_Cb_GC_WT_G1 | control | Ground.Control | 9.9722 | 7.0214 | 7.1558 | -2.9508 | | OSD-563 | RR-10 | cerebellum | RR10_Cb_GC_WT_G3 | control | Ground.Control | 8.769 | 7.018 | 5.9016 | -1.751 | | OSD-563 | RR-10 | cerebellum | RR10_Cb_GC_WT_G5 | control | Ground.Control | 9.3133 | 6.9435 | 6.0321 | -2.3698 | | OSD-563 | RR-10 | cerebellum | RR10_Cb_GC_WT_G7 | control | Ground.Control | 9.3564 | 6.3885 | 5.9088 | -2.9679 | | OSD-563 | RR-10 | cerebellum | RR10_Cb_GC_WT_G9 | control | Ground.Control | 9.2898 | 6.3798 | 5.3917 | -2.91 | | OSD-564 | RR-10 | hippocampus | RR10_HPC_FLT_WT_F1 | exposed | Space.Flight | 10.3627 | 5.7823 | 6.5283 | -4.5805 | | OSD-564 | RR-10 | hippocampus | RR10_HPC_FLT_WT_F3 | exposed | Space.Flight | 10.1818 | 6.7492 | 6.8757 | -3.4327 | | OSD-564 | RR-10 | hippocampus | RR10_HPC_FLT_WT_F5 | exposed | Space.Flight | 10.7115 | 7.0266 | 7.4117 | -3.6849 | | OSD-564 | RR-10 | hippocampus | RR10_HPC_FLT_WT_F7 | exposed | Space.Flight | 10.399 | 6.5971 | 6.8109 | -3.8019 | | OSD-564 | RR-10 | hippocampus | RR10_HPC_FLT_WT_F9 | exposed | Space.Flight | 10.519 | 6.6383 | 6.8038 | -3.8807 | | OSD-564 | RR-10 | hippocampus | RR10_HPC_GC_WT_G1 | control | Ground.Control | 10.1652 | 7.0506 | 7.2067 | -3.1146 | | OSD-564 | RR-10 | hippocampus | RR10_HPC_GC_WT_G3 | control | Ground.Control | 10.0143 | 7.157 | 7.1375 | -2.8573 | | OSD-564 | RR-10 | hippocampus | RR10_HPC_GC_WT_G5 | control | Ground.Control | 10.1516 | 7.4766 | 7.2318 | -2.675 | | OSD-564 | RR-10 | hippocampus | RR10_HPC_GC_WT_G7 | control | Ground.Control | 10.1416 | 7.2191 | 7.2521 | -2.9226 | | OSD-564 | RR-10 | hippocampus | RR10_HPC_GC_WT_G9 | control | Ground.Control | 10.3577 | 6.8659 | 6.7118 | -3.4918 | | OSD-612 | RR-10 | cerebral hemisphere | RR10_BRN_FLT_WT_F1 | exposed | Space.Flight | 10.7045 | 6.5675 | 7.7019 | -4.137 | | OSD-612 | RR-10 | cerebral hemisphere | RR10_BRN_FLT_WT_F3 | exposed | Space.Flight | 10.5792 | 7.4565 | 7.6487 | -3.1227 | | OSD-612 | RR-10 | cerebral hemisphere | RR10_BRN_FLT_WT_F5 | exposed | Space.Flight | 10.1401 | 6.9566 | 7.1079 | -3.1835 | | OSD-612 | RR-10 | cerebral hemisphere | RR10_BRN_FLT_WT_F7 | exposed | Space.Flight | 10.5383 | 7.1252 | 7.307 | -3.4131 | | OSD-612 | RR-10 | cerebral hemisphere | RR10_BRN_GC_WT_G1 | control | Ground.Control | 8.8582 | 6.8062 | 6.2161 | -2.052 | | OSD-612 | RR-10 | cerebral hemisphere | RR10_BRN_GC_WT_G3 | control | Ground.Control | 9.2518 | 6.713 | 6.3252 | -2.5388 | | OSD-612 | RR-10 | cerebral hemisphere | RR10_BRN_GC_WT_G5 | control | Ground.Control | 9.602 | 7.5626 | 6.8905 | -2.0393 | | OSD-612 | RR-10 | cerebral hemisphere | RR10_BRN_GC_WT_G7 | control | Ground.Control | 10.8115 | 7.093 | 7.6175 | -3.7184 | | OSD-612 | RR-10 | cerebral hemisphere | RR10_BRN_GC_WT_G9 | control | Ground.Control | 10.1667 | 6.8455 | 7.2612 | -3.3211 | | OSD-561 | RRRM-2 | cerebellum | RRRM2_Cb_FLT_ISS-T_OLD_FO12 | exposed | 29.week...Space.Flight...On.Earth | 8.5552 | 4.9857 | 5.2708 | -3.5695 | | OSD-561 | RRRM-2 | cerebellum | RRRM2_Cb_FLT_ISS-T_OLD_FO13 | exposed | 29.week...Space.Flight...On.Earth | 8.423 | 6.5559 | 6.1147 | -1.8672 | | OSD-561 | RRRM-2 | cerebellum | RRRM2_Cb_FLT_ISS-T_OLD_FO15 | exposed | 29.week...Space.Flight...On.Earth | 8.6297 | 5.9118 | 6.0409 | -2.7179 | | OSD-561 | RRRM-2 | cerebellum | RRRM2_Cb_FLT_ISS-T_OLD_FO18 | exposed | 29.week...Space.Flight...On.Earth | 8.8355 | 6.1067 | 5.9639 | -2.7288 | | OSD-561 | RRRM-2 | cerebellum | RRRM2_Cb_FLT_ISS-T_YNG_FY3 | exposed | 12.week...Space.Flight...On.ISS | 7.6727 | 5.5255 | 5.2868 | -2.1472 | | OSD-561 | RRRM-2 | cerebellum | RRRM2_Cb_FLT_ISS-T_YNG_FY4 | exposed | 12.week...Space.Flight...On.ISS | 8.3606 | 5.67 | 5.417 | -2.6905 | | OSD-561 | RRRM-2 | cerebellum | RRRM2_Cb_FLT_ISS-T_YNG_FY6 | exposed | 12.week...Space.Flight...On.ISS | 8.6921 | 4.9099 | 5.3996 | -3.7822 | | OSD-561 | RRRM-2 | cerebellum | RRRM2_Cb_FLT_ISS-T_YNG_FY9 | exposed | 12.week...Space.Flight...On.ISS | 9.083 | 4.9335 | 5.7308 | -4.1495 | | OSD-561 | RRRM-2 | cerebellum | RRRM2_Cb_FLT_ISS-T_YNG_FY10 | exposed | 12.week...Space.Flight...On.ISS | 8.5225 | 4.5156 | 5.1676 | -4.0069 | | OSD-561 | RRRM-2 | cerebellum | RRRM2_Cb_FLT_LAR_OLD_FO2 | exposed | 29.week...Space.Flight...On.Earth | 9.0506 | 6.5701 | 6.3627 | -2.4806 | | OSD-561 | RRRM-2 | cerebellum | RRRM2_Cb_FLT_LAR_OLD_FO3 | exposed | 29.week...Space.Flight...On.Earth | 9.1147 | 6.2915 | 5.8816 | -2.8232 | | OSD-561 | RRRM-2 | cerebellum | RRRM2_Cb_FLT_LAR_OLD_FO5 | exposed | 29.week...Space.Flight...On.Earth | 8.4578 | 7.3496 | 6.072 | -1.1082 | | OSD-561 | RRRM-2 | cerebellum | RRRM2_Cb_FLT_LAR_YNG_FY7 | exposed | 12.week...Space.Flight...On.Earth | 9.192 | 6.4473 | 6.1896 | -2.7446 | | OSD-561 | RRRM-2 | cerebellum | RRRM2_Cb_FLT_LAR_YNG_FY10 | exposed | 12.week...Space.Flight...On.Earth | 8.8566 | 7.7629 | 6.4509 | -1.0937 | | OSD-561 | RRRM-2 | cerebellum | RRRM2_Cb_GC_ISS-T_OLD_GO14 | control | 29.week...Ground.Control...On.Earth | 8.7571 | 7.5929 | 6.2651 | -1.1642 | | OSD-561 | RRRM-2 | cerebellum | RRRM2_Cb_GC_ISS-T_OLD_GO15 | control | 29.week...Ground.Control...On.Earth | 8.6691 | 5.6186 | 6.1246 | -3.0505 | | OSD-561 | RRRM-2 | cerebellum | RRRM2_Cb_GC_ISS-T_OLD_GO20 | control | 29.week...Ground.Control...On.Earth | 8.5603 | 5.9242 | 5.8391 | -2.6361 | | OSD-561 | RRRM-2 | cerebellum | RRRM2_Cb_GC_ISS-T_YNG_GY5 | control | 12.week...Ground.Control...On.Earth | 8.7207 | 6.3273 | 6.1299 | -2.3933 | | OSD-561 | RRRM-2 | cerebellum | RRRM2_Cb_GC_ISS-T_YNG_GY8 | control | 12.week...Ground.Control...On.Earth | 7.3179 | 6.7577 | 5.1065 | -0.5601 | | OSD-561 | RRRM-2 | cerebellum | RRRM2_Cb_GC_ISS-T_YNG_GY10 | control | 12.week...Ground.Control...On.Earth | 8.0755 | 6.375 | 5.7057 | -1.7004 | | OSD-561 | RRRM-2 | cerebellum | RRRM2_Cb_GC_LAR_OLD_GO12 | control | 29.week...Ground.Control...On.Earth | 8.4924 | 4.7958 | 5.6485 | -3.6967 | | OSD-561 | RRRM-2 | cerebellum | RRRM2_Cb_GC_LAR_OLD_GO13 | control | 29.week...Ground.Control...On.Earth | 8.4112 | 6.6242 | 5.6865 | -1.787 | | OSD-561 | RRRM-2 | cerebellum | RRRM2_Cb_GC_LAR_OLD_GO15 | control | 