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Table 4 Genomic information and reason for inclusion in the original 422-gene signature for the 34 genes selected in the prediction model

From: Prediction of chemo-response in serous ovarian cancer

Annotation Expression Copy number DNA Methylation miRNA expression
Symbol Name Entrez-ID chr Start Length Fold-change (CR/IR) Presence cytoband Methylated Genes Methylation Status (CR/IR) miRNA CR/IR expression
LRRC8D leucine rich repeat containing 8 family, member D 55144 1 90286572 115417 1.13       
OLFML3 olfactomedin-like 3 56944 1 114522029 2846 0.76       
DPT dermatopontin 1805 1 168664694 33748 0.9       
FAP fibroblast activation protein, alpha 2191 2 163027199 72846 0.7       
RNF13 ring finger protein 13 11342 3 149530474 149451   Gain 3q22.1-q29 CRKRS 1.19   
SLC7A11 solute carrier family 7, (cationic amino acid transporter, y + system) member 11 23657 4 139085247 78256   Loss 4q13.3-q35.2     
TRIO triple functional domain (PTPRF interacting) 7204 5 14143828 365630 1.18 Gain 5p15.33-p13.1     
DROSHA drosha, ribonuclease type III 29102 5 31400601 131681 1.16 Gain 5p15.33-p13.1     
RPS23 ribosomal protein S23 6228 5 81569138 5097 0.96 Loss 5q11.2-q21.1 UNQ9217 1.15 miR-22 0.8
SYNE1 spectrin repeat containing, nuclear envelope 1 23345 6 152442821 196658   Loss 6q15-q27 LAD1, NFATC2, SLC1A2, STEAP4 0.77 miR-22, miR-200b 1.22
STEAP4 STEAP family member 4 79689 7 87905743 30466     SYNE1 0.82   
PRSS1 protease, serine, 1 (trypsin 1) 5644 7 142457318 3609 1.32 Gain 7q32.1-q36.3     
PRSS2 protease, serine, 2 (trypsin 2) 5645 7 142479907 1471 1.34 Gain 7q32.1-q36.3     
ST18 suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein) 9705 8 53023391 299048 0.97 Gain 8p11.21-q24.3     
RPS20 ribosomal protein S20 6224 8 56980738 6402   Gain 8p11.21-q24.3    miR-135b 1.22
ZBTB10 zinc finger and BTB domain containing 10 65986 8 81398447 36163 1.2 Gain 8p11.21-q24.3    miR-708 1.2
MTAP methylthioadenosine phosphorylase 4507 9 21802634 63335 1.12 Loss 9p21.3-p21.2     
GCNT1 glucosaminyl (N-acetyl) transferase 1, core 2 2650 9 79056581 65751 1.17       
C10orf26 WBP1L - chromosome 10 open reading frame 26 54838 10 104503726 72295 0.87 No      
MYO7A myosin VIIA 4647 11 76839309 86977 1.08 Gain 11q13.5-q14.1     
PDGFD platelet derived growth factor D 80310 11 103777913 257114 0.76 No      
KLRAP1 killer cell lectin-like receptor subfamily A pseudogene 1 10748 12 10741076 11358   Gain 12p13.33-p11.21    miR-22 0.8
NUAK1 NUAK family, SNF1-like kinase, 1 9891 12 106457124 76687 0.75 No      
POLE polymerase (DNA directed), epsilon 5426 12 133200347 63598 1.14 No      
ENTPD5 ectonucleoside triphosphate diphosphohydrolase 5 957 14 74433180 52846 1.13 No      
THBS1 thrombospondin 1 7057 15 39873279 16389   Loss 15q11.1-q21.1 CORO6, LAD1, NFATC2, SLC1A2, SNAI1 0.74 miR-22, miR-641, miR-200b 1.22
CCPG1 cell cycle progression 1 9236 15 55647437 53137 0.84 Loss 15q21.3     
PDPR pyruvate dehydrogenase phosphatase regulatory subunit 55066 16 70147528 47656 1.04 Loss 16q12.2-q24.3     
RHOT1 ras homolog gene family, member T1 55288 17 30469472 83274 0.87 Gain 17p13.3-q21.2     
MLX MAX-like protein X 6945 17 40719077 6144 0.88 No      
COPZ2 coatomer protein complex, subunit zeta 2 51226 17 46103532 11620 0.78 No      
MATK megakaryocyte-associated tyrosine kinase 4145 19 3777966 8449 0.93 No      
TIMP3 TIMP metallopeptidase inhibitor 3 7078 22 33196801 62227 0.7 Loss 22q11.22    miR-22 0.8
MCM5 minichromosome maintenance complex component 5 4174 22 35796115 24380 1.19 Loss 22q11.22-q13.33     
  1. In the Expression, Copy number, DNA methylation, and miRNA expression, only those with significant differential values between CR and IR were represented. Some genes had more than one biological difference
  2. Copy number shows the chromosomal region (cytoband) that was significantly correlated with gene expression in the 422-gene signature. DNA Methylation and miRNA expression shows the initial variables that were significantly correlated to gene expression in the 422-gene signature