Mullins Molecular Retrovirology Lab

  • Department of Microbiology
  • School of Medicine
  • University of Washington
University of Washington/Fred Hutch Center for AIDS Research

Citation Information

van ’t Wout AB, Lehrman GK, Mikheeva SA, O'Keeffe GC, Katze MG, Bumgarner RE, Geiss GK, Mullins JI (2003). Cellular gene expression upon human immunodeficiency virus type 1 infection of CD4(+)-T-cell lines. Journal of virology, 77(2), 1392-402. (pubmed)

Abstract

The expression levels of approximately 4,600 cellular RNA transcripts were assessed in CD4(+)-T-cell lines at different times after infection with human immunodeficiency virus type 1 strain BRU (HIV-1(BRU)) using DNA microarrays. We found that several classes of genes were inhibited by HIV-1(BRU) infection, consistent with the G(2) arrest of HIV-1-infected cells induced by Vpr. These included genes involved in cell division and transcription, a family of DEAD-box proteins (RNA helicases), and all genes involved in translation and splicing. However, the overall level of cell activation and signaling was increased in infected cells, consistent with strong virus production. These included a subgroup of transcription factors, including EGR1 and JUN, suggesting they play a specific role in the HIV-1 life cycle. Some regulatory changes were cell line specific; however, the majority, including enzymes involved in cholesterol biosynthesis, of changes were regulated in most infected cell lines. Compendium analysis comparing gene expression profiles of our HIV-1 infection experiments to those of cells exposed to heat shock, interferon, or influenza A virus indicated that HIV-1 infection largely induced specific changes rather than simply activating stress response or cytokine response pathways. Thus, microarray analysis confirmed several known HIV-1 host cell interactions and permitted identification of specific cellular pathways not previously implicated in HIV-1 infection. Continuing analyses are expected to suggest strategies for impacting HIV-1 replication in vivo by targeting these pathways.

Supplemental Data

Raw Data: van ’t Wout et al

retrieve raw data

Supplemental Data: van ’t Wout et al.

Supplement S1. Supplement S2. Supplement S3.

Supplement S1. Gene groups up regulated (red) or down regulated (green) by HIV-1BRU infection of CCRF-CEM cells.** Genes involved in cell signaling and communication were mostly up regulated, whereas genes involved in gene and protein expression were mostly down regulated.

suppdata.JPG

Category Up (%) Down (%) Total (%)
Cell Division 4 (2) 13 (5) 17 (4)
Cell/Organism Defense 2 (1) 3 (1) 5 (1)
Gene/Protein Expression 28 (17) 91 (37) 119 (29)
Metabolism 30 (18) 41 (17) 71 (17)
Signaling/Communication 56 (34) 26 (11) 82 (20)
Structure/Motility 15 (9) 9 (4) 24 (6)
Unknown 30 (18) 61 (25) 91 (22)
Total 165 244 409
Group Up (%) Down (%) Total (%)
Cell division 4 (2) 13 (5) 17 (4)
Defense 2 (1) 3 (1) 5 (1)
DNA binding 1 (1) 10 (4) 11 (3)
Protein processing 7 (4) 11 (5) 18 (4)
Ribosomal 1 (1) 6 (2) 7 (2)
RNA binding 2 (1) 8 (3) 10 (2)
RNA helicase 0 (0) 7 (3) 7 (2)
Splicing 0 (0) 8 (3) 8 (2)
Translation 0 (0) 10 (4) 10 (2)
Transcription 17 (10) 31 (13) 48 (12)
Enzyme 22 (13) 31 (13) 53 (13)
Transporter 8 (5) 10 (4) 18 (4)
Apoptosis 3 (2) 1 (0) 4 (1)
Channel 3 (2) 1 (0) 4 (1)
Kinase 6 (4) 4 (2) 10 (2)
Ligand 4 (2) 0 (0) 4 (1)
Phosphatase 1 (1) 4 (0) 5 (1)
Receptor 22 (13) 8 (3) 30 (7)
Transducer 17 (10) 8 (3) 25 (6)
Adhesion 4 (2) 6 (2) 10 (2)
Cytoskeleton 11 (7) 3 (1) 14 (3)
Unknown 30 (18) 61 (25) 91 (22)
Total 165 244 409

