Table 4:

Lynx1^−/− plasticity signature

RP	FC	pfp	p value	Probe_id	Symbol	mm_Entrez_ID	hs_Entrez_ID	Gene_name
1.2599	6.1102	0	0	ILMN_1213274	Ydjc	69101	150223	YdjC homolog (bacterial)
26.1378	1.722	0	0	ILMN_2744660	Igh-6	NA	NA	NA
87.0435	1.5896	0.0325	0	ILMN_1259747	Il33	77125	90865	Interleukin-33
79.5578	1.583	0.0233	0	ILMN_1231445	Inmt	21743	11185	Indolethylamine N-methyltransferase
99.1693	1.5584	0.0189	0	ILMN_1252675	D230019G01Rik	NA	NA	NA
95.5604	1.5581	0.0267	0	ILMN_2499166	Tmem65	74868	157378	Transmembrane protein 65
98.106	1.5481	0.0213	0	ILMN_1251713	Car12	76459	771	Carbonic anyhydrase 12
94.6178	1.5436	0.032	0	ILMN_1244887	Gria4	NA	NA	NA
96.4906	1.5339	0.0229	0	ILMN_2649671	Ipas	53417	64344	Hypoxia-inducible factor 3, α subunit
122.0152	1.5276	0.035	0	ILMN_2680188	Bai1	107831	575	Brain-specific angiogenesis inhibitor 1
137.2649	1.5013	0.04	0	ILMN_2968369	Kcnip1	70357	30820	Kv channel-interacting protein 1
128.559	1.4989	0.0418	0	ILMN_2744657	Igh-6	NA	NA	NA
135.6589	1.4911	0.0425	0	ILMN_3049896	Evi2b	NA	NA	NA
295.2115	−1.4885	0.0464	3.00E-04	ILMN_2847144	Hist1h2ak	319169	221613	Histone cluster 1, H2ak
271.4427	−1.5015	0.0389	2.00E-04	ILMN_2619455	Mcat	223722	27349	Malonyl CoA:ACP acyltransferase (mitochondrial)
309.8626	−1.5083	0.0494	3.00E-04	ILMN_2700265	Pex11a	18631	8800	Peroxisomal biogenesis factor 11 alpha
310.3477	−1.5135	0.0487	3.00E-04	ILMN_1254828	A730014O07Rik	NA	NA	NA
306.798	−1.5145	0.049	3.00E-04	ILMN_2684693	Dusp3	72349	1845	Dual-specificity phosphatase 3 (vaccinia virus phosphatase VH1-related)
307.0792	−1.5179	0.0488	3.00E-04	ILMN_2869715	Nell2	54003	4753	NEL-like 2
277.2855	−1.5191	0.0393	2.00E-04	ILMN_2491589	Vgll4	232334	9686	Vestigial like 4 (Drosophila)
311.6705	−1.5218	0.0487	4.00E-04	ILMN_2568488	A530089A20Rik	218914	23063	Wings apart-like homolog (Drosophila)
300.5669	−1.5221	0.0474	3.00E-04	ILMN_2768841	Rab22a	NA	NA	NA
312.3161	−1.5221	0.0484	4.00E-04	ILMN_3163448	Cdh8	12564	1006	Cadherin 8
261.4704	−1.5237	0.0365	2.00E-04	ILMN_1214071	Ifitm1	68713	NA	Interferon-induced transmembrane protein 1
273.6424	−1.5279	0.0394	2.00E-04	ILMN_2757232	Aqp4	11829	361	aquaporin 4
285.8745	−1.5314	0.0422	3.00E-04	ILMN_1241551	Nell2	54003	4753	NEL-like 2
240.2307	−1.534	0.0322	2.00E-04	ILMN_2629112	Asah3l	230379	340485	Alkaline ceramidase 2
295.481	−1.5354	0.046	3.00E-04	ILMN_2688728	Pcyt1a	13026	5130	Phosphate cytidylyltransferase 1, choline, α isoform
249.2494	−1.5366	0.0328	2.00E-04	ILMN_3151149	Cpne8	66871	144402	Copine VIII
273.9191	−1.5385	0.0391	2.00E-04	ILMN_2657911	Cnot4	53621	4850	CCR4-NOT transcription complex, subunit 4
