Data Mining for Biomarker Development: A Review of Tissue Specificity Analysis

Clinics in Laboratory Medicine

Volumn 28, Issue 1, 2008, Pages 127-143

  Klee, Eric W ^a  

^a MAYO CLINIC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER;

DATA MINING; ENTROPY; GENE EXPRESSION PROFILING; GENOME; PRIORITY JOURNAL; REVIEW; SEQUENCE ANALYSIS; TISSUE SPECIFICITY; TRANSCRIPTOMICS;

BIOLOGICAL MARKERS; DATABASES, FACTUAL; GENE EXPRESSION PROFILING; HUMANS; MEDICAL INFORMATICS; ORGAN SPECIFICITY; SOFTWARE;

EID: 37849011977     PISSN: 02722712     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cll.2007.10.009     Document Type: Review

References (56)

1. National Cancer Institute 2007. The nation's investment in cancer research. A plan and budget proposal for fiscal year 2008. Pub. L. No. 92-218, NIH Publication No. 06-6090.
2. Batchelder K., and Miller P. A change in the market-investing in diagnostics. Nat Biotechnol 24 8 (2006) 922-926
3. Ozdemir V., Williams-Jones B., Glatt S., et al. Shifting emphasis from pharmacogenomics to theragnostics. Nat Biotechnol 24 8 (2006) 942-946
4. Rifai N., Gillette M.A., and Carr S.A. Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat Biotechnol 24 8 (2006) 971-983
5. Cho W.C. Contribution of oncoproteomics to cancer biomarker discovery. Mol Cancer 6 1 (2007) 25
6. Bharti A., Ma P.C., and Salgia R. Biomarker discovery in lung cancer-promises and challenges of clinical proteomics. Mass Spectrom Rev (2007)
7. He Y.D. Genomic approach to biomarker identification and its recent applications. Cancer Biomark 2 3-4 (2006) 103-133
8. Adams M.D., Kellye J.M., Gocayne J.D., et al. Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252 5013 (1991) 1651-1656
9. Velculescu V.E., Zhang L., Vogelstein B., et al. Serial analysis of gene expression. Science 270 5235 (1995) 484-487
10. Brenner S., Johnson M., Bridgham J., et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 18 6 (2000) 630-634
11. Jongeneel C.V., Iseli C., Stevenson B.J., et al. Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencing. Proc Natl Acad Sci U S A 100 8 (2003) 4702-4705
12. Pontius J.U., Wagner L., and Schuler G.D. UniGene: a unified view of the transcriptome. The NCBI handbook (2003), National Center for Biotechnology Information, Bethesda (MD)
13. Boguski M.S., Lowe T.M., and Tolstoshev C.M. dbEST-database for "expressed sequence tags". Nat Genet 4 4 (1993) 332-333
14. Adams M.D., Kerlavage A.R., Fields C., et al. 3,400 new expressed sequence tags identify diversity of transcripts in human brain. Nat Genet 4 3 (1993) 256-267
15. Boon K., Osorio E.C., Greenhut S.F., et al. An anatomy of normal and malignant gene expression. Proc Natl Acad Sci U S A 99 17 (2002) 11287-11292
16. Beaty R.M., Edwards J.B., Boon K., et al. PLXDC1 (TEM7) is identified in a genome-wide expression screen of glioblastoma endothelium. J Neurooncol 81 3 (2007) 241-248
17. Jongeneel C.V., Delorenzi M., Iseli C., et al. An atlas of human gene expression from Massively Parallel Signature Sequencing (MPSS). Genome Res 15 7 (2005) 1007-1014
18. Su A.I., Cooke M.P., Ching K.A., et al. Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci U S A 99 7 (2002) 4465-4470
19. Greller L.D., and Tobin F.L. Detecting selective expression of genes and proteins. Genome Res 9 3 (1999) 282-296
20. Stekel D.J., Git Y., and Falciani F. The comparison of gene expression from multiple cDNA libraries. Genome Res 10 12 (2000) 2055-2061
21. Castensson A., Emilsson L., Preece P., et al. High-resolution quantification of specific mRNA levels in human brain autopsies and biopsies. Genome Res 10 8 (2000) 1219-1229
22. Lai C., Chou C., Ch'ang L., et al. Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics. Genome Res 10 5 (2000) 703-713
23. Walker M.G., Volkmuth W., Sprinzak E., et al. Prediction of gene function by genome-scale expression analysis: prostate cancer-associated genes. Genome Res 9 12 (1999) 1198-1203
24. Ewing R.M., Kahla A.B., Poirot O., et al. Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression. Genome Res 9 10 (1999) 950-959
25. Skrabanek L., and Campagne F. TissueInfo: high-throughput identification of tissue expression profiles and specificity. Nucleic Acids Res 29 21 (2001) E102
26. Altschul S.F., Gish W., Miller W., et al. Basic local alignment search tool. J Mol Biol 215 (1990) 403-410
27. Zhang Z., Schwartz S., Wagner L., et al. A greedy algorithm for aligning DNA sequences. J Comput Biol 7 (2000) 203-214
28. Brown A.C., Kai K., May M.E., et al. ExQuest, a novel method for displaying quantitative gene expression from ESTs. Genomics 83 3 (2004) 528-539
