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Table 4 Gene expression trends of LongSAGE tags that consistently and significantly altered expression in CR prostate cancer*

From: LNCaP Atlas: Gene expression associated with in vivoprogression to castration-recurrent prostate cancer

  13N 15N 13R    
  AS§ RADII CR¶ AS RAD CR AS RAD CR    
Tag Sequence S1885 S1886 S1887 S1888 S1889 S1890 S1891 S1892 S1893 Trend‡ Gene** Accession§§
TCTAGAGAACACTGTGC 12† 79 382 7 67 136 7 52 200 A ACPP‡‡ NM_001099
TAATTTTTCTAAGGTGT 101 311 648 119 397 895 120 546 918 A C1ORF80 ENSG00000186063
TGAGAGAGGCCAGAACA 8 39 150 4 39 144 7 33 95 A N/A Genomic
CTCATAAGGAAAGGTTA 637 952 1680 653 1170 1540 688 1620 1930 A RNF208 BC090061
GATTTCTATTTGTTTTT 89 169 446 116 208 339 86 311 555 A SERINC5 ENSG00000164300
GTTGGGAAGACGTCACC 426 571 742 273 417 741 262 363 495 A STEAP1 NM_012449
GAGGATCACTTGAGGCC 191 299 449 134 189 589 187 203 314 B AMACR‡‡ BC009471
TTGTTGATTGAAAATTT 219 197 528 273 197 479 232 391 586 B AMD1‡‡ NM_001634
TTTGCTTTTGTTTTGTT 53 16 169 34 51 129 7 28 72 B AQP3 NM_004925
GTTCGACTGCCCACCAG 45 28 101 52 47 122 34 42 106 B ASAH1†† NM_177924
TAATAAACAGGTTTTTA 426 232 648 332 315 700 138 250 491 B ASAH1‡‡ NM_177924
TCACAGCTGTGAAGATC 85 110 277 161 71 258 310 438 945 B BTG1 NM_001731
AAAAGAGAAAGCACTTT 24 75 199 19 35 85 15 90 552 B CAMK2N1 NM_018584
CAAAACAGGCAGCTGGT 4 71 169 15 83 162 37 75 268 B CAMK2N1†† NM_018584
AGGAGGAAGAATGGACT 33 59 187 49 67 247 26 42 223 B CCNH NM_001239
TTTTAAAAATATAAAAT 89 83 243 97 130 269 64 170 382 B COMT NM_000754
GAATGAAATAAAAAATA 134 252 626 209 240 357 116 160 272 B DHRS7 NM_016029
AAAGTGCATCCTTTCCC 118 146 318 153 220 394 288 231 646 B FGFRL1 NM_001004356
AAACTGAATAAGGAGAA 24 51 236 19 51 438 19 146 283 B GALNT3 NM_004482
TTTAAGGAAACATTTGA 4 4 75 4 4 81 0 0 57 B GALNT3†† NM_004482
CCAACCGTGCTTGTACT 191 327 521 202 279 534 172 363 510 B GLO1 NM_006708
GAGGGCCGGTGACATCT 300 378 1170 321 476 1230 254 447 1030 B H2AFJ NM_177925
TATCATTATTTTTACAA 57 63 161 67 63 181 75 94 181 B HSD17B4 NM_000414
AATGCACTTATGTTTGC 16 8 64 22 16 77 19 28 98 B N/A No map
ACCTTCGCAGGGGAGAG 0 0 19 0 4 41 0 5 34 B N/A Genomic
ATAACCTGAAAGGAAAG 0 16 56 7 4 74 0 28 87 B N/A No map
GTGATGTGCACCTGTTG 0 0 38 4 0 30 0 5 45 B N/A No map
GTTTGGAGGTACTAAAG 20 43 94 34 87 169 34 90 234 B N/A Genomic
TTTTCAAAAATTGGAAA 0 35 180 7 4 59 0 19 61 B N/A No map
GAAAAATTTAAAGCTAA 394 397 569 433 598 788 853 862 1060 B NGFRAP1 NM_206917
CAAATTCAGGGAGCACA 0 4 139 4 16 228 0 14 136 B OPRK1 NM_000912
CTATTGTCTGAACTTGA 0 8 109 0 12 70 0 9 227 B OR51E2 BC020768
ATGCTAATTATGGCAAT 4 12 75 4 8 74 0 5 57 B PCGEM1 NR_002769
CAGAAAGCATCCCTCAC 4 43 195 0 16 111 7 33 264 B PLA2G2A‡‡ NM_000300
