Table 1 Top-ranked genes (n=111) for the features of RAG-1^−/− brain in comparison with wild-type

From: CD4⁺ but not CD8⁺ T cells revert the impaired emotional behavior of immunocompromised RAG-1-deficient mice

Gene symbol	Probe ID	EntrezID	RAG score (gene score)	FC (RAG-WT)	FC (RAG-OTII)	P-value adj.RAG vs WT	P-value adj.RAG vs OTII
Mageb16	1 054 5096	71 967	−2.040851531	−1.382	−2.412	0.080489	0.022479
Vmn2r42	1 055 9883	22 310	−1.93209053	−2.152	−1.793	0.021505	0.020203
Mir300	10 398 412	723 833	−1.88308172	−1.677	−2.085	0.017506	0.016937
9530091C08Rik	10 586 718	320 440	−1.794710154	−1.667	−2.619	0.104888	0.032618
Phxr4	10 583 203	18 689	−1.697861707	−1.052	−2.198	0.236372	0.040404
Mir539	10 398 418	723 917	−1.68592755	−1.867	−1.625	0.032518	0.037203
A130014H13Rik	10 402 560	319 630	−1.666278107	−1.767	−2.305	0.029595	0.018413
Mir380	10 398 388	723 859	−1.579352318	−1.198	−1.896	0.039846	0.018076
Mir487b	10 398 416	723 940	−1.515646393	−1.591	−1.606	0.029403	0.025115
Gm9911	10 578 017	10 010 1427	−1.495726048	−1.097	−1.857	0.171881	0.045496
Tbrg3	10 430 929	21 378	−1.480314578	−1.246	−1.955	0.059237	0.02181
Mir323	10 398 390	723 839	−1.459997834	−1.189	−1.849	0.084182	0.027581
Mir680-2	10 602 221	751 551	−1.436650249	−1.111	−2.109	0.136616	0.028476
Mir665	10 398 338	751 555	−1.426506241	−1.668	−1.866	0.0336	0.023984
Mir376b	10 398 408	723 934	−1.390698725	−1.236	−1.411	0.034845	0.023984
Krtap2-4	10 390 913	71 453	−1.383924657	−1.713	−2.176	0.049788	0.026248
F830001A07Rik	10 586 722	320 055	−1.360180695	−1.16	−1.984	0.170697	0.043923
Mir382	10 398 420	723 912	−1.358674308	−1.517	−1.887	0.029403	0.01938
Mir154	10 398 428	387 172	−1.302334846	−1.148	−1.479	0.022707	0.016937
Gm10048	10 529 953	625 026	−1.295861539	−1.173	−1.861	0.06009	0.02181
Mir329	10 398 392	723 842	−1.295645605	−1.373	−1.719	0.043559	0.024869
Ephb1	10 596 115	270 190	−1.28329288	−1.144	−1.534	0.044139	0.022479
D230041D01Rik	10 548 727	1 000 38615	−1.249725567	−1.103	−1.502	0.050443	0.023984
Mir679	10 398 396	751 539	−1.239666734	−1.275	−1.743	0.092767	0.038914
Mir344	10 564 235	723 931	−1.227043517	−1.01	−1.991	0.109837	0.023058
4931406H21Rik	10 413 216	77 592	−1.20459512	−1.236	−1.209	0.030727	0.027375
Mir9-1	10 493 191	387 133	−1.188744017	−1.132	−1.618	0.04865	0.02181
Mir341	10398350	723 846	−1.185006997	−1.323	−2.14	0.109543	0.032187
Snord95	10 375 501	1 002 16540	−1.140100065	−1.165	−1.229	0.049459	0.037703
Tra2a	10 544 638	101 214	−1.085592515	−1.154	−1.518	0.05765	0.027615
Gm5887	10 542 834	545 893	−1.068780678	−1.213	−1.068	0.023897	0.024869
Snord37	10 365 003	100 217 454	−1.052485206	−1.061	−0.627	0.017506	0.02181
Mir543	10 398 400	723 881	−1.046459099	−1.036	−1.118	0.021685	0.017462
Myh9	10 430 245	17 886	−0.951892542	−1.048	−0.884	0.021822	0.021872
Il11ra1	10 504 106	16 157	−0.935378718	−1.033	−1.167	0.02919	0.021613
Vwf	10 541 910	22 371	−0.913653403	−1.116	−1.213	0.024473	0.019653