29. Zhang Y., Eberhard D.A., Frantz G.D., et al. GEPIS-quantitative gene expression profiling in normal and cancer tissues. Bioinformatics 20 15 (2004) 2390-2398
30. Zhang Y., Luoh S.M., Hon L., et al. GeneHub-GEPIS: digital expression profiling for normal and cancer tissues based on an integrated gene database. NAR 35 (2007) W152-W158
31. Schug J., Schuller W.P., Kappen C., et al. Promoter features related to tissue specificity as measured by Shannon Entropy. Genome Biol 6 4 (2005) R33
32. The Computational Biology and Informatics Laboratory. AllGenes: a Web site providing access to an integrated database of known and predicted human (release 9.0, 2004) and mouse genes (release 10.0, 2004). Center for Bioinformatics, University of Pennsylvania. Available at: http://www.allgenes.org. Accessed November 19, 2007.
33. Liang S., Li Y., Be X., et al. Detecting and profiling tissue-selective genes. Physiol Genomics 26 2 (2006) 158-162
34. Kadota K., Nishimura S., Bono H., et al. Detection of genes with tissue-specific expression patterns using Akaike's information criterion procedure. Physiol Genomics 12 3 (2003) 251-259
35. Akaike H. Information theory and an extension of the maximum likelihood principle. Proc: 2nd Int symp information theory. Budapest; 1973. p. 267-81.
36. Miki R., Kadota K., Bono H., et al. Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays. Proc Natl Acad Sci U S A 98 5 (2001) 2199-2204
37. Kadota K., Ye J., Nakai Y., et al. ROKU: a novel method for identification of tissue-specific genes. BMC Bioinformatics 7 (2006) 294
38. Saito-Hisaminato A., Katagiri T., Kakiuchi S., et al. Genome-wide profiling of gene expression in 29 normal human tissues with a cDNA microarray. DNA Res 9 2 (2002) 35-45
39. Hsiao L.L., Dangond F., Yoshida T., et al. A compendium of gene expression in normal human tissues. Physiol Genomics 7 2 (2001) 95-96
40. Misra J., Schmitt W., Hwang D., et al. Interactive exploration of microarray gene expression patterns in a reduced dimensional space. Genome Res 12 7 (2002) 1112-1120
41. Vasmatzis G., Klee E., Kube D.M., et al. Quantitating tissue specificity of human genes to facilitate biomarker discovery. Bioinformatics 23 11 (2007) 1348-1355
42. Gupta S., Vingron M., and Haas S.A. T-STAG: resource and Web-interface for tissue-specific transcripts and genes. Nucleic Acids Res 33 Web Server issue (2005) W654-W658
43. Wang J., and Liang P. DigiNorthern, digital expression analysis of query genes based on ESTs. Bioinformatics 19 5 (2003) 653-654
44. Madden S.F., O'Donovan B., Furney S.J., et al. Digital extractor: analysis of digital differential display output. Bioinformatics 19 12 (2003) 1594-1595
45. Huminiecki L., and Bicknell R. In silico cloning of novel endothelial-specific genes. Genome Res 10 11 (2000) 1796-1806
46. Huminiecki L., Lloyd A.T., and Wolfe K.H. Congruence of tissue expression profiles from gene expression atlas, SAGEmap and TissueInfo databases. BMC Genomics 4 1 (2003) 31
47. Campagne F., and Skrabanek L. Mining expressed sequence tags identifies cancer markers of clinical interest. BMC Bioinformatics 7 (2006) 481
48. Wang X.S., Zhang Z., Wang H.C., et al. Rapid identification of UCA1 as a very sensitive and specific unique marker for human bladder carcinoma. Clin Cancer Res 12 16 (2006) 4851-4858
49. Wang A.G., Yoon S.Y., Oh J.H., et al. Identification of intrahepatic cholangiocarcinoma related genes by comparison with normal liver tissues using expressed sequence tags. Biochem Biophys Res Commun 345 3 (2006) 1022-1032
50. Yoon S.Y., Kim J.M., Oh J.H., et al. Gene expression profiling of human HBV- and/or HCV-associated hepatocellular carcinoma cells using expressed sequence tags. Int J Oncol 29 2 (2006) 315-327
51. Huang Z.G., Ran Z.H., Lu W., et al. Analysis of gene expression profile in colon cancer using the cancer genome anatomy project and RNA interference. Chin J Dig Dis 7 2 (2006) 97-102
52. Aouacheria A., Navratil V., Barthelaix A., et al. Bioinformatic screening of human ESTs for differentially expressed genes in normal and tumor tissues. BMC Genomics 7 (2006) 94
53. Laterza O.F., Modur V.R., Crimmins D.L., et al. Identification of novel brain biomarkers. Clin Chem 52 9 (2006) 1713-1721
54. Asmann Y.W., Kosari F., Wang K., et al. Identification of differentially expressed genes in normal and malignant prostate by electronic profiling of expressed sequence tags. Cancer Res 62 11 (2002) 3308-3314
55. Megy K., Audic S., and Claverie J.M. Heart-specific genes revealed by expressed sequence tag (EST) sampling. Genome Biol 3 12 (2002) RESEARCH0074:1-11
56. Klee E.W., Finlay J., McDonald C., et al. Bioinformatics methods for prioritizing serum biomarker candidates. Clin Chem 52 11 (2006) 2162-2164