309.8885	−1.5389	0.049	3.00E-04	ILMN_1257190	2900083I11Rik	58212	NA	Serine/arginine repetitive matrix 3
269.2151	−1.5392	0.0385	2.00E-04	ILMN_2639849	Cbln4	228942	140689	Cerebellin 4 precursor protein
290.2289	−1.5404	0.0445	3.00E-04	ILMN_1255457	Crebbp	12914	1387	CREB binding protein
256.2379	−1.5408	0.0356	2.00E-04	ILMN_3072536	Eif5	217869	1983	Eukaryotic translation initiation factor 5
242.1891	−1.542	0.0315	2.00E-04	ILMN_1249000	1500015O10Rik	78896	84417	RIKEN cDNA 1500015O10 gene
306.5435	−1.5432	0.0494	3.00E-04	ILMN_1214405	Cnksr2	245684	22866	Connector enhancer of kinase suppressor of Ras 2
278.6573	−1.5516	0.0393	2.00E-04	ILMN_2751988	Kitl	17311	4254	Kit ligand
274.1734	−1.5518	0.0391	2.00E-04	ILMN_2673566	Eif4ebp2	13688	1979	Eukaryotic translation initiation factor 4E binding protein 2
274.7663	−1.5538	0.0391	2.00E-04	ILMN_1216085	B230387C07Rik	106585	23253	Ankyrin repeat domain 12
267.3929	−1.5547	0.0379	2.00E-04	ILMN_2703913	Mtf2	17765	22823	Metal response element binding transcription factor 2
218.0454	−1.5569	0.03	1.00E-04	ILMN_2535881	Macrod2	72899	140733	MACRO domain containing 2
298.574	−1.5571	0.0468	3.00E-04	ILMN_1246494	LOC381445	26422	26960	Neurobeachin
240.5714	−1.5576	0.0318	2.00E-04	ILMN_1225224	Ttc14	67120	151613	Tetratricopeptide repeat domain 14
257.4399	−1.5601	0.0364	2.00E-04	ILMN_1259724	Man1b	17156	10905	Mannosidase, α, class 1A, member 2
225.5851	−1.5603	0.0305	1.00E-04	ILMN_1227376	BC042720	329178	285175	unc-80 homolog (Caenorhabditis elegans)
233.0899	−1.5645	0.0306	1.00E-04	ILMN_2741677	Bach1	12013	571	BTB and CNC homology 1
241.988	−1.5645	0.0319	2.00E-04	ILMN_1230312	A830054O04Rik	NA	NA	NA
309.3927	−1.5684	0.0497	3.00E-04	ILMN_2793638	H2-Tw3	NA	NA	NA
275.3065	−1.5696	0.0391	2.00E-04	ILMN_2757889	Zfp91-cntf	NA	NA	NA
225.8264	−1.5706	0.0301	1.00E-04	ILMN_2654822	Chd4	107932	1108	Chromodomain helicase DNA binding protein 4
247.466	−1.5728	0.0324	2.00E-04	ILMN_2731854	Creg2	263764	200407	Cellular repressor of E1A-stimulated genes 2
218.4269	−1.5755	0.0297	1.00E-04	ILMN_1221598	9330133O14Rik	NA	NA	NA
259.2859	−1.578	0.0363	2.00E-04	ILMN_1227149	Meg3	17263	NA	Maternally expressed 3
245.0182	−1.579	0.032	2.00E-04	ILMN_2601176	Meg3	17263	NA	Maternally expressed 3
246.2646	−1.5793	0.0323	2.00E-04	ILMN_1230605	Gm336	212285	116984	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2
225.2295	−1.5805	0.0309	1.00E-04	ILMN_2638066	Gria3	53623	2892	Glutamate receptor, ionotropic, AMPA3 (alpha 3)
224.7568	−1.5808	0.0311	1.00E-04	ILMN_1253224	Dhcr24	74754	1718	24-Dehydrocholesterol reductase