Supplement S2. Genes regulated by HIV-1BRU infection of CCRF-CEM cells. Tables, sorted by functional category, depict gene order in hierarchical cluster (S1), IMAGE consortium clone number, gene name, functional group and mean and standard deviation of the array ratios in the four 24 hour infection experiments.

Cell Division

No. Image Name Group Mean S.D.
18 66919 APC7 cell cycle -0.14 0.04
22 788645 G3BP cell cycle -0.14 0.09
134 22918 P40 cell cycle -0.14 0.04
34 247925 DRIM cell cycle -0.11 0.05
189 842806 CDK4 cell cycle -0.11 0.03
41 724615 CHC1 cell cycle -0.10 0.04
184 358736 GSPT2 cell cycle -0.09 0.03
1 292806 CSE1L cell cycle -0.08 0.03
54 843049 MCM4 cell cycle -0.08 0.03
109 784830 D123 cell cycle -0.08 0.06
215 214572 CDK6 cell cycle -0.06 0.09
171 159118 ARHG cell cycle -0.05 0.08
176 809557 MCM3 cell cycle -0.04 0.09
368 841332 ARHGDIB cell cycle 0.08 0.01
355 249705 DSS1 cell cycle 0.09 0.07
360 823691 CCNG2 cell cycle 0.15 0.04
267 207288 INSIG1 cell cycle 0.26 0.06

Cell/Organism Defense

No. Image Name Group Mean S.D.
12 207029 PTMA defense -0.14 0.04
273 703581 PRG1 defense 0.16 0.01
66 824031 HSJ2 heat shock -0.19 0.03
59 781341 HSPE1 heat shock -0.13 0.04
293 546600 HLJ1 heat shock 0.14 0.04