Malat1	10 465 244	72 289	−0.881007189	−1.116	−1.756	0.136615	0.04157
Celsr3	10 589 130	107 934	−0.876228519	−1.171	−1.127	0.02257	0.019787
Dock6	10 591 614	319 899	−0.837490045	−1.295	−1.147	0.014287	0.016937
Dock6	10 591 630	319 899	−0.808120768	−1.142	−0.959	0.021097	0.018349
Dock6	10 591 612	319 899	−0.805918085	−1.083	−1.032	0.021505	0.017355
Trank1	10 589 761	320 429	−0.803294001	−1.008	−1.337	0.062753	0.029244
Pkd1	10 442 495	18 763	−0.798266404	−1.173	−1.073	0.020247	0.016937
Snhg11	10 478 073	319 317	−0.792852186	−1.038	−0.89	0.03061	0.03547
Fn1	10 355 403	14 268	−0.75577708	−1.188	−1.149	0.018698	0.016937
Leng8	10 549 615	232 798	−0.755496969	−1.053	−1.088	0.029574	0.024595
Mll2	10 432 298	381 022	−0.679798747	−1.088	−0.886	0.017506	0.016937
Erdr1	10 608 711	170 942	−0.516986696	−1.069	−0.546	0.019742	0.035677
Mkks	10 488 048	59 030	0.457287879	1.043	0.341	0.022707	0.18131
Dynlt1c	10 548 785	100 040 563	0.459997269	1.004	0.654	0.017506	0.01714
Rpl10a	10 355 173	19 896	0.485867583	1.117	0.793	0.021854	0.029315
Nsa2	10 411 363	59 050	0.552510543	1.192	0.814	0.018273	0.020521
Atp6v1f	10 536 895	66 144	0.573664963	1.027	1.039	0.021685	0.018076
Rpsa	10 385 034	16 785	0.573730493	1.054	0.675	0.017506	0.017355
Plrg1	10 492 757	53 317	0.578165545	1.006	0.899	0.017506	0.016937
Hsd17b10	10 602 592	15 108	0.594214684	1.012	0.98	0.021685	0.018382
Snrpd2	10 367 073	107 686	0.601279671	1.014	0.881	0.021505	0.019125
Ly6c2	10 429 573	100 041 546	0.616556062	1.066	0.885	0.024294	0.027767
Bloc1s1	10 373 594	14 533	0.639650101	1.016	1.1	0.021993	0.017462
Rpp38	10 479 749	227 522	0.640345029	1.128	0.834	0.017506	0.018347
Wdr61	10 593 740	66 317	0.668426554	1.012	1.07	0.022823	0.01851
Cd53	10 501 063	12 508	0.668970684	1.139	0.627	0.021505	0.040581
Tm4sf1	10 498 273	17 112	0.675247588	1.016	0.827	0.017506	0.016937
Rpl29	10 505 090	19 944	0.686092788	1.1	1.086	0.030792	0.026878
Adh5	10 496 475	11 532	0.693727155	1.039	1.025	0.017802	0.016937
Nkain4	10 490 551	58 237	0.698189047	1.015	1.213	0.021505	0.016937
Rpl11	10 454 097	67 025	0.70163422	1.163	1.003	0.039409	0.046635
Rpl11	10 517 457	67 025	0.706880397	1.009	0.903	0.021685	0.020078
Ndufa2	10 458 386	17 991	0.706987075	1.075	1.157	0.017506	0.016937
Trim13	10 415 784	66 597	0.708945695	1.285	0.768	0.021505	0.034966
Rpl10a	10 443 360	19 896	0.711172011	1.402	1.194	0.021505	0.018349
Tspan6	10 606 609	56 496	0.71734053	1.097	1.001	0.017506	0.016937
Slc39a12	10 469 389	277 468	0.724078447	1.08	1.054	0.018698	0.016937
Txndc9	10 396 064	98 258	0.737153463	1.094	1.077	0.021505	0.017462
Kcnj13	10 356 403	100 040 591	0.746292444	1.237	1.062	0.017506	0.016937
S100a10	10 493 995	20 194	0.749982194	1.295	1.167	0.017506	0.016937
Trappc1	10 377 508	245 828	0.753853858	1.109	1.257	0.022707	0.017462
Ly6c1	10 429 568	17 067	0.755009369	1.168	1.228	0.032378	0.025501
Slc19a3	10 356 145	80 721	0.76123195	1.042	0.765	0.02554	0.037851