TAATTTTAGTGCTTTGA 16 75 154 37 59 162 4 57 132 B PTGFR NM_000959
TTGTTTGTAAATAGAAT 0 12 94 0 4 162 0 14 72 B QKI NM_206853
TAAACACTGTAAAATCC 0 4 75 0 4 66 0 0 42 B QKI†† NM_206853
AGCAGATCAGGACACTT 20 35 112 15 16 140 15 42 98 B S100A10 NM_002966
CTGCCATAACTTAGATT 37 55 161 93 63 192 56 99 264 B SBDS NM_016038
TGGCTGAGTTTATTTTT 20 24 79 41 8 96 4 42 147 B SFRS2B NM_032102
GAAGATTAATGAGGGAA 126 142 277 108 130 402 101 188 325 B SNX3 NM_003795
ATGGTACTAAATGTTTT 16 47 124 37 28 88 11 19 76 B SPIRE1 NM_020148
TATATATTAAGTAGCCG 45 39 101 45 75 133 41 75 178 B STEAP2‡‡ NM_152999
CAACAATATATGCTTTA 24 32 82 75 32 136 26 99 212 B STEAP2†† NM_152999
TTTCATTGCCTGAATAA 24 43 150 34 59 114 22 61 178 B TACC1‡‡ NM_006283
TTGGCCAGTCTGCTTTC 8 16 67 4 4 77 0 5 38 B TMEM30A ENSG00000112697
ATATCACTTCTTCTAGA 12 4 26 7 4 26 0 52 140 C ADAM2‡‡ NM_001464
ATGTGTGTTGTATTTTA 812 338 768 1010 315 1020 269 702 865 C BNIP3 NM_004052
CCACGTTCCACAGTTGC 601 291 599 530 346 700 381 339 559 C ENO2 NM_001975
CTGATCTGTGTTTCCTC 16 0 26 0 4 41 19 0 34 C HLA-B BC013187
AGCCCTACAAACAACTA 382 441 596 508 456 619 400 631 1010 C MT-ND3 ENSG00000198840
ATATTTTCTTTGTGGAA 20 12 90 7 0 48 4 0 23 C N/A No map
CAAGCATCCCCGTTCCA 2400 2130 2440 2730 1720 2250 1020 2010 2340 C N/A ENSG00000211459
GTTGTAAAATAAACTTT 118 83 172 228 87 247 112 203 378 C N/A Genoic
TTGGATTTCCAAAGCAG 12 0 19 0 0 33 0 0 26 C N/A Genomic
TCTTTTAGCCAATTCAG 138 181 420 381 326 468 389 334 457 C NKX3-1†† NM_006167
TGATTGCCCTTTCATAT 73 39 86 86 39 107 108 99 181 C P4HA1 NM_000917
GTAACAAGCTCTGGTAT 28 16 56 49 24 66 11 19 72 C PJA2 NM_014819
ACAGTGCTTGCATCCTA 85 75 139 108 98 203 101 118 196 C PPP2CB NM_004156
AGGCGAGATCAATCCCT 57 39 101 37 24 122 131 66 268 C PSMA7 NM_002792
TATTTTGTATTTATTTT 73 59 180 93 51 111 22 94 253 C SLC25A4 NM_001151
TTATGGATCTCTCTGCG 1050 1260 1820 1140 1300 2260 1990 1010 1530 C SPON2 NM_012445
CAGTTCTCTGTGAAATC 767 515 1060 855 503 914 467 608 1200 C TMEM66 NM_016127
AAATAAATAATGGAGGA 138 59 255 82 118 284 165 90 159 C TRPM8 NM_024080
ATGTTTAATTTTGCACA 61 87 154 157 59 195 217 85 344 C WDR45L NM_019613
GGGCCCCAAAGCACTGC 861 543 1180 1020 657 1590 1240 739 937 E C19orf48 NM_199249
TCCCCGTGGCTGTGGGG 1670 1390 2290 1740 1410 1720 3370 970 1180 E DHCR24‡‡ BC004375
GCATCTGTTTACATTTA 487 201 345 444 208 468 684 226 423 E ELOVL5 NM_021814
GAAATTAGGGAAGCCTT 317 153 311 310 181 542 359 193 298 E ENDOD1 XM_290546
GGATGGGGATGAAGTAA 2780 1160 4780 2950 1350 3620 2930 1230 1890 E KLK3‡‡ NM_001648
TGAAAAGCTTAATAAAT 313 142 322 474 181 332 273 179 314 E TPD52 NM_001025252
GTTGTGGTTAATCTGGT 1770 634 1270 1800 806 1190 2480 659 960 F B2M NM_004048
GAAACAAGATGAAATTC 4380 1170 2260 5300 1110 2720 3750 2220 2830 F PGK1 NM_000291
AGCACCTCCAGCTGTAC 2150 1130 648 2060 1560 939 1560 1200 722 G EEF2 NM_001961
