Differential gene expression profiling analysis in workers occupationally exposed to benzene

Science of the Total Environment

Volumn 472, Issue , 2014, Pages 872-879

  Gao, Ai ^a   Yang, Jing ^a   Yang, Gengxia ^a   Niu, Piye ^a   Tian, Lin ^a  

^a CAPITAL MEDICAL UNIVERSITY   (China)

Author keywords

Benzene; Bioinformatics analysis; Gene expression profiling; Microarray analysis

Indexed keywords

BIOCHEMISTRY; BIOINFORMATICS; CELL DEATH; CELL MEMBRANES; ENZYME ACTIVITY; GENE EXPRESSION; IMMUNE SYSTEM; NUCLEIC ACIDS; PIGMENTS; SIGNAL TRANSDUCTION;

ACUTE MYELOID LEUKEMIA; BIOINFORMATICS ANALYSIS; DIFFERENTIAL GENE EXPRESSIONS; ENVIRONMENTAL CONTAMINANT; GENE EXPRESSION PROFILING; HEMATOPOIETIC CELL LINEAGES; INFLAMMATORY RESPONSE; MICROARRAY ANALYSIS;

BENZENE;

B LYMPHOCYTE RECEPTOR; BENZENE; BIOLOGICAL MARKER; MESSENGER RNA; T LYMPHOCYTE RECEPTOR;

BENZENE; BIOINFORMATICS; BIOMARKER; GENE EXPRESSION; IMMUNE RESPONSE; OCCUPATIONAL EXPOSURE; RNA; TOXICITY;

ADULT; ARTICLE; BLOOD TOXICITY; CONTROLLED STUDY; GENE; GENE EXPRESSION PROFILING; GENETIC VARIABILITY; GNAI3 GENE; HLA DMA GENE; HLA DMB GENE; HUMAN; IMMUNE RESPONSE; INTOXICATION; KRAS GENE; MICROARRAY ANALYSIS; NFKB1 GENE; NRAS GENE; NUCLEOTIDE SEQUENCE; OCCUPATIONAL EXPOSURE; PIK3CG GENE; PIK3R1 GENE; PIK3R2 GENE; PLCG2 GENE; PRIORITY JOURNAL; PTPN6 GENE; RNA EXTRACTION; SIGNAL TRANSDUCTION; SOCS4 GENE; SYK GENE;

BENZENE; BIOINFORMATICS ANALYSIS; GENE EXPRESSION PROFILING; MICROARRAY ANALYSIS;

ADULT; AIR POLLUTANTS, OCCUPATIONAL; BENZENE; BIOLOGICAL MARKERS; FEMALE; GENE EXPRESSION PROFILING; HLA-D ANTIGENS; HUMANS; MALE; OCCUPATIONAL EXPOSURE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA, MESSENGER;

EID: 84890418788     PISSN: 00489697     EISSN: 18791026     Source Type: Journal    
DOI: 10.1016/j.scitotenv.2013.11.089     Document Type: Article

References (34)

1. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29.
2. Bollati V., Baccarelli A., Hou L., Bonzini M., Fustinoni S., Cavallo D., et al. Changes in DNA methylation patterns in subjects exposed to low-dose benzene. Cancer Res 2007, 67:876-880.
3. Clarke R., Ressom H.W., Wang A., Xuan J., Liu M.C., Gehan E.A., et al. The properties of high-dimensional data spaces: implications for exploring gene and protein expression data. Nat Rev Cancer 2008, 8:37-49.
4. Draghici S., Khatri P., Tarca A.L., Amin K., Done A., Voichita C., et al. A systems biology approach for pathway level analysis. Genome Res 2007, 17:1537-1545.
5. Dupuy D., Bertin N., Hidalgo C.A., Venkatesan K., Tu D., Lee D., et al. Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans. Nat Biotechnol 2007, 25:663-668.
6. Forrest M.S., Lan Q., Hubbard A.E., Zhang L., Vermeulen R., Zhao X., et al. Discovery of novel biomarkers by microarray analysis of peripheral blood mononuclear cell gene expression in benzene-exposed workers. Environ Health Perspect 2005, 113:801-807.
7. Gao A., Zuo X., Song S., Guo W., Tian L. Epigenetic modification involved in benzene-induced apoptosis through regulating apoptosis-related genes expression. Cell Biol Int 2011, 35:391-396.
8. Glass D.C., Gray C.N., Jolley D.J., Gibbons C., Sim M.R., Fritschi L., et al. Leukemia risk associated with low-level benzene exposure. Epidemiology 2003, 14:569-577.
9. Irons R.D., Chen Y., Wang X., Ryder J., Kerzic P.J. Acute myeloid leukemia following exposure to benzene more closely resembles de novo than therapy related-disease. Genes Chromosomes Cancer 2013, 52:887-894.
10. Jansen R., Greenbaum D., Gerstein M. Relating whole-genome expression data with protein-protein interactions. Genome Res 2002, 12:37-46.
11. Kanehisa M., Goto S., Kawashima S., Okuno Y., Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res 2004, 32:D277-D280.
12. Lagorio S., Ferrante D., Ranucci A., Negri S., Sacco P., Rondelli R., et al. Exposure to benzene and childhood leukaemia: a pilot case-control study. BMJ Open 2013, 3(2).
13. Lan Q., Zhang L., Li G., Vermeulen R., Weinberg R.S., Dosemeci M., et al. Hematotoxicity in workers exposed to low levels of benzene. Science 2004, 306:1774-1776.
14. Lan Q., Zhang L., Shen M., Smith M.T., Li G., Vermeulen R., et al. Polymorphisms in cytokine and cellular adhesion molecule genes and susceptibility to hematotoxicity among workers exposed to benzene. Cancer Res 2005, 65(20):9574-9581.
15. Li C., Li H. Network-constrained regularization and variable selection for analysis of genomic data. Bioinformatics 2008, 24:1175-1182.
16. Li G., Yin S. Progress of epidemiological and molecular epidemiological studies on benzene in China. Ann N Y Acad Sci 2006, 1076:800-809.
17. McHale C.M., Zhang L., Lan Q., Li G., Hubbard A.E., Forrest M.S., et al. Changes in the peripheral blood transcriptome associated with occupational benzene exposure identified by cross-comparison on two microarray platforms. Genomics 2009, 93:343-349.
18. McHale C.M., Zhang L., Lan Q., Vermeulen R., Li G., Hubbard A.E., et al. Global gene expression profiling of a population exposed to a range of benzene levels. Environ Health Perspect 2011, 119:628-634.
19. Miller L.D., Long P.M., Wong L., Mukherjee S., McShane L.M., Liu E.T. Optimal gene expression analysis by microarrays. Cancer Cell 2002, 2(5):353-361.
20. Pesatori A.C., Garte S., Popov T., Georgieva T., Panev T., Bonzini M., et al. Early effects of low benzene exposure on blood cell counts in Bulgarian petrochemical workers. Med Lav 2009, 100:83-90.
21. Ramoni M.F., Sebastiani P., Kohane I.S. Cluster analysis of gene expression dynamics. Proc Natl Acad Sci U S A 2002, 99(14):9121-9126.
22. Reiner A., Yekutieli D., Benjamini Y. Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics 2003, 19(3):368-375.
23. Sarma S.N., Kim Y.J., Ryu J.C. Differential gene expression profiles of human leukemia cell lines exposed to benzene and its metabolites. Environ Toxicol Pharmacol 2011, 32(2):285-295.
24. Schlitt T., Palin K., Rung J., Dietmann S., Lappe M., Ukkonen E., et al. From gene networks to gene function. Genome Res 2003, 13:2568-2576.
25. Shen M., Zhang L., Lee K.M., Vermeulen R., Hosgood H.D., Li G., et al. Polymorphisms in genes involved in innate immunity and susceptibility to benzene-induced hematotoxicity. Exp Mol Med 2011, 43(6):374-378.
26. Snyder R. Leukemia and benzene. Int J Environ Res Public Health 2012, 9:2875-2893.
27. Spirin V., Mirny L.A. Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci U S A 2003, 100:12123-12128.
28. Swaen G.M., van Amelsvoort L., Twisk J.J., Verstraeten E., Slootweg R., Collins J.J., et al. Low level occupational benzene exposure and hematological parameters. Chem Biol Interact 2010, 184:94-100.
29. Wei Z., Li H. A Markov random field model for network-based analysis of genomic data. Bioinformatics 2007, 23:1537-1544.
30. Wright G.W., Simon R.M. A random variance model for detection of differential gene expression in small microarray experiments. Bioinformatics 2003, 19:2448-2455.
31. Xiao S., Mo D., Wang Q., Jia J., Qin L., Yu X., et al. Aberrant host immune response induced by highly virulent PRRSV identified by digital gene expression tag profiling. BMC Genomics 2010, 11:544.
32. Yi M., Horton J.D., Cohen J.C., Hobbs H.H., Stephens R.M. Whole Pathway Scope: a comprehensive pathway-based analysis tool for high-throughput data. BMC Bioinformatics 2006, 7:30.
33. Zhang J.D., Wiemann S. KEGG graph: a graph approach to KEGG PATHWAY in R and bioconductor. Bioinformatics 2009, 25:1470-1471.
34. Zhang L., McHale C.M., Rothman N., Li G., Ji Z., Vermeulen R., et al. Systems biology of human benzene exposure. Chem Biol Interact 2010, 184(1-2):86-93.