Gene/Protein Expression

No. Image Name Group Mean S.D.
111 293576 TARDBP dna binding -0.13 0.02
107 27548 NUP153 dna binding -0.12 0.09
36 205445 H1F0 dna binding -0.11 0.04
63 950574 TAF dna binding -0.11 0.06
149 144894 MMS19L dna binding -0.09 0.01
180 773599 RBBP4 dna binding -0.06 0.01
208 129506 SSRP1 dna binding -0.06 0.02
163 789091 H2AFL dna binding -0.04 0.08
231 240151 ID2 dna binding 0.01 0.07
222 136073 BRD4 dna binding 0.04 0.11
351 753447 DDB2 dna binding 0.09 0.04
193 204111 HMGE protein processing -0.16 0.05
186 840517 PSME3 protein processing -0.15 0.08
64 788574 GCN5L2 protein processing -0.14 0.05
93 839682 UBE2N protein processing -0.11 0.04
60 243343 CCT2 protein processing -0.09 0.02
126 840325 UBL4 protein processing -0.09 0.03
197 43884 PPIF protein processing -0.08 0.08
21 232612 LMAN1 protein processing -0.06 0.06
27 123700 USP7 protein processing -0.06 0.03
174 241900 PPIA protein processing -0.06 0.02
218 843140 KDELR2 protein processing -0.02 0.03
354 51814 CSTB protein processing 0.08 0.03
283 760298 PRSC1 protein processing 0.10 0.06
332 83083 ITIH3 protein processing 0.12 0.08
320 139573 RNPEP protein processing 0.13 0.06
335 143887 SPUVE protein processing 0.14 0.08
272 243202 CTSE protein processing 0.16 0.05
257 898035 CTSB protein processing 0.17 0.09
142 125148 RNAC ribosomal -0.21 0.05
137 824568 MRPL4 ribosomal -0.16 0.03
127 321354 HSPC228 ribosomal -0.15 0.03
144 246041 MRPS35 ribosomal -0.15 0.04
200 44255 RPML3 ribosomal -0.10 0.10
86 292232 RPS15A ribosomal -0.08 0.03
259 562867 RRS1 ribosomal 0.28 0.05
132 236055 PAI-RBP1 rna binding -0.20 0.04
147 841352 RBMX rna binding -0.16 0.05
113 842820 PABPC4 rna binding -0.11 0.05
112 897594 RNPS1 rna binding -0.09 0.03
83 26711 NCBP2 rna binding -0.08 0.02
89 703739 NCBP1 rna binding -0.07 0.03
16 782449 PCBP2 rna binding -0.05 0.02
204 124138 NXF1 rna binding -0.05 0.04
405 33690 CPSF6 rna binding 0.01 0.03
362 814526 RNPC1 rna binding 0.18 0.05
65 814117 DDX21 rna helicase -0.22 0.06
148 127925 DDX18 rna helicase -0.14 0.03
48 838373 DDX9 rna helicase -0.11 0.01
19 241880 DDX24 rna helicase -0.09 0.04
37 250519 DDX? rna helicase -0.09 0.06
194 773192 DDX1 rna helicase -0.05 0.02
237 741841 DDX11 rna helicase -0.05 0.11
157 202904 HSSG1 splicing -0.19 0.05
47 80399 SFRS1 splicing -0.15 0.02
146 47681 SFRS10 splicing -0.15 0.03
58 950092 SFRS3 splicing -0.11 0.03
170 123400 FBP2 splicing -0.04 0.09
219 345208 ELAVL1 splicing -0.03 0.06
246 898265 SFRS5 splicing 0.01 0.07
226 48530 PPIG splicing 0.03 0.06
183 812965 MYC transcription -0.39 0.07
91 843016 P130 transcription -0.24 0.05
82 823851 AEBP1 transcription -0.20 0.07
185 782811 HMGIY transcription -0.19 0.04
158 126702 ZNF202 transcription -0.17 0.04
74 824602 IFI16 transcription -0.16 0.04
136 713839 TFAP4 transcription -0.16 0.05
72 814101 TFDP2 transcription -0.15 0.01
28 280735 TBP transcription -0.13 0.03
57 949971 ATF4 transcription -0.13 0.01
103 773188 NR1D2 transcription -0.13 0.04
145 789049 NFYA transcription -0.13 0.04
172 809892 SEMA3B transcription -0.12 0.08
182 321708 TFDP1 transcription -0.12 0.06
52 322759 SNAPC5 transcription -0.10 0.01
99 786048 E2F4 transcription -0.10 0.01
119 711680 ZNFN1A1 transcription -0.10 0.03
85 825478 ZNF146 transcription -0.09 0.04
162 365930 TAF7 transcription -0.08 0.05
165 785816 ILF3 transcription -0.08 0.03
195 785845 TFAM transcription -0.08 0.05
203 361171 HTATIP transcription -0.07 0.10
214 809648 ZNF162 transcription -0.07 0.11
78 781018 SMARCB1 transcription -0.06 0.04
161 511814 ZNF38 transcription -0.06 0.03
96 80772 NCOR2 transcription -0.05 0.03
201 230218 GCN5L1 transcription -0.05 0.04
239 244058 JPO1 transcription -0.04 0.08
205 756272 TCF7 transcription -0.03 0.05
409 131626 NFRKB transcription -0.02 0.08
220 142395 HCFC1 transcription 0.01 0.08
225 773215 RUNX1 transcription 0.02 0.08
241 111981 LRRFIP1 transcription 0.03 0.11
397 280882 FLI1 transcription 0.03 0.04
398 297731 ZNF9 transcription 0.05 0.07
290 774082 ASCL1 transcription 0.06 0.02
378 287300 MLLT10 transcription 0.07 0.20
256 71727 TAL1 transcription 0.09 0.06
279 241412 ELF1 transcription 0.09 0.05
345 789357 RELB transcription 0.10 0.03
406 214068 GATA3 transcription 0.10 0.07
286 229723 SP140 transcription 0.12 0.04
324 741067 SMARCD2 transcription 0.12 0.03
310 196501 ARP transcription 0.17 0.06
348 45291 DRPLA transcription 0.18 0.03
297 246722 TNRC3 transcription 0.21 0.04
372 358531 JUN transcription 0.30 0.16
336 840944 EGR1 transcription 0.36 0.18
55 511586 HNRPA1 translation -0.13 0.02
100 204614 EIF4A1 translation -0.13 0.04
88 840384 GRSF1 translation -0.11 0.03
8 214577 RPP20 translation -0.10 0.02
73 327350 HNRPA2B1 translation -0.10 0.04
156 358457 HNRPH1 translation -0.10 0.03
117 949934 HNRPA0 translation -0.08 0.05
24 380394 EIF1AY translation -0.07 0.03
153 307532 EIF4A2 translation -0.07 0.06
187 236305 HARS translation -0.07 0.02

