Article Figures & Data
Figures
- Fig. 1.
Outline for the construction of the transcriptome map.
- Fig. 2.
Transcriptome map of NSCLC based on SAGE. Expression is shown for eight SAGE libraries consisting of two each of NHBE, squamous cell carcinomas, SAEC, and adenocarcinomas. The number of gene expression in each tissue type was the sum of tag values from the two libraries of the same tissue or cell type and then normalized to per 100,000 tags. The levels of gene expression are displayed from 0 to 100 with the expression levels over 100 shown as 100. Vertical bars indicate the clustered regions of genes with increased (red) or decreased (green) expression levels, respectively. The average, median, and maximum expression levels of all genes was 14.7, 3.3, and 6452.6 for squamous cell carcinoma; 14.4, 3.9, and 1738.1 for NHBE cell; 17.8, 4.7, and 3279.6 for adenocarcinoma; and 14.9, 4.6, and 1481.3 for SAEC cell libraries. Yellow, orange, and dark brown shading on the chromosome diagrams represent centromeric, variable regions, and stalk, respectively.
- Fig. 2B.
(continued).
Tables
- Table 1
Validation of differentially expressed gene clusters by Monte-Carlo simulation
Squamous cell carcinoma Adenocarcinoma Overexpressed in tumor Underexpressed in tumor Overexpressed in tumor Underexpressed in tumor Observed number of clusters in genomea 16 30 41 23 Expected average number (±S.D.) 6.5 ± 2.4 15 ± 3.3 38.7 ± 4.0 11.5 ± 2.8 P b 0.000064 0.000006 0.5652 0.00004 Average tumor/normal ratio (range) 3.15 (2.76–3.52) 0.65 (0.43–0.78) 4.16 (1.54–4.39) 0.50 (0.27–0.62) -
a The values shown are higher than the actual number of gene clusters because all of the chromosomes were regarded as a continuum and a few clusters had boundaries between chromosomes.
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b The probability to obtain the observed or greater differences between the expected average numbers versus the actual numbers of clusters identified by chance alone.
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- Table 2
Clustering of differentially expressed genes between squamous cell carcinoma and normal bronchial epithelial cells on SAGE-based transcriptome map
Information on the genes included in each cluster can be found at http://lpg.nci.nih.gov/LPG/jen/proj1.
Cluster no. Cytogenetic band Chromosomal positiona Status Number of genes Median T/N ratio Notable genes/tumor suppressor/oncogenesb Referencesc Total Increased Decreased No change 1 1p36.2–p36.3 Chr1:2205808–7866192 − 20 1 12 7 0.43 [TP73] (5 , 7 , 29 , 42) 2 1p36.1 Chr1:17749951–23736394 − 20 2 11 7 0.59 (5) 4 2p22–p23 Chr2:27865382–33722776 − 23 4 14 5 0.73 5 2p11.2–q11.1 Chr2:80547374–96027377 − 25 1 18 6 0.52 6 2q14.2–q21 Chr2:121891208–136835134 − 22 2 12 8 0.75 8 2q35–q36 Chr2:223459509–231867469 − 20 3 12 5 0.70 (7 , 9) 9 2q37 Chr2:238670940–247114424 − 22 3 14 5 0.60 (7 , 9 , 43) 10 3p22–p24 Chr3:29156374–43672061 − 22 2 13 7 0.76 MLH1 11 3p21 Chr3:50161501–53381366 − 21 6 12 3 0.74 (5 , 7 , 9 , 31 , 44) 12 3p21 Chr3:55712479–58579957 − 28 4 15 9 0.78 SEMA3B, FUS1, RASSF1 (5 , 7 , 9 , 32 33 34 35 36 , 44) 16 4p15.3–p16 Chr4:6772157–18506596 − 16 1 11 4 0.58 (7 , 9 , 43) 20 5q35 Chr5:185901250–191841574 − 26 4 15 7 0.64 24 9p13–p21 Chr9:35863844–38031975 − 20 2 12 6 0.62 [11.5 Mb telomeric to CDKN2A] (5 6 7 , 9 , 11 , 42) 27 10q24 Chr10:104155005–111136770 − 39 7 24 8 0.68 [Centromeric to PTEN] (5 , 9 , 38 , 39) 28 11q13 Chr11:79065935–84562231 − 23 7 12 4 0.70 [2.7 Mb telomeric to CCND1] 29 12q13 Chr12:55578725–59469204 − 29 5 17 7 0.70 KRT7, KRT5, KRT6A, KRT1, KRT4, KRT8, HOXC, PFDN5 32 16q12.2–q21 Chr16:64645711–68405819 − 25 4 14 7 0.66 MT2A, MT1E, MMP15, [2.6 Mb centromeric to CDH1] 33–35d 17q21 Chr17:42070147–54387502 − 78 7 41 30 0.72 KRT17, KRT19, KRT14, KRT16, [BRCA1], WNT3, HOXB7 36 17q25 Chr17:81703388–85614916 − 18 4 12 2 0.57 [TOC], SEC14L1, TIMP2 37 19p13.3 Chr19:3149667–5728422 − 25 4 14 7 0.74 [0.9 Mb centromeric to APCL] (5 , 7 , 11) 38 19p13.1 Chr19:17718229–21340745 − 20 2 12 6 0.76 39 19q13.1 Chr19:36880234–46441554 − 40 7 25 8 0.60 40 19q13.1–q13.2 Chr19:51112826–54555604 − 22 5 12 5 0.59 (5 , 7) 41 19q13.3 Chr19:59444162–63343735 − 41 0 26 15 0.60 42 20q12–q13.1 Chr20:41509642–49168634 − 38 10 22 6 0.61 43 20q13.3 Chr20:62621763–64468901 − 17 5 10 2 0.58 3 1q42–q43 Chr1:259270782–274578830 + 23 12 2 9 3.20 (6 , 7 , 9 10 11 , 44) 7 2q31–q32 Chr2:172570929–194025818 + 29 15 1 13 2.76 (10 , 45) 13–14 3q25–q26.3 Chr3:162192762–193593987 + 37 20 3 14 3.52 PIK3CA, SKIL (6 , 7 , 9 10 11 , 42 , 44) 15 3q27–q29 Chr3:197917861–215639073 + 53 31 4 18 3.52 TP63 (6 , 7 , 9 10 11 , 42 , 44) 17 4q21–q24 Chr4:80267829–105587989 + 30 16 7 7 3.05 18–19 5p11–q13 Chr5:1663141–72954158 + 64 39 7 18 3.41 (6 , 7 , 9 10 11) 21 7p14–p22 Chr7:4316431–30797633 + 39 23 4 12 3.29 ( 6 , 10 , 44 , 46) 22–23 8q21.1–q24.1 Chr8:77518537–128248010 + 56 30 4 22 2.96 [4.3 Mb centromeric to MYC] (6 , 7 , 9 10 11 , 42 , 44) 25 9p12–q22 Chr9:40952402–91352574 + 30 16 2 12 3.16 26 9q31–q32 Chr9:107340066–115634147 + 21 13 3 5 3.17 30 13q12–q14 Chr13:23162216–39892274 + 27 14 6 7 2.81 31 14q23–q24 Chr14:55160283–65335623 + 25 13 2 10 2.97 -
a Chromosomal positions are indicated as nucleotide coordinates based on the UCSC Human Genome Working Draft (April 1, 2001 freeze).
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b Genes in brackets are within the cluster but not observed in the lung SAGE libraries.
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c Publications with results consistent with those observed in this study.
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d Gaps up to 1.3 Mb exist among the clusters.
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Volume 62, Issue 12