Bloc1s1	10 457 924	14 533	0.763087509	1.124	1.198	0.021505	0.016937
Tmem100	10 380 285	67 888	0.763927693	1.001	0.715	0.021589	0.026199
P2ry13	10 498 367	74 191	0.766062492	1.278	0.969	0.017506	0.017355
Hddc2	10 362 394	69 692	0.799560244	1.01	1.071	0.021505	0.016937
Sncg	10 418 921	20 618	0.812109509	1.236	1.33	0.011381	0.012815
Churc1	10 396 694	211 151	0.830334656	1.017	1.336	0.037868	0.021562
Scrg1	10 571 865	20 284	0.838580022	1.22	1.228	0.025882	0.022109
Rpl29	10 490 824	19 944	0.8434953	1.052	1.155	0.039564	0.028208
Hsd11b1	10 361 234	15 483	0.850759562	1.097	1.145	0.017506	0.016937
Snrpd2	10 498 595	107 686	0.851183191	1.075	1.138	0.026256	0.021562
Pgcp	10 423 556	54 381	0.868297012	1.256	1.28	0.017506	0.016937
Tpmt	10 409 021	22 017	0.88208296	1.027	1.412	0.021822	0.016937
Cd63	10 367 436	12 512	0.888313271	1.17	1.461	0.022707	0.016937
5730469M10Rik	10 419 082	70 564	0.895272141	1.268	1.91	0.03237	0.017355
Ly86	10 404 606	17 084	0.897001413	1.274	1.271	0.021685	0.018349
Akr1b10	10 537 157	67 861	0.902194098	1.175	1.305	0.021505	0.016937
Lgals1	10 425 161	16 852	0.912182029	1.268	1.398	0.021505	0.016937
N6amt2	10 420 385	68 043	0.91317463	1.241	1.256	0.021685	0.018347
Arhgdib	10 548 892	11 857	0.929045264	1.003	1.328	0.058924	0.027787
Ly6a	10 429 564	110 454	0.94058187	1.438	1.499	0.025555	0.021402
Fcer1g	10 360 070	14 127	0.963847748	1.2	1.306	0.055767	0.039132
Akr1c18	10 407 435	105 349	0.964325333	1.047	0.762	0.024294	0.036537
Serpinb9	10 404 429	20 723	0.966649984	1.023	0.968	0.017506	0.016937
Rfc4	10 438 690	106 344	0.99077814	1.162	1.23	0.020247	0.016937
Serpinb1a	10 408 557	66 222	1.057850202	1.247	1.558	0.017506	0.013705
Gstk1	10 537 712	76 263	1.150030127	1.592	1.697	0.021505	0.016937
Rpl11	1 050 2745	67 025	1.167088017	1.307	1.558	0.037379	0.023823
Stxbp4	1 038 9795	20 913	1.173500167	1.086	1.948	0.091593	0.023603
Rpl11	1 045 1301	67 025	1.243624445	1.26	1.699	0.053335	0.025053
Ppia	1 054 5337	268 373	1.52055618	1.462	1.698	0.034726	0.023458
Mela	1 058 2545	17 276	3.221879948	4.675	2.776	0.002256	0.016937
Rpl36	10 378 783	54 217	3.792674002	2.358	3.245	0.109543	0.045167

Abbreviations: FC, fold change; WT, wild type.
The table shows the identity and statistical values of the top-ranked genes that were used for heatmap analysis (Figure 9b) and calculating the similarity score (RAG score) for the RAG-1^−/− phenotype compared with the wild-type one (Figure 9c). Genes are ordered according to their relative contributions to the RAG score (i.e. the association with RAG-1^−/− or WT; positive values indicate association with RAG-1^−/−, whereas negative ones indicate association with WT). See Figure 9a for how genes were selected.
Probe ID is affymetrix ID.
FC is logged value.

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Table 1 Top-ranked genes (n=111) for the features of RAG-1^−/− brain in comparison with wild-type

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