Metabolism

No. Image Name Group Mean S.D.
101 180244 ABCC8 transporter -0.16 0.04
3 841703 TFRC transporter -0.14 0.06
110 153006 SLC19A1 transporter -0.14 0.08
188 308682 ABCF2 transporter -0.13 0.03
167 825451 P115 transporter -0.12 0.18
105 320903 SLC25A6 transporter -0.10 0.04
45 825677 ASNA1 transporter -0.09 0.03
213 815285 ERPROT213 transporter -0.07 0.08
20 250667 RAB9 transporter -0.06 0.06
198 80946 ABCE1 transporter -0.05 0.20
339 245853 AP2B1 transporter 0.05 0.04
371 898253 RCN2 transporter 0.05 0.05
370 199286 ATP11B transporter 0.06 0.03
275 841340 ABCB2 transporter 0.08 0.03
307 49352 ANXA7 transporter 0.08 0.03
322 842784 SLC25A3 transporter 0.08 0.02
358 139540 OSPBL3 transporter 0.08 0.03
292 121981 SLC2A3 transporter 0.19 0.04
154 79502 MAT2A enzyme -0.20 0.04
7 796646 ODC1 enzyme -0.17 0.03
2 49464 UNG enzyme -0.16 0.05
116 25679 SRD5A1 enzyme -0.16 0.09
92 813280 ADSL enzyme -0.14 0.03
5 814615 MTHFD2 enzyme -0.13 0.03
40 242687 B3GNT1 enzyme -0.13 0.03
125 813711 ADH5 enzyme -0.13 0.03
190 300103 NAGLU enzyme -0.13 0.03
51 760344 UMPS enzyme -0.12 0.02
151 812155 RABGGTB enzyme -0.12 0.05
199 126243 HMBS enzyme -0.12 0.14
14 46182 CTPS enzyme -0.11 0.05
30 127509 GBE1 enzyme -0.11 0.07
179 179232 PP enzyme -0.11 0.04
33 357091 HS6ST enzyme -0.10 0.02
50 813830 CYC1 enzyme -0.10 0.02
129 145132 MPDU1 enzyme -0.10 0.02
10 898123 GART enzyme -0.09 0.04
62 755239 METTL1 enzyme -0.09 0.03
121 530875 TKT enzyme -0.09 0.04
26 841370 GOT2 enzyme -0.08 0.07
29 810316 IDH3A enzyme -0.08 0.05
166 299360 FBP1 enzyme -0.08 0.02
115 782800 UQCRFS1 enzyme -0.07 0.02
108 826077 PDHB enzyme -0.05 0.05
238 725533 STE enzyme -0.05 0.10
196 292236 GPI enzyme -0.03 0.04
210 202535 MT1G enzyme -0.02 0.07
244 28012 OGT enzyme -0.01 0.10
393 121628 HAO1 enzyme 0.00 0.08
232 769645 NDST2 enzyme 0.02 0.04
395 66728 FECH enzyme 0.05 0.05
337 840990 GSTM4 enzyme 0.07 0.05
344 212165 PRDX2 enzyme 0.07 0.05
304 144852 PCL1 enzyme 0.08 0.02
329 897983 AOP2 enzyme 0.09 0.03
278 774036 GSTTLp28 enzyme 0.10 0.03
305 213890 DECR1 enzyme 0.10 0.05
327 897835 OXA1L enzyme 0.10 0.04
308 824024 NMOR2 enzyme 0.12 0.06
309 211780 HEXB enzyme 0.12 0.03
312 248454 ERP70 enzyme 0.14 0.06
300 196992 AKR1C1 enzyme 0.15 0.03
266 124781 SQLE enzyme 0.16 0.09
326 123474 SCD enzyme 0.22 0.04
260 739901 CYP51 enzyme 0.23 0.01
316 840878 DHCR24 enzyme 0.24 0.04
333 770355 LSS enzyme 0.24 0.15
261 247901 HSD17B7 enzyme 0.26 0.06
264 36393 ACAT2 enzyme 0.26 0.06
373 80410 FDPS enzyme 0.31 0.08
294 44975 IDI1 enzyme 0.35 0.11