29.week...Ground.Control...On.Earth | 9.1449 | 6.6972 | 6.3509 | -2.4477 | | OSD-561 | RRRM-2 | cerebellum | RRRM2_Cb_GC_LAR_YNG_GY1 | control | 12.week...Ground.Control...On.Earth | 8.9099 | 6.6396 | 5.8211 | -2.2703 | | OSD-561 | RRRM-2 | cerebellum | RRRM2_Cb_GC_LAR_YNG_GY4 | control | 12.week...Ground.Control...On.Earth | 8.7412 | 6.5039 | 5.8945 | -2.2373 | | OSD-561 | RRRM-2 | cerebellum | RRRM2_Cb_GC_LAR_YNG_GY5 | control | 12.week...Ground.Control...On.Earth | 8.8412 | 7.285 | 6.0929 | -1.5562 | | OSD-562 | RRRM-2 | hippocampus | RRRM2_HPC_FLT_ISS-T_OLD_FO11 | exposed | 29.week...Space.Flight...On.ISS | 9.428 | 5.722 | 6.6653 | -3.706 | | OSD-562 | RRRM-2 | hippocampus | RRRM2_HPC_FLT_ISS-T_OLD_FO12 | exposed | 29.week...Space.Flight...On.ISS | 8.927 | 6.6454 | 6.1183 | -2.2816 | | OSD-562 | RRRM-2 | hippocampus | RRRM2_HPC_FLT_ISS-T_OLD_FO13 | exposed | 29.week...Space.Flight...On.ISS | 9.2513 | 6.0052 | 6.346 | -3.2461 | | OSD-562 | RRRM-2 | hippocampus | RRRM2_HPC_FLT_ISS-T_OLD_FO15 | exposed | 29.week...Space.Flight...On.ISS | 9.4236 | 5.7111 | 6.6287 | -3.7125 | | OSD-562 | RRRM-2 | hippocampus | RRRM2_HPC_FLT_ISS-T_OLD_FO18 | exposed | 29.week...Space.Flight...On.Earth | 9.2357 | 6.5639 | 5.934 | -2.6717 | | OSD-562 | RRRM-2 | hippocampus | RRRM2_HPC_FLT_ISS-T_YNG_FY3 | exposed | 12.week...Space.Flight...On.ISS | 8.1608 | 5.4998 | 6.4223 | -2.661 | | OSD-562 | RRRM-2 | hippocampus | RRRM2_HPC_FLT_ISS-T_YNG_FY4 | exposed | 12.week...Space.Flight...On.ISS | 8.2887 | 5.2172 | 6.0482 | -3.0716 | | OSD-562 | RRRM-2 | hippocampus | RRRM2_HPC_FLT_ISS-T_YNG_FY6 | exposed | 12.week...Space.Flight...On.ISS | 9.5444 | 5.4263 | 6.3232 | -4.1181 | | OSD-562 | RRRM-2 | hippocampus | RRRM2_HPC_FLT_ISS-T_YNG_FY10 | exposed | 12.week...Space.Flight...On.Earth | 9.3532 | 5.4446 | 6.3629 | -3.9086 | | OSD-562 | RRRM-2 | hippocampus | RRRM2_HPC_FLT_LAR_OLD_FO2 | exposed | 29.week...Space.Flight...On.Earth | 9.6642 | 6.402 | 6.9763 | -3.2622 | | OSD-562 | RRRM-2 | hippocampus | RRRM2_HPC_FLT_LAR_OLD_FO3 | exposed | 29.week...Space.Flight...On.Earth | 9.7203 | 6.7776 | 6.7488 | -2.9427 | | OSD-562 | RRRM-2 | hippocampus | RRRM2_HPC_FLT_LAR_OLD_FO5 | exposed | 29.week...Space.Flight...On.Earth | 9.6755 | 6.589 | 6.6795 | -3.0865 | | OSD-562 | RRRM-2 | hippocampus | RRRM2_HPC_FLT_LAR_YNG_FY6 | exposed | 12.week...Space.Flight...On.Earth | 9.1724 | 5.2863 | 6.1751 | -3.8861 | | OSD-562 | RRRM-2 | hippocampus | RRRM2_HPC_FLT_LAR_YNG_FY7 | exposed | 12.week...Space.Flight...On.Earth | 9.5767 | 5.8639 | 5.8767 | -3.7128 | | OSD-562 | RRRM-2 | hippocampus | RRRM2_HPC_FLT_LAR_YNG_FY10 | exposed | 12.week...Space.Flight...On.Earth | 9.5039 | 6.3069 | 6.8576 | -3.197 | | OSD-562 | RRRM-2 | hippocampus | RRRM2_HPC_GC_ISS-T_OLD_GO12 | control | 29.week...Ground.Control...On.Earth | 8.9982 | 5.464 | 6.2292 | -3.5341 | | OSD-562 | RRRM-2 | hippocampus | RRRM2_HPC_GC_ISS-T_OLD_GO15 | control | 29.week...Ground.Control...On.Earth | 9.2314 | 6.4148 | 6.522 | -2.8166 | | OSD-562 | RRRM-2 | hippocampus | RRRM2_HPC_GC_ISS-T_OLD_GO20 | control | 29.week...Ground.Control...On.ISS | 9.4114 | 5.5903 | 6.622 | -3.8211 | | OSD-562 | RRRM-2 | hippocampus | RRRM2_HPC_GC_ISS-T_YNG_GY5 | control | 12.week...Ground.Control...On.Earth | 9.0807 | 5.679 | 6.6293 | -3.4017 | | OSD-562 | RRRM-2 | hippocampus | RRRM2_HPC_GC_ISS-T_YNG_GY8 | control | 12.week...Ground.Control...On.Earth | 8.774 | 5.3154 | 6.1475 | -3.4587 | | OSD-562 | RRRM-2 | hippocampus | RRRM2_HPC_GC_ISS-T_YNG_GY10 | control | 12.week...Ground.Control...On.Earth | 9.3757 | 5.4599 | 6.2485 | -3.9158 | | OSD-562 | RRRM-2 | hippocampus | RRRM2_HPC_GC_LAR_OLD_GO12 | control | 29.week...Ground.Control...On.Earth | 9.3717 | 6.0827 | 6.4339 | -3.289 | | OSD-562 | RRRM-2 | hippocampus | RRRM2_HPC_GC_LAR_OLD_GO13 | control | 29.week...Ground.Control...On.Earth | 9.6199 | 6.0679 | 6.5517 | -3.552 | | OSD-562 | RRRM-2 | hippocampus | RRRM2_HPC_GC_LAR_OLD_GO15 | control | 29.week...Ground.Control...On.Earth | 9.2916 | 6.8242 | 6.2265 | -2.4674 | | OSD-562 | RRRM-2 | hippocampus | RRRM2_HPC_GC_LAR_YNG_GY1 | control | 12.week...Ground.Control...On.Earth | 9.632 | 6.1723 | 6.6319 | -3.4597 | | OSD-562 | RRRM-2 | hippocampus | RRRM2_HPC_GC_LAR_YNG_GY4 | control | 12.week...Ground.Control...On.Earth | 9.3265 | 6.4931 | 6.7465 | -2.8334 | | OSD-562 | RRRM-2 | hippocampus | RRRM2_HPC_GC_LAR_YNG_GY5 | control | 12.week...Ground.Control...On.Earth | 9.9311 | 6.4498 | 6.8364 | -3.4813 | | OSD-613 | RRRM-2 | cerebral hemisphere | RRRM2_BRN_FLT_ISS-T_OLD_FO14 | exposed | Space.Flight...29.week | 11.3885 | 6.6803 | 8.1975 | -4.7082 | | OSD-613 | RRRM-2 | cerebral hemisphere | RRRM2_BRN_FLT_ISS-T_OLD_FO16 | exposed | Space.Flight...29.week | 11.0636 | 6.9351 | 7.992 | -4.1285 | | OSD-613 | RRRM-2 | cerebral hemisphere | RRRM2_BRN_FLT_ISS-T_OLD_FO17 | exposed | Space.Flight...29.week | 11.2149 | 7.0353 | 8.2362 | -4.1796 | | OSD-613 | RRRM-2 | cerebral hemisphere | RRRM2_BRN_FLT_ISS-T_OLD_FO19 | exposed | Space.Flight...29.week | 11.3222 | 6.9042 | 8.3579 | -4.418 | | OSD-613 | RRRM-2 | cerebral hemisphere | RRRM2_BRN_FLT_ISS-T_OLD_FO20 | exposed | Space.Flight...29.week | 11.0609 | 6.9391 | 7.9144 | -4.1218 | | OSD-613 | RRRM-2 | cerebral hemisphere | RRRM2_BRN_FLT_ISS-T_YNG_FY2 | exposed | Space.Flight...12.week | 11.292 | 6.1749 | 7.4521 | -5.1171 | | OSD-613 | RRRM-2 | cerebral hemisphere | RRRM2_BRN_FLT_ISS-T_YNG_FY5 | exposed | Space.Flight...12.week | 11.1247 | 6.585 | 8.004 | -4.5397 | | OSD-613 | RRRM-2 | cerebral hemisphere | RRRM2_BRN_FLT_ISS-T_YNG_FY7 | exposed | Space.Flight...12.week | 10.8435 | 6.0802 | 7.3182 | -4.7634 | | OSD-613 | RRRM-2 | cerebral hemisphere | RRRM2_BRN_FLT_ISS-T_YNG_FY8 | exposed | Space.Flight...12.week | 11.1861 | 6.8684 | 7.9508 | -4.3177 | | OSD-613 | RRRM-2 | cerebral hemisphere | RRRM2_BRN_GC_ISS-T_OLD_GO13 | control | Ground.Control...29.week | 11.3931 | 7.1761 | 8.1427 | -4.2171 | | OSD-613 | RRRM-2 | cerebral hemisphere | RRRM2_BRN_GC_ISS-T_OLD_GO16 | control | Ground.Control...29.week | 11.1973 | 6.7046 | 7.9917 | -4.4928 | | OSD-613 | RRRM-2 | cerebral hemisphere | RRRM2_BRN_GC_ISS-T_OLD_GO18 | control | Ground.Control...29.week | 11.3397 | 6.668 | 8.3023 | -4.6717 | | OSD-613 | RRRM-2 | cerebral hemisphere | RRRM2_BRN_GC_ISS-T_OLD_GO19 | control | Ground.Control...29.week | 11.1503 | 6.8585 | 8.1709 | -4.2918 | | OSD-613 | RRRM-2 | cerebral hemisphere | RRRM2_BRN_GC_ISS-T_YNG_GY1 | control | Ground.Control...12.week | 11.095 | 6.4312 | 8.2691 | -4.6637 | | OSD-613 | RRRM-2 | cerebral hemisphere | RRRM2_BRN_GC_ISS-T_YNG_GY2 | control | Ground.Control...12.week | 11.3813 | 7.0008 | 8.2607 | -4.3806 | | OSD-613 | RRRM-2 | cerebral hemisphere | RRRM2_BRN_GC_ISS-T_YNG_GY4 | control | Ground.Control...12.week | 11.1569 | 7.4407 | 8.1266 | -3.7162 | | OSD-613 | RRRM-2 | cerebral hemisphere | RRRM2_BRN_GC_ISS-T_YNG_GY7 | control | Ground.Control...12.week | 11.1559 | 6.4993 | 7.9657 | -4.6566 | | OSD-613 | RRRM-2 | cerebral hemisphere | RRRM2_BRN_GC_ISS-T_YNG_GY9 | control | Ground.Control...12.week | 11.344 | 6.9805 | 8.308 | -4.3635 | | OSD-374 | proton | hippocampus | Mouse_hippocampus_9-10 | exposed | proton | 9.795 | 5.235 | 6.1823 | -4.56 | | OSD-374 | proton | hippocampus | Mouse_hippocampus_11-12 | exposed | proton | 9.9378 | 4.2275 | 6.3653 | -5.7104 | | OSD-374 | proton | hippocampus | Mouse_hippocampus_13-14 | exposed | proton | 9.8287 | 5.2757 | 5.9605 | -4.553 | | OSD-374 | proton | hippocampus | Mouse_hippocampus_15-16 | exposed | proton | 9.8121 | 5.5449 | 6.2747 | -4.2672 | | OSD-374 | proton | hippocampus | Mouse_hippocampus_1-2 | control | sham.irradiated | 9.9154 | 4.6297 | 6.3115 | -5.2858 | | OSD-374 | proton | hippocampus | Mouse_hippocampus_3-4 | control | sham.irradiated | 9.939 | 5.6451 | 5.9829 | -4.2939 | | OSD-374 | proton | hippocampus | Mouse_hippocampus_5-6 | control | sham.irradiated | 9.7668 | 5.6631 | 6.1916 | -4.1037 | | OSD-374 | proton | hippocampus | Mouse_hippocampus_7-8 | control | sham.irradiated | 9.8274 | 4.375 | 6.9026 | -5.4524 | | OSD-611 | Si-28 | hippocampus | Mouse_hippocampus_6 | exposed | Si.28.ion.radiation...0.6.gray | 8.0642 | 2.6851 | 4.6623 | -5.3791 | | OSD-611 | Si-28 | hippocampus | Mouse_hippocampus_7 | exposed | Si.28.ion.radiation...0.6.gray | 7.7508 | 3.2255 | 4.8547 | -4.5253 | | OSD-611 | Si-28 | hippocampus | Mouse_hippocampus_8 | exposed | Si.28.ion.radiation...0.3.gray | 7.624 | 3.5438 | 5.3453 | -4.0802 | | OSD-611 | Si-28 | hippocampus | Mouse_hippocampus_9 | exposed | Si.28.ion.radiation...0.3.gray | 7.6313 | 3.1647 | 4.9005 | -4.4666 | | OSD-611 | Si-28 | hippocampus | Mouse_hippocampus_10 | exposed | Si.28.ion.radiation...0.3.gray | 7.6172 | 3.265 | 4.7052 | -4.3522 | | OSD-611 | Si-28 | hippocampus | Mouse_hippocampus_11 | exposed | Si.28.ion.radiation...0.3.gray | 7.6819 | 2.6458 | 4.8774 | -5.036 | | OSD-611 | Si-28 | hippocampus | Mouse_hippocampus_12 | exposed | Si.28.ion.radiation...0.3.gray | 7.6451 | 2.5789 | 4.7501 | -5.0662 | | OSD-611 | Si-28 | hippocampus | Mouse_hippocampus_1 | control | sham.irradiated...0.gray | 7.8091 | 2.7331 | 4.5665 | -5.076 | | OSD-611 | Si-28 | hippocampus | Mouse_hippocampus_3 | control | sham.irradiated...0.gray | 7.8604 | 3.0704 | 5.096 | -4.79 | | OSD-611 | Si-28 | hippocampus | Mouse_hippocampus_4 | control | sham.irradiated...0.gray | 7.5311 | 2.893 | 4.6474 | -4.6381 | | OSD-202 | Co-57 LDR | brain | Mmus_C57-6J_BRN_HLLC_IR_1mon_Rep1_M50 | exposed | cobalt.57.gamma.radiation...Normally.Loaded.Control...1.month | 8.5226 | 4.2549 | 4.9876 | -4.2677 | | OSD-202 | Co-57 LDR | brain | Mmus_C57-6J_BRN_HLLC_IR_1mon_Rep2_M51 | exposed | cobalt.57.gamma.radiation...Normally.Loaded.Control...1.month | 8.4274 | 3.9254 | 4.5994 | -4.502 | | OSD-202 | Co-57 LDR | brain | Mmus_C57-6J_BRN_HLLC_IR_1mon_Rep3_M52 | exposed | cobalt.57.gamma.radiation...Normally.Loaded.Control...1.month | 8.5997 | 4.8146 | 5.2098 | -3.7851 | | OSD-202 | Co-57 LDR | brain | Mmus_C57-6J_BRN_HLLC_IR_1mon_Rep4_M53 | exposed | cobalt.57.gamma.radiation...Normally.Loaded.Control...1.month | 8.5137 | 3.9521 | 5.1091 | -4.5616 | | OSD-202 | Co-57 LDR | brain | Mmus_C57-6J_BRN_HLLC_IR_1mon_Rep5_M54 | exposed | cobalt.57.gamma.radiation...Normally.Loaded.Control...1.month | 8.3185 | 3.7477 | 5.1015 | -4.5709 | | OSD-202 | Co-57 LDR | brain | Mmus_C57-6J_BRN_HLLC_IR_1mon_Rep6_M55 | exposed | cobalt.57.gamma.radiation...Normally.Loaded.Control...1.month | 8.4511 | 4.0267 | 4.8333 | -4.4244 | | OSD-202 | Co-57 LDR | brain | Mmus_C57-6J_BRN_HLLC_IR_4mon_Rep1_M75 | exposed | cobalt.57.gamma.radiation...Normally.Loaded.Control...4.month | 8.2238 | 3.5777 | 4.9426 | -4.6461 | | OSD-202 | Co-57 LDR | brain | Mmus_C57-6J_BRN_HLLC_IR_4mon_Rep2_M80 | exposed | cobalt.57.gamma.radiation...Normally.Loaded.Control...4.month | 8.2997 | 3.8073 | 4.7052 | -4.4924 | | OSD-202 | Co-57 LDR | brain | Mmus_C57-6J_BRN_HLLC_IR_4mon_Rep3_M81 | exposed | cobalt.57.gamma.radiation...Normally.Loaded.Control...4.month | 8.3175 | 4.1626 | 4.8016 | -4.1549 | | OSD-202 | Co-57 LDR | brain | Mmus_C57-6J_BRN_HLLC_IR_4mon_Rep4_M82 | exposed | cobalt.57.gamma.radiation...Normally.Loaded.Control...4.month | 8.1253 | 3.2842 | 4.4925 | -4.8412 | | OSD-202 | Co-57 LDR | brain | Mmus_C57-6J_BRN_HLLC_IR_4mon_Rep5_M84 | exposed | cobalt.57.gamma.radiation...Normally.Loaded.Control...4.month | 8.2351 | 4.4028 | 4.6023 | -3.8323 | | OSD-202 | Co-57 LDR | brain | Mmus_C57-6J_BRN_HLLC_IR_4mon_Rep6_M89 | exposed | cobalt.57.gamma.radiation...Normally.Loaded.Control...4.month | 8.3992 | 4.1178 | 4.963 | -4.2814 | | OSD-202 | Co-57 LDR | brain | Mmus_C57-6J_BRN_HLLC_IRC_1mon_Rep1_M62 | control | non.irradiated...Normally.Loaded.Control...1.month | 8.6735 | 4.2869 | 5.4623 | -4.3867 | | OSD-202 | Co-57 LDR | brain | Mmus_C57-6J_BRN_HLLC_IRC_1mon_Rep2_M63 | control | non.irradiated...Normally.Loaded.Control...1.month | 8.7836 | 4.2411 | 5.3476 | -4.5425 | | OSD-202 | Co-57 LDR | brain | Mmus_C57-6J_BRN_HLLC_IRC_1mon_Rep3_M64 | control | non.irradiated...Normally.Loaded.Control...1.month | 8.097 | 3.884 | 3.7722 | -4.213 | | OSD-202 | Co-57 LDR | brain | Mmus_C57-6J_BRN_HLLC_IRC_1mon_Rep4_M65 | control | non.irradiated...Normally.Loaded.Control...1.month | 