Table 3.

Correlation of early gene expression with vaccine-induced Env-specific neutralizing antibodies.

Parameter	Spearman Correlation
	week 14			week 32			week 34
	r	p	q	r	p	q	r	p	q
D1 DEG
SERPING1	0.1500	0.5934	0.8379	0.2000	0.4738	0.7881	0.2679	0.3334	0.7378
C3AR1	0.3107	0.2592	0.6848	0.3786	0.1649	0.6147	0.3464	0.2061	0.6313
IL1RN	0.2393	0.3892	0.7592	0.3250	0.2370	0.6739	0.4393	0.1032	0.5737
TNFAIP6	0.3214	0.2425	0.6804	0.3607	0.1870	0.6212	0.5214	0.0488	0.5158
PLAUR	-0.4750	0.0759	0.5415	-0.5143	0.0524	0.5158	-0.1929	0.4901	0.7907
FPR2	0.1429	0.6115	0.8548	0.1857	0.5067	0.7907	0.3714	0.1735	0.6182
SOCS3	0.4821	0.0711	0.5358	0.5357	0.0422	0.5158	0.4571	0.0888	0.5470
OAS1	0.4179	0.1227	0.7907	0.1929	0.4901	0.7378	-0.3714	0.1735	0.5900
TNFSF10	0.2893	0.2949	0.7046	0.4107	0.1297	0.5900	0.3893	0.1525	0.6055
CCR1	0.0179	0.9540	0.9803	0.0714	0.8025	0.9365	0.4679	0.0808	0.5470
LILRA3	0.4071	0.1334	0.5900	0.4500	0.0944	0.5506	0.5357	0.0422	0.5158
IFITM1	0.5964	0.0213	0.5158	0.6429	0.0116	0.4927	0.5000	0.0602	0.5158
ARG2	0.3393	0.2161	0.6415	0.3750	0.1692	0.6169	0.4179	0.1227	0.5900
CD82	0.2607	0.3469	0.7378	0.3107	0.2592	0.6848	0.2929	0.2888	0.7021
IRF7	0.3929	0.1485	0.6004	0.4429	0.1002	0.5650	0.5679	0.0297	0.5158
IFI35	-0.1964	0.4819	0.7881	-0.2500	0.3678	0.7433	0.1607	0.5667	0.8284
NFKBIA	0.1893	0.4983	0.7907	0.2571	0.3538	0.7378	0.3607	0.1870	0.6212
CSF3R	0.3393	0.2160	0.6415	0.3821	0.1607	0.6147	0.5179	0.0506	0.5158
DDIT3	0.2857	0.3012	0.7047	0.2964	0.2827	0.6999	0.6464	0.0110	0.4927
GP1BB	0.0321	0.9132	0.9557	0.0536	0.8525	0.9506	0.2071	0.4578	0.7876
CLU	-0.2214	0.4266	0.7633	-0.1964	0.4819	0.7880	-0.1929	0.4901	0.7907
TNFAIP3	0.1893	0.4983	0.8824	0.1286	0.6482	0.7907	0.4714	0.0783	0.5470
IL1RL1	-0.0964	0.7337	0.9117	-0.1536	0.5844	0.8379	0.1893	0.4983	0.7907
HLA-DMA	-0.4286	0.1127	0.5771	-0.3786	0.1649	0.6147	-0.2536	0.3607	0.7379
KIT	-0.4786	0.0735	0.5358	-0.5464	0.0376	0.5158	-0.2214	0.4266	0.7633
D1 Shared Pathway Genes c
IL2RA	0.0893	0.7532	0.9189	0.1250	0.6575	0.8895	0.1214	0.6669	0.8932
CSF2RB	0.2214	0.4266	0.7633	0.3286	0.2317	0.6722	0.4071	0.1334	0.5900
FCGR1A	0.2393	0.3892	0.7592	0.3179	0.2479	0.6804	0.3643	0.1824	0.6212
DUSP4	-0.3429	0.2111	0.6408	-0.2214	0.4266	0.7633	-0.1607	0.5667	0.8284
HLA-DQB1	-0.6857	0.0061	0.4927	-0.6964	0.0051	0.4927	-0.4571	0.0888	0.5470
HLA-DRB1	0.0714	0.8025	0.9365	0.1500	0.5934	0.8379	-0.0070	0.9847	0.9980
D1 Cytokine Genes d
IFNA2	-0.3786	0.1649	0.6147	-0.4321	0.1094	0.5737	-0.1500	0.5934	0.8379