Signaling/Communication

No. Image Name Group Mean S.D.
6 198904 APMCF1 apoptosis -0.14 0.05
340 814381 DAP apoptosis 0.08 0.07
302 841498 DAXX apoptosis 0.10 0.03
347 810039 DAD1 apoptosis 0.18 0.04
114 72050 CLNS1A channel -0.08 0.01
296 796341 CLCN3 channel 0.09 0.02
408 51640 CNTN1 channel 0.10 0.03
356 45272 CLCN6 channel 0.14 0.08
9 122091 CSNK2A1 kinase -0.08 0.05
211 230385 PIP5K2B kinase -0.07 0.05
235 713080 CLK2 kinase -0.07 0.10
216 128833 PRKWNK1 kinase -0.05 0.10
247 275180 SMG1 kinase 0.03 0.10
315 302031 SLK kinase 0.08 0.01
376 841308 MYLK kinase 0.08 0.11
377 756452 TYK2 kinase 0.09 0.09
271 138737 DYRK2 kinase 0.12 0.04
270 33826 MAP2K1 kinase 0.17 0.05
255 809776 IL16 ligand 0.07 0.06
303 700302 OSTF1 ligand 0.09 0.06
396 770670 TNFAIP3 ligand 0.09 0.31
364 460398 MIP1A ligand 0.12 0.04
11 825442 PTP4A2 phosphatase -0.15 0.04
35 950607 SET phosphatase -0.13 0.03
32 129840 PPP2CA phosphatase -0.11 0.02
120 42739 PTP4A1 phosphatase -0.09 0.06
382 240099 PTPRA phosphatase 0.06 0.11
70 878838 GRM3 receptor -0.18 0.06
209 782789 AVPR1A receptor -0.16 0.13
140 241530 EPHA2 receptor -0.13 0.06
118 80109 HLA-DQA1 receptor -0.09 0.05
76 40365 SCAP receptor -0.08 0.03
90 768496 EBI3 receptor -0.08 0.04
77 840978 CD81 receptor -0.07 0.06
229 757440 IL10RA receptor -0.04 0.11
384 838359 GUCY1B3 receptor 0.05 0.04
350 711857 FGFR1 receptor 0.07 0.05
353 714453 IL4RA receptor 0.09 0.04
392 296757 GYPA receptor 0.10 0.11
343 713145 CD44 receptor 0.12 0.11
375 137017 EGFR receptor 0.12 0.00
388 774409 ENG receptor 0.12 0.13
249 290124 IFNGR1 receptor 0.13 0.03
274 208001 CD59 receptor 0.13 0.03
374 810242 C3AR1 receptor 0.13 0.05
268 785575 IFNGR2 receptor 0.14 0.07
253 788185 TNFRSF10B receptor 0.15 0.05
277 231675 EVI2A receptor 0.15 0.06
306 841149 TGFBR2 receptor 0.15 0.06
265 842860 IL10RB receptor 0.16 0.03
281 813254 F2R receptor 0.19 0.09
334 810017 PLAUR receptor 0.19 0.08
269 504226 CD53 receptor 0.24 0.07
291 35828 DTR receptor 0.26 0.06
325 825295 LDLR receptor 0.30 0.04
289 770014 TRA@ receptor 0.33 0.03
251 704459 CD69 receptor 0.40 0.15
17 754275 ARHGEF12 transducer -0.19 0.08
49 230235 NGB transducer -0.18 0.03
46 783629 HUMAUAG transducer -0.13 0.03
75 711450 P84 transducer -0.12 0.02
79 813158 DRG2 transducer -0.09 0.02
67 842980 DRG1 transducer -0.08 0.01
175 30093 RANBP1 transducer -0.07 0.09
202 45544 TAGLN2 transducer -0.04 0.11
404 39808 PIK3R1 transducer 0.03 0.06
400 240249 APLP2 transducer 0.08 0.03
280 210522 PDE7A transducer 0.09 0.05
282 815774 SLA transducer 0.09 0.06
285 810986 PPP1R11 transducer 0.09 0.02
301 33049 CRY1 transducer 0.09 0.01
346 81315 SEC4L transducer 0.09 0.12
369 563444 GNAS1 transducer 0.11 0.05
295 135083 GRP58 transducer 0.12 0.02
367 49873 MCF2L transducer 0.12 0.17
298 898148 IQGAP1 transducer 0.13 0.02
361 382773 MYOZ2 transducer 0.14 0.05
399 841008 GBP1 transducer 0.14 0.08
349 470379 STAC transducer 0.15 0.08
287 108177 P85SPR transducer 0.16 0.05
328 813707 RGS16 transducer 0.17 0.05
311 154482 SERPINB1 transducer 0.18 0.04