8.1746 | 3.7289 | 4.7131 | -4.4457 | | OSD-202 | Co-57 LDR | brain | Mmus_C57-6J_BRN_HLLC_IRC_1mon_Rep5_M66 | control | non.irradiated...Normally.Loaded.Control...1.month | 8.3623 | 3.5027 | 4.9039 | -4.8597 | | OSD-202 | Co-57 LDR | brain | Mmus_C57-6J_BRN_HLLC_IRC_1mon_Rep6_M67 | control | non.irradiated...Normally.Loaded.Control...1.month | 8.5325 | 4.0732 | 4.7138 | -4.4593 | | OSD-202 | Co-57 LDR | brain | Mmus_C57-6J_BRN_HLLC_IRC_4mon_Rep1_M83 | control | non.irradiated...Normally.Loaded.Control...4.month | 8.2389 | 3.2067 | 4.8464 | -5.0322 | | OSD-202 | Co-57 LDR | brain | Mmus_C57-6J_BRN_HLLC_IRC_4mon_Rep2_M85 | control | non.irradiated...Normally.Loaded.Control...4.month | 7.9742 | 3.7389 | 4.4827 | -4.2353 | | OSD-202 | Co-57 LDR | brain | Mmus_C57-6J_BRN_HLLC_IRC_4mon_Rep3_M95 | control | non.irradiated...Normally.Loaded.Control...4.month | 8.5332 | 4.0736 | 4.3317 | -4.4597 | | OSD-202 | Co-57 LDR | brain | Mmus_C57-6J_BRN_HLLC_IRC_4mon_Rep4_M97 | control | non.irradiated...Normally.Loaded.Control...4.month | 8.1949 | 3.6229 | 4.6762 | -4.5721 | ## Code ### composition.py ```python import pandas as pd,numpy as np,json,glob,re from scipy import stats e2s=json.load(open('ens2sym.json')) H=["P2ry12","Tmem119","Sall1","Fcrls","Olfml3","Gpr34","Hexb","Siglech","Cx3cr1","Csf1r"] P=["Ms4a7","Lyz2","Mrc1","F13a1","Pf4","Lyve1","Cd163","Ms4a6c","Clec12a","Ccr2"] I=["Il1b","Tnf","Cd68","Nlrp3","Casp1","Aif1","Tyrobp","Trem2"] MISSION={352:"RR-3",525:"RR-23",563:"RR-10",564:"RR-10",612:"RR-10",561:"RRRM-2",562:"RRRM-2",613:"RRRM-2",374:"proton",611:"Si-28",202:"Co-57 LDR"} TIS={352:"brain",525:"cerebellum",563:"cerebellum",564:"hippocampus",612:"cerebral hemisphere",561:"cerebellum",562:"hippocampus",613:"cerebral hemisphere",374:"hippocampus",611:"hippocampus",202:"brain"} def g(x,y): nx,ny=len(x),len(y); sp=np.sqrt(((nx-1)*x.var(ddof=1)+(ny-1)*y.var(ddof=1))/(nx+ny-2)) d=(x.mean()-y.mean())/sp if sp>0 else 0; return d*(1-3/(4*(nx+ny)-9)) rows=[];persample=[] for i in MISSION: nc=pd.read_csv(glob.glob(f"{i}__*Normalized*")[0],index_col=0); st=pd.read_csv(glob.glob(f"{i}__*SampleTable*")[0],index_col=0) nc.index=[e2s.get(x,x) for x in nc.index]; L=np.log2(nc+1) idx=lambda G:L.loc[[x for x in G if x in L.index]].mean() Hs,Ps,Is=idx(H),idx(P),idx(I); C=Ps-Hs cond=st['condition'].astype(str) if i in (374,611,202): trt=cond.str.contains(r'irradiated|gray|proton|Si-28|radiation',case=False)&~cond.str.contains(r'non.irradiated|sham',case=False) ctl=cond.str.contains(r'non.irradiated|sham',case=False) if i==202: # isolate radiation effect in normally loaded animals nl=cond.str.contains('Normally.Loaded',case=False); trt&=nl; ctl&=nl else: trt=cond.str.contains('Space.Flight',case=False); ctl=cond.str.contains('Ground.Control',case=False) st=st[~st.index.str.contains('techrep')]; trt=trt[st.index]; ctl=ctl[st.index] a=[s for s in st.index[trt] if s in L.columns]; b=[s for s in st.index[ctl] if s in L.columns] for s in a+b: persample.append({"osd":f"OSD-{i}","mission":MISSION[i],"tissue":TIS[i],"sample":s,"group":"exposed" if