204.3878	−1.5825	0.0256	1.00E-04	ILMN_2544603	2610015J01Rik	67039	NA	RNA binding motif protein 25
190.3687	−1.5853	0.0233	1.00E-04	ILMN_2593230	Mllt4	17356	4301	Myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4
190.5304	−1.5853	0.0225	1.00E-04	ILMN_2519673	Vwf	22371	7450	Von Willebrand factor homolog
194.1056	−1.5868	0.0229	1.00E-04	ILMN_1215713	Egr4	13656	1961	Early growth response 4
220.9951	−1.5896	0.0293	1.00E-04	ILMN_1239599	Bat2d	226562	23215	Proline-rich coiled-coil 2C
218.0063	−1.5911	0.0304	1.00E-04	ILMN_2637413	Dbpht2	386753	NA	DNA binding protein with his-thr domain
185.7923	−1.5957	0.023	1.00E-04	ILMN_1247295	Hook1	77963	51361	Hook homolog 1 (Drosophila)
225.437	−1.5957	0.0309	1.00E-04	ILMN_2520582	Plxna4	243743	91584	Plexin A4
204.4627	−1.6008	0.0249	1.00E-04	ILMN_2674890	Tbl1x	21372	6907	Transducin (β)-like 1 X-linked
198.2794	−1.6018	0.0238	1.00E-04	ILMN_2541675	LOC382128	319675	85459	RIKEN cDNA 5830418K08 gene
202.278	−1.6049	0.0251	1.00E-04	ILMN_2690603	Spp1	20750	6696	Secreted phosphoprotein 1
204.4135	−1.6064	0.0252	1.00E-04	ILMN_1224992	Gcap14	72972	54462	Coiled-coil serine rich 2
236.1982	−1.609	0.0309	2.00E-04	ILMN_1235124	Thsd4	207596	79875	Thrombospondin, type I, domain containing 4
193.5829	−1.616	0.0231	1.00E-04	ILMN_2737867	Mtap1b	17755	4131	Microtubule-associated protein 1B
219.8212	−1.616	0.0296	1.00E-04	ILMN_1254547	Nr4a2	18227	4929	Nuclear receptor subfamily 4, group A, member 2
174.6364	−1.6168	0.0212	1.00E-04	ILMN_1235652	Usp37	319651	57695	Ubiquitin-specific peptidase 37
190.4584	−1.6202	0.0229	1.00E-04	ILMN_1255854	Mtap9	213582	79884	Microtubule-associated protein 9
183.2527	−1.6215	0.0226	1.00E-04	ILMN_3114632	Ddx6	13209	1656	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6
168.6428	−1.6221	0.0204	1.00E-04	ILMN_2561533	Vps13a	271564	23230	Vacuolar protein sorting 13A (yeast)
169.7224	−1.6236	0.0204	1.00E-04	ILMN_1241229	Bat2d	226562	23215	Proline-rich coiled-coil 2C
161.0071	−1.6316	0.0176	0	ILMN_1231734	Nsd1	18193	64324	Nuclear receptor-binding SET-domain protein 1
228.5556	−1.6327	0.0303	1.00E-04	ILMN_1259781	A430041B07Rik	328108	23116	Family with sequence similarity 179, member B
164.2141	−1.6332	0.0193	1.00E-04	ILMN_1250030	Cdc42ep1	104445	11135	CDC42 effector protein (Rho GTPase binding) 1
186.6603	−1.6332	0.0229	1.00E-04	ILMN_2795040	Hist1h2ad	NA	NA	NA
189.467	−1.6364	0.0239	1.00E-04	ILMN_1216322	Hmgcs2	15360	3158	3-Hydroxy-3-methylglutaryl-coenzyme A synthase 2
189.7896	−1.6367	0.0235	1.00E-04	ILMN_2646070	Mtap1a	17754	4130	Microtubule-associated protein 1 A