Structure/Motility

No. Image Name Group Mean S.D.
181 235135 ITGA4 adhesion -0.14 0.01
160 346545 LAMB1 adhesion -0.08 0.03
206 359747 LGALS7 adhesion -0.08 0.06
38 342721 ITGB2 adhesion -0.07 0.06
228 40751 CDH8 adhesion -0.07 0.07
230 145112 ICAM1 adhesion 0.01 0.09
366 897531 MCAM adhesion 0.05 0.12
401 136536 PCDHGA8 adhesion 0.05 0.05
254 810859 NK4 adhesion 0.08 0.07
365 469969 ITGAV adhesion 0.09 0.07
71 112525 SYNCOILIN cytoskeleton -0.16 0.04
44 825323 CKAP1 cytoskeleton -0.10 0.01
236 470930 ACTR2 cytoskeleton -0.05 0.10
383 868368 TMSB4X cytoskeleton 0.01 0.16
394 340558 ARPC5 cytoskeleton 0.03 0.06
386 131362 MSN cytoskeleton 0.06 0.06
387 81129 MYH9 cytoskeleton 0.06 0.04
288 840511 VIM cytoskeleton 0.09 0.05
323 713886 CNN2 cytoskeleton 0.09 0.02
276 40562 SGCB cytoskeleton 0.10 0.03
331 194161 ACTN4 cytoskeleton 0.13 0.06
299 840788 TMSB10 cytoskeleton 0.14 0.03
250 841059 CAPG cytoskeleton 0.25 0.13
318 770080 PXN cytoskeleton 0.29 0.09