GCACAAGAAGATTAAAA 536 228 124 762 425 195 838 278 174 G GAS5 NR_002578
CCGCTGCGTGAGGGCAG 451 169 56 429 197 44 516 94 0 G HES6 NM_018645
GCCCAGGTCACCCACCC 585 55 4 519 79 7 456 66 0 G LOC644844 XM_927939
ATGCAGCCATATGGAAG 2650 386 82 2470 216 129 1210 259 98 G ODC1 NM_002539
CGCTGGTTCCAGCAGAA 1420 811 479 1250 959 553 800 589 374 G RPL11 NM_000975
AAGACAGTGGCTGGCGG 2650 1730 1220 2460 1860 1350 2120 1630 1270 G RPL37A‡‡ NM_000998
TTCTTGTGGCGCTTCTC 925 543 217 1030 708 273 1130 419 306 G RPS11†† NM_001015
GGTGAGACACTCCAGTA 463 252 165 485 346 192 363 245 159 G SLC25A6 NM_001636
AGGTTTTGCCTCATTCC 982 515 281 1200 491 243 688 782 166 H ABHD2 NM_007011
TGAAGGAGCCGTCTCCA 317 272 187 392 295 199 366 259 140 H ATP5G2 NM_001002031
CTCAGCAGATCCAAGAG 191 185 67 254 232 66 142 231 79 H C17orf45 NM_152350
CTGTGACACAGCTTGCC 308 397 172 209 307 125 295 226 110 H CCT2 NM_006431
TCTGCACCTCCGCTTGC 495 606 277 426 570 276 366 471 204 H EEF1A2 NM_001958
GCCCAAGGACCCCCTGC 114 114 38 138 98 41 101 42 4 H FLNA‡‡ NM_001456
TTATGGGATCTCAACGA 564 425 180 642 452 317 430 490 253 H GNB2L1 NM_006098
TCTGCAAAGGAGAAGTC 81 102 38 105 87 26 165 80 30 H HMGB2 NM_002129
CTTGTGAACTGCACAAC 268 228 124 231 177 103 273 160 57 H HN1 NM_016185
TCTGAAGTTTGCCCCAG 313 291 150 254 299 155 187 226 72 H MAOA NM_000240
TTAATTGATAGAATAAA 483 350 199 422 287 103 273 235 83 H MAOA NM_000240
GGCAGCCAGAGCTCCAA 1200 1260 420 1050 672 350 681 819 23 H MARCKSL1 NM_023009
CCCTGCCTTGTCCCTCT 353 240 112 310 263 107 176 193 102 H MDK NM_001012334
CTGTGGATGTGTCCCCC 649 476 169 459 389 214 430 297 117 H N/A No map
CTCCTCACCTGTATTTT 1120 771 262 1220 979 313 666 730 261 H RPL13A‡‡ NM_012423
GCAGCCATCCGCAGGGC 1980 1770 809 2300 1730 928 2150 1570 1020 H RPL28 NM_000991
GGATTTGGCCTTTTTGA 3470 2070 1370 4170 2910 1540 2800 2870 2500 H RPLP2‡‡ NM_001004
TCTGTACACCTGTCCCC 2320 1670 850 1930 1880 825 2130 1490 1120 H RPS11 NM_001015
GCTTTTAAGGATACCGG 1510 1050 626 1860 1120 593 1550 1550 960 H RPS20‡‡ NM_001023
CCCCAGCCAGTCCCCAC 921 519 281 788 664 357 1100 438 291 H RPS3 NM_001005
CCCCCAATGCTGAGGCC 89 138 26 90 94 30 90 80 30 H SF3A2 NM_007165
GCCGCCATCTCCGAGAG 195 102 30 168 118 55 172 108 30 H TKT NM_001064
GGCCATCTCTTCCTCAG 349 307 202 317 346 173 277 254 121 H YWHAQ NM_006826
AGGCTGTGTTCCTCCGT 16 39 11 34 67 22 26 38 8 I ACY1 NM_000666
TGCCTCTGCGGGGCAGG 446 649 427 399 664 424 501 462 317 I CD151 NM_004357
GGCACAGTAAAGGTGGC 175 216 142 332 350 173 456 316 204 I CUEDC2 NM_024040
TCACACAGTGCCTGTCG 49 71 7 30 47 15 34 66 4 I CXCR7 NM_001047841
TGTGAGGGAAGCTGCTT 53 87 15 67 102 52 52 90 42 I FKBP10 BC016467
TGCTTTGCTTCATTCTG 28 63 26 22 79 26 49 118 61 I GRB10 NM_005311
GTACTGTATGCTTGCCA 170 212 82 134 153 88 123 188 113 I KPNB1‡‡ NM_002265