s in a else "control","condition":cond[s],"homeostatic":round(Hs[s],4),"peripheral":round(Ps[s],4),"inflammatory":round(Is[s],4),"composition_P_minus_H":round(C[s],4)}) def t(v): x,y=v[a].values,v[b].values; return round(g(x,y),2),float(stats.ttest_ind(x,y,equal_var=False).pvalue) rows.append({"osd":f"OSD-{i}","mission":MISSION[i],"tissue":TIS[i],"n_exp":len(a),"n_ctl":len(b), "g_homeostatic":t(Hs)[0],"p_homeostatic":t(Hs)[1],"g_peripheral":t(Ps)[0],"p_peripheral":t(Ps)[1], "g_composition":t(C)[0],"p_composition":t(C)[1],"g_inflammatory":t(Is)[0],"p_inflammatory":t(Is)[1], "r_comp_vs_infl":round(float(np.corrcoef(C[a+b],Is[a+b])[0,1]),2)}) R=pd.DataFrame(rows); pd.DataFrame(persample).to_csv('microglia_composition_per_sample.csv',index=False); R.to_csv('microglia_composition_by_dataset.csv',index=False) pd.set_option('display.width',250); print(R.to_string(index=False,float_format=lambda x:f"{x:.3g}")) # mission-level (one value per mission: mean g of its tissues; Stouffer across independent missions) sf=R[R.mission.isin(["RR-3","RR-23","RR-10","RRRM-2"])] for k in ["composition","peripheral","homeostatic","inflammatory"]: z=[];gs=[] for m,grp in sf.groupby('mission'): zz=[stats.norm.isf(p/2)*np.sign(gg) for p,gg in zip(grp['p_'+k],grp['g_'+k])] z.append(np.mean(zz)); gs.append(grp['g_'+k].mean()) Z=sum(z)/np.sqrt(len(z)); print(k,"missions",len(z),"mean g",round(np.mean(gs),2),"Stouffer Z",round(Z,2),"p",f"{2*stats.norm.sf(abs(Z)):.3g}","signs",[round(x,2) for x in gs]) ``` ### robust.py ```python import pandas as pd,numpy as np,json,glob from scipy import stats exec(open('composition.py').read().split("rows=[];persample=[]")[0]) SFm={352:"RR-3",525:"RR-23",563:"RR-10",564:"RR-10",612:"RR-10",561:"RRRM-2",562:"RRRM-2",613:"RRRM-2"} D={} for i in SFm: nc=pd.read_csv(glob.glob(f"{i}__*Normalized*")[0],index_col=0); st=pd.read_csv(glob.glob(f"{i}__*SampleTable*")[0],index_col=0) st=st[~st.index.str.contains('techrep')]; nc.index=[e2s.get(x,x) for x in nc.index]; L=np.log2(nc+1) c=st['condition'].astype(str); a=[s for s in st.index[c.str.contains('Space.Flight')] if s in L.columns]; b=[s for s in st.index[c.str.contains('Ground.Control')] if s in L.columns] D[i]=(L,a,b) def Z(Hs,Ps,perm=None,rng=None): zm={} for i,(L,a,b) in D.items(): C=L.loc[[x for x in Ps if x in L.index]].mean()-L.loc[[x for x in Hs if x in L.index]].mean() aa,bb=a,b if perm: s=list(a+b); rng.shuffle(s); aa,bb=s[:len(a)],s[len(a):] t=stats.ttest_ind(C[aa].values,C[bb].values,equal_var=False) zm.setdefault(SFm[i],[]).append(stats.norm.isf(t.pvalue/2)*np.sign(t.statistic)) z=[np.mean(v) for v in zm.values()]; return sum(z)/np.sqrt(len(z)) z0=Z(H,P); print("observed Z",round(z0,2)) lo=[(g,round(Z([x for x in H if x!=g],P),2)) for g in H]+[(g,round(Z(H,[x for x in P if x!=g]),2)) for g in P] print("leave-one-marker-out Z range",min(v for _,v in lo),max(v for _,v in lo)); print(lo) rng=np.random.default_rng(0); null=[Z(H,P,True,rng) for _ in range(2000)] print("permutation p (two-sided)",(np.sum(np.abs(null)>=abs(z0))+1)/2001) ```