Unknown

No. Image Name Group Mean S.D.
135 130005 FLJ14494 unknown -0.22 0.05
80 43977 KIAA0182 unknown -0.21 0.04
56 81331 EST_81331 unknown -0.20 0.09
4 196866 FLJ13340 unknown -0.19 0.09
139 151261 MGC5627 unknown -0.19 0.04
25 108425 EST_108425 unknown -0.18 0.03
43 108422 EST_108422 unknown -0.18 0.03
94 154654 EST_154654 unknown -0.18 0.11
102 142944 FLJ20037 unknown -0.18 0.06
69 245147 EST_245147 unknown -0.17 0.02
98 34106 KIAA0153 unknown -0.17 0.04
15 47647 FLJ20397 unknown -0.16 0.04
138 470232 EST_470232 unknown -0.16 0.04
159 193122 MGC5306 unknown -0.16 0.06
31 669471 EST_669471 unknown -0.15 0.04
39 195387 EST_195387 unknown -0.14 0.02
53 173878 EST_173878 unknown -0.14 0.03
131 324255 EST_324255 unknown -0.14 0.04
23 346484 FLJ22351 unknown -0.13 0.07
42 195051 STRAIT11499 unknown -0.13 0.04
87 809779 KIAA0239 unknown -0.13 0.07
143 195903 FLJ20624 unknown -0.13 0.05
150 133158 MGC5297 unknown -0.13 0.04
61 129293 EST_129293 unknown -0.12 0.05
81 262920 H41 unknown -0.12 0.03
155 128875 SCA2 unknown -0.12 0.03
13 202919 DKFZp762N0610 unknown -0.11 0.05
123 306380 MGC4276 unknown -0.11 0.04
130 754046 DXS9879E unknown -0.11 0.02
141 134172 FLJ13855 unknown -0.11 0.05
128 138021 FLJ10563 unknown -0.10 0.06
164 142689 EST_142689 unknown -0.10 0.07
192 293901 EST_293901 unknown -0.10 0.04
106 123815 KIAA1259 unknown -0.09 0.06
133 293599 FLJ10290 unknown -0.09 0.03
68 812144 FLJ20580 unknown -0.08 0.00
84 135561 FLJ20188 unknown -0.08 0.03
104 202339 EST_202339 unknown -0.08 0.03
122 826166 HRIHFB2206 unknown -0.08 0.04
124 203469 KIAA0697 unknown -0.08 0.03
152 66406 DKFZp762E1312 unknown -0.08 0.04
178 814776 MGC14433 unknown -0.08 0.02
169 135273 EST_135273 unknown -0.07 0.17
177 130243 FLJ11036 unknown -0.07 0.10
191 232908 PX19 unknown -0.07 0.02
207 127194 FLJ13195 unknown -0.07 0.03
95 825013 SSP29 unknown -0.06 0.06
168 296155 EST_296155 unknown -0.06 0.07
97 49404 KIAA0218 unknown -0.05 0.04
245 195127 EST_195127 unknown -0.05 0.12
173 235056 EST_235056 unknown -0.04 0.05
240 202034 MGC14439 unknown -0.04 0.04
212 208161 GW128 unknown -0.03 0.05
227 123614 C20ORF55 unknown -0.03 0.05
243 111549 EST_111549 unknown -0.02 0.08
224 212704 KIAA0170 unknown -0.01 0.07
221 239958 KIAA0618 unknown 0.00 0.06
407 140197 LOC51299 unknown 0.01 0.03
217 124808 EST_124808 unknown 0.02 0.14
223 126466 KIAA0467 unknown 0.02 0.06
233 115307 EST_115307 unknown 0.03 0.06
248 111571 HP1-BP74 unknown 0.03 0.04
391 131563 EST_131563 unknown 0.04 0.10
242 206949 EST_206949 unknown 0.05 0.08
359 142397 EST_142397 unknown 0.06 0.05
381 294647 EST_294647 unknown 0.06 0.14
385 122126 EST_122126 unknown 0.06 0.05
284 144924 C6ORF5 unknown 0.07 0.03
234 140792 EST_140792 unknown 0.08 0.04
380 144951 EST_144951 unknown 0.08 0.05
263 206544 EST_206544 unknown 0.09 0.04
313 52431 TDE1 unknown 0.09 0.03
338 210415 EST_210415 unknown 0.09 0.04
379 66391 EST_66391 unknown 0.09 0.12
258 360079 OS-9 unknown 0.11 0.02
262 755299 ETR101 unknown 0.11 0.07
321 136909 EST_136909 unknown 0.11 0.06
330 292528 FLJ23306 unknown 0.11 0.06
341 248256 KIAA1691 unknown 0.11 0.05
342 47475 PIR121 unknown 0.12 0.06
403 213280 EST_213280 unknown 0.12 0.16
252 202213 EST_202213 unknown 0.13 0.06
357 67037 EST_67037 unknown 0.13 0.17
352 243817 EST_243817 unknown 0.14 0.01
402 502067 KIAA0342 unknown 0.16 0.09
319 135673 EST_135273 unknown 0.17 0.08
363 113284 EST_113284 unknown 0.18 0.06
317 292388 LOC55977 unknown 0.19 0.04
314 726678 KIAA0275 unknown 0.23 0.07
389 110996 EST_110996 unknown 0.26 0.14
390 110582 EST_110582 unknown 0.28 0.09