IL6	-0.4321	0.1094	0.5737	-0.3964	0.1446	0.6003	-0.1000	0.7241	0.9098
IL18	-0.3893	0.1525	0.6055	-0.4607	0.0861	0.5470	-0.2286	0.4114	0.7633
IFNG	-0.4607	0.0861	0.5470	-0.5071	0.0562	0.5158	-0.5000	0.0602	0.5158
MCP1	-0.2321	0.4039	0.7633	-0.2107	0.4498	0.7820	0.2250	0.4190	0.7633
D1 Cytokine Proteins
IFN-α	-0.1321	0.6389	0.8785	-0.0464	0.8726	0.9547	-0.2036	0.4657	0.7880
IL-6	0.0643	0.8196	0.9557	0.0304	0.9158	0.9450	-0.2574	0.3514	0.7378
IL-18	-0.1250	0.6575	0.8898	-0.0429	0.8828	0.9547	-0.2679	0.3334	0.7378
IFN-γ	0.3378	0.2170	0.6415	0.4004	0.1394	0.5996	0.0840	0.7654	0.9220
MCP-1	-0.0321	0.9132	0.9557	0.1786	0.5235	0.7960	-0.3500	0.2012	0.6314
IL-1RA	-0.2000	0.4738	0.7880	-0.2036	0.4657	0.7880	-0.0786	0.7827	0.9263
D3 DEG
CLU	-0.3978	0.1602	0.6147	-0.1780	0.5423	0.8141	-0.0901	0.7616	0.9220
GP1BB	-0.1736	0.5526	0.8239	0.0945	0.7500	0.9189	0.0154	0.9637	0.9833
BCL2L1	0.0769	0.7965	0.9360	0.4330	0.1239	0.5900	-0.0153	0.9637	0.9833
IL1RL1	-0.0374	0.9035	0.9557	0.0637	0.8319	0.9451	-0.6835	0.0088	0.4927
ILR2	-0.3275	0.2530	0.6848	-0.2088	0.4731	0.7881	-0.6132	0.0224	0.5158
D3 Shared Pathway Genes
HLA-C	0.0154	0.9638	0.9833	-0.0901	0.7616	0.9220	0.4681	0.0938	0.5506
FCGR1A	-0.4110	0.1458	0.6003	-0.3802	0.1808	0.6212	-0.3407	0.2335	0.6724
D3 Cytokine Genes
IFNA2	-0.1165	0.6930	0.9029	-0.3099	0.2806.	0.6999	-0.5297	0.0543	0.5158
IL6	-0.1121	0.7042	0.9060	-0.2615	0.3656	0.7433	-0.1692	0.5629	0.8284
IL18	-0.3011	0.2951	0.7046	-0.3319	0.2464	0.6804	- 0.8242	0.0005	0.3471
IFNG	0.0418	0.8915	0.9547	-0.0505	0.8676	0.9547	-0.4286	0.1281	0.5900
MCP1	-0.0549	0.8557	0.9506	-0.0022	1.0000	1.0000	-0.4945	0.0750	0.5411
IL1RN	-0.2307	0.4265	0.7633	-0.0725	0.8083	0.9400	-0.0417	0.8915	0.9547
D3 Cytokine Proteins
IFN-α	0.3439	0.2484	0.6804	0.4044	0.1706	0.6181	0.4237	0.1494	0.6005
IL-6	0.2096	0.5000	0.7907	-0.0262	0.9487	0.9764	0.0262	0.9487	0.9764
IL-18	-0.1848	0.5243	0.7960	0.0726	0.8049	0.9377	-0.1210	0.6784	0.8944
IFN-g	-0.2077	0.4732	0.7881	-0.0530	0.8581	0.9517	-0.0972	0.7402	0.9136
MCP-1	-0.1077	0.7156	0.9098	-0.0066	0.9879	0.9983	-0.3319	0.2464	0.6804
IL-1RA	-0.5328	0.0532	0.5158	-0.4811	0.0843	0.5470	0.0023	1.0000	1.0000

^abold font corresponds to p < 0.05.

^bbold and italic font corresponds to p < 0.01.

^cGenes shared between the top five scoring pathways on D1 also included IL1RN, SOCS3, IFITM1, IRF7, and NFKBIA, genes that are included in the DEG.

^dThe gene encoding IL-1RA is ILRN that is included in the DEG.