173.3318	−1.6391	0.0212	1.00E-04	ILMN_1229727	Gpr123	52389	84435	G-protein-coupled receptor 123
182.5954	−1.642	0.0227	1.00E-04	ILMN_2715848	Slitrk4	245446	139065	SLIT and NTRK-like family, member 4
154.7165	−1.6445	0.0157	0	ILMN_2481391	Zfp326	54367	284695	Zinc finger protein 326
144.623	−1.6461	0.0132	0	ILMN_1224129	Dennd3	105841	22898	DENN/MADD domain containing 3
175.2067	−1.6461	0.0208	1.00E-04	ILMN_2445958	Tssc8	63830	NA	KCNQ1 overlapping transcript 1
201.9407	−1.6496	0.0253	1.00E-04	ILMN_3059326	Sparc	20692	6678	Secreted acidic cysteine-rich glycoprotein
153.5956	−1.6636	0.0154	0	ILMN_3031781	Arid5b	71371	84159	AT-rich interactive domain 5B (MRF1-like)
140.1691	−1.6694	0.0126	0	ILMN_2481389	Zfp326	54367	284695	Zinc finger protein 326
134.6324	−1.67	0.0109	0	ILMN_1257525	Cpeb3	208922	22849	Cytoplasmic polyadenylation element binding protein 3
135.784	−1.6706	0.0108	0	ILMN_1237548	5830407P18Rik	NA	NA	NA
158.0665	−1.6714	0.0161	0	ILMN_1220048	A330086O21Rik	434089	NA	Predicted gene 10010
131.7096	−1.672	0.0116	0	ILMN_1254296	Chd1	12648	1105	Chromodomain helicase DNA binding protein 1
134.8336	−1.6821	0.0106	0	ILMN_2654932	Pdap1	231887	11333	PDGFA-associated protein 1
156.3313	−1.6827	0.016	0	ILMN_2457731	A930010C08Rik	NA	NA	NA
124.0646	−1.6846	0.0117	0	ILMN_2747381	Ddx24	27225	57062	DEAD (Asp-Glu-Ala-Asp) box polypeptide 24
138.2192	−1.6875	0.0114	0	ILMN_1248181	Zbtb7a	16969	51341	Zinc finger and BTB domain containing 7a
109.4147	−1.7232	0.0089	0	ILMN_2492395	2900064A13Rik	NA	NA	NA
127.2584	−1.7307	0.0116	0	ILMN_1251488	A430041B07Rik	328108	23116	Family with sequence similarity 179, member B
93.3629	−1.7373	0.0064	0	ILMN_1218471	3-Sep	24050	55964	Septin 3
93.4053	−1.747	0.0062	0	ILMN_2675914	R3hdm1	226412	23518	R3H domain containing 1
124.2134	−1.7587	0.0113	0	ILMN_2680128	Zc3h13	67302	NA	Zinc finger CCCH type containing 13
80.5466	−1.7652	0.0055	0	ILMN_1239042	Ankhd1	108857	54882	Ankyrin repeat and KH domain containing 1
86.1003	−1.7765	0.0054	0	ILMN_3162820	Odz4	23966	26011	Teneurin transmembrane protein 4
82.5619	−1.7931	0.0057	0	ILMN_1236820	9430047F21Rik	NA	NA	NA
134.4843	−1.794	0.0112	0	ILMN_2750515	Fos	14281	2353	FBJ osteosarcoma oncogene
71.9896	−1.8054	0.0055	0	ILMN_1258834	Chd1	12648	1105	Chromodomain helicase DNA binding protein 1
141.8688	−1.8109	0.0128	0	ILMN_3035795	Mllt3	70122	4300	Myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3
271.3241	−1.8126	0.0392	2.00E-04	ILMN_2965669	Xlr4a	NA	NA	NA
58.7952	−1.8477	0.0031	0	ILMN_2589525	Cpeb3	208922	22849	Cytoplasmic polyadenylation element binding protein 3