Supplement S3. Comparison of regulated gene signatures in HIV-1BRU infections of CD4+ T cell-lines. Table depicts numbers of regulated genes (P=0.005) for each cell line, number of common- and anti-regulated genes for each comparison and correlation coefficient (‍R‍) for either all observations or the genes in the common signature. * Anti-correlated gene names listed in table below.

Compare Query Target Common Anti R all R common
CEM#1-CEM#2 361 616 224 4 0.922 0.992
CEM#1-CEM#3 341 290 121 1 0.891 0.994
CEM#2-CEM#3 574 290 161 2 0.871 0.992
CEM HI-CEM#1 274 361 121 1 0.941 0.997
CEM HI-CEM#2 274 616 152 4 0.910 0.991
CEM HI-CEM#3 256 290 99 0 0.903 0.997
CEM#2-CEMss 616 257 141 2* 0.858 0.985
CEM#2-CEMfh 616 378 209 0 0.866 0.980
CEM#2-Jurkat 616 440 156 15* 0.704 0.960
CEM#2-SupT1 616 447 179 6* 0.716 0.963
CEMss-CEMfh 257 378 156 0 0.903 0.579
CEMss-Jurkat 257 440 68 4* 0.676 0.984
CEMss-SupT1 257 447 95 2 0.716 0.985
CEMfh-Jurkat 378 440 102 5* 0.688 0.971
CEMfh-SupT1 378 447 133 5* 0.726 0.966
Jurkat-SupT1 440 447 129 7* 0.602 0.957
Compare Anti-correlated genes
CEM#2-CEMss HSU79266, STE
CEM#2-Jurkat GCKR, RPML3, RCN2, H2AFL, PX19, BCL2A1, PPP1CA, MCM3, MYBL2, TCF7, EST_131877, BIRC3, ELAVL1, ACVR1, ACTB
CEM#2-SupT1 SLA, EGR1, PTPRA, STRAIT11499, SCAMP3, LOC51299
CEMss-Jurkat RPML3, GBP1, PCYT2, TCF7
CEMfh-Jurkat XRCC1, DTYMK, RPML3, CD5, TCF7
CEMss-SupT1 PRKACA, STRAIT11499
CEMfh-SupT1 EST_120823, EST_139962, STRAIT11499, IGF2, GALNT2
Jurkat-SupT1 OPRK1, BRF2, EGR1, STRAIT11499, BCL2A1, TCF7, CXCR4