GTGGCAGTGGCCAGTTG 106 193 97 123 173 96 94 137 76 I N/A ENSG00000138744
GGGGAGCCCCGGGCCCG 61 63 26 30 51 18 34 57 0 I NAT14 NM_020378
TGTTCAGGACCCTCCCT 28 67 26 60 63 26 60 28 0 I NELF NM_015537
TTTTCCTGGGGATCCTC 41 130 15 37 87 33 56 104 45 I PCOTH NM_001014442
GAAACCCGGTAGTCTAG 41 75 4 37 75 26 52 151 30 I PLCB4 NM_000933
GTCTGACCCCAGGCCCC 126 205 82 119 193 103 157 179 38 I PPP2R1A NM_014225
GGCCCGAGTTACTTTTC 231 150 75 161 232 136 142 160 45 I RPL35A†† NM_000996
GTTCGTGCCAAATTCCG 881 696 390 1100 712 523 497 782 461 I RPL35A‡‡ NM_000996
TTACCATATCAAGCTGA 877 535 311 1130 598 405 636 791 578 I RPL39‡‡ NM_001000
GCTGCAGCACAAGCGGC 268 244 127 45 216 125 157 71 11 I RPS18†† NM_022551
AGCTCTTGGAGGCACCA 203 319 206 142 421 243 269 259 162 I SELENBP1 NM_003944
TGCTGGTGTGTAAGGGG 69 102 45 82 87 37 105 75 30 I SH3BP5L NM_030645
GAGAGTAACAGGCCTGC 191 150 71 112 181 111 108 165 64 I SYNC1 NM_030786
CTGAAAACCACTCAAAC 394 508 225 306 547 236 310 381 200 I TFPI NM_006287
TAAAAAAGGTTTCATCC 183 248 127 86 130 66 142 268 87 I TFPI NM_006287
CTCCCTCCTCTCCTACC 28 32 4 30 39 7 71 24 0 I TK1 NM_003258
CATTTTCTAATTTTGTG 544 744 236 407 771 181 288 664 185 J N/A No map
TGATTTCACTTCCACTC 3480 5260 3910 3700 6110 3590 3040 5960 2600 K MT-CO3 ENSG00000198938
TTTCTGTCTGGGGAAGG 130 236 82 123 201 111 101 188 113 K PIK3CD NM_005026
GCCGCTACTTCAGGAGC 256 370 199 224 330 169 142 316 38 K RAMP1 NM_005855
ATGGTTACACTTTTGGT 93 161 94 75 208 118 60 226 95 K UTX NM_021140
CACTACTCACCAGACGC 2820 3900 3020 2740 4290 2440 2620 3120 1260 K VPS13B†† ENSG00000132549
CTAAGACTTCACCAGTC 7120 11000 9730 6390 10900 8330 3610 8870 7850 L N/A ENSG00000210082
  1. * Statistics according to the Audic and Claverie test statistic (p ≤ 0.05)
  2. † Tag count per 1 million = (observed tag count/total tags in the library) × 1,000,000
  3. ‡ Trends are visually represented from A to P in Additional file 1, Figure S3. In addition to p-value considerations, significantly different trends were also required to display uniform directions of change in each biological replicate.
  4. § AS, Androgen-sensitive
  5. II RAD, Responsive to androgen-deprivation
  6. ¶ CR, Castration-recurrent
  7. ** Human Genome Nomenclature Committee (HGNC)-approved gene names were used when possible. Non-HGNC-approved gene names were not italicized.
  8. †† Tag maps antisense to gene
  9. ‡‡ Gene is known to display this expression trend in castration-recurrence
  10. §§ Accession numbers were displayed following the priority (where available): RefSeq > Mammalian Gene Collection > Ensembl Gene. If the tag mapped to more than one transcript variant of the same gene, the accession number of the lowest numerical transcript variant was displayed.