108.4816	−1.8546	0.0093	0	ILMN_2803674	S100a9	20202	6280	S100 calcium-binding protein A9 (calgranulin B)
73.6082	−1.8653	0.0057	0	ILMN_2639442	Rock2	19878	9475	Rho-associated coiled-coil containing protein kinase 2
65.4886	−1.8737	0.0032	0	ILMN_2617920	1110017D15Rik	73721	84688	RIKEN cDNA 1110017D15 gene
48.1193	−1.9436	0.0021	0	ILMN_1217776	Mll5	69188	55904	Lysine (K)-specific methyltransferase 2E
53.5131	−1.9814	0.0027	0	ILMN_2702303	Ch25h	12642	9023	Cholesterol 25-hydroxylase
43.2714	−2.0064	0.0015	0	ILMN_2649773	Slc38a5	209837	92745	Solute carrier family 38, member 5
37.5276	−2.0092	9.00E-04	0	ILMN_1244343	B230369L08Rik	223697	25777	Sad1 and UNC84 domain containing 2
41.0522	−2.0325	0.0017	0	ILMN_1226085	Syt1	NA	NA	NA
30.3722	−2.0661	0.0011	0	ILMN_1256701	2900016B01Rik	74901	9920	Kelch repeat and BTB (POZ) domain containing 11
33.181	−2.0665	0.001	0	ILMN_2778076	2210021J22Rik	72355	150383	Cysteine-rich, DPF motif domain containing 1
61.2262	−2.0942	0.0029	0	ILMN_2668333	Prg4	96875	NA	Proteoglycan 4 (megakaryocyte stimulating factor, articular superficial zone protein)
61.9241	−2.1057	0.0033	0	ILMN_2623983	Egr2	13654	1959	Early growth response 2
18.8649	−2.4826	0.0014	0	ILMN_2652500	Lrg1	76905	116844	Leucine-rich alpha-2-glycoprotein 1
13.3721	−2.4851	0	0	ILMN_2654906	Mgat3	17309	4248	Mannoside acetylglucosaminyltransferase 3
25.6626	−2.6212	0.0012	0	ILMN_2710905	S100a8	20201	6279	S100 calcium binding protein A8 (calgranulin A)
6.5864	−3.7552	0	0	ILMN_2712075	Lcn2	16819	3934	Lipocalin 2
4.4996	−4.7574	0	0	ILMN_1243615	Gramd4	223752	23151	GRAM domain containing 4
3.677	−5.3591	0	0	ILMN_1223734	Atf4	11911	468	Activating transcription factor 4
2.1886	−7.3314	0	0	ILMN_2507182	Tomm22	223696	56993	Translocase of outer mitochondrial membrane 22 homolog (yeast)
1	−13.9276	0	0	ILMN_1256369	Lynx1	23936	66004	Ly6/neurotoxin 1

V1 transcriptomes were profiled with microarray from Lynx1^−/− mice (the plasticity brake Lynx1 is genetically deleted to allow experience-dependent plasticity even in adulthood) to generate the Lynx1^−/− plasticity differential expression signature. Using RankProd differential expression (DE) analysis, V1 of adult Lynx1^−/− male mice >P60 was compared with adult wild-type mice (> P60; n = 3 each group) to identify 132 DE probes, which mapped to 107 unique mouse Entrez IDs. For downstream analysis, mouse Entrez IDs were mapped to human orthologs using the Mouse Genome Informatics homology reference to yield a 98 gene Lynx1^−/− plasticity signature. FC, fold change. RP, rank product. pfp, percent false positive (i.e. false discovery rate).