Comparability of gene expression in human blood, immune and carcinoma cells

Applied Mathematics and Computation

Volumn 205, Issue 1, 2008, Pages 178-184

  Yang, Xinan ^a   Sun, Xiao ^a   Xie, Jianming ^a   Lu, Zuhong ^a  

^a SOUTHEAST UNIVERSITY   (China)

Author keywords

Bioinformatics; Co expression; Computational diagnostics; Gene co regulation; Immune cell; Leukemia; Lymphoma; Microarrays; Peripheral blood

Indexed keywords

ABERRATIONS; BIOACTIVITY; BIOASSAY; BIOINFORMATICS; BLOOD; CELLS; COBALT; COBALT COMPOUNDS; CYTOLOGY; DIAGNOSIS; GENE EXPRESSION; HISTOLOGY; MICROARRAYS; OPTICAL PROPERTIES; STATISTICAL METHODS;

CO-EXPRESSION; COMPUTATIONAL DIAGNOSTICS; IMMUNE CELL; LEUKEMIA; LYMPHOMA; PERIPHERAL BLOOD;

TISSUE;

EID: 54049123223     PISSN: 00963003     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.amc.2008.05.023     Document Type: Article

References (20)

1. Elshimali Y.I., and Grody W.W. The clinical significance of circulating tumor cells in the peripheral blood. Diagn. Mol. Pathol. 15 4 (2006)
2. Sullivan P.F., Fan C., and Perou C.M. Evaluating the comparability of gene expression in blood and brain. Am. J. Med. Genet. B Neuropsychiatr. Genet. 141 3 (2006) 261-268
3. Su A.I., Wiltshire T., Batalov S., Lapp H., Ching K.A., Block D., Zhang J., Soden R., Hayakawa M., Kreiman G., Cooke M.P., Walker J.R., and Hogenesch J.B. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl. Acad. Sci. USA 101 16 (2004) 6062-6067
4. Jiang Z., and Gentleman R. Extensions to gene set enrichment. Bioinformatics 23 3 (2007) 306-313
5. S. Scheid, C. Lottaz, A toolbox for performing and illustrating microarray data analyses - users guide to the R package compdiagtools. CompDiag Technical Report 01(2005).
6. Lottaz C., and Spang R. Molecular decomposition of complex clinical phenotypes using biologically structured analysis of microarray data. Bioinformatics 21 9 (2005) 1971-1978
7. Storey J.D., and Tibshirani R. Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. USA 100 16 (2003) 9440-9445
8. Scheid S., and Spang R. A stochastic downhill search algorithm for estimating the local false discovery rate. IEEE/ACM Trans. Comput. Biol. Bioinform. 1 3 (2004) 98-108
9. Golub T.R., Slonim D.K., Tamayo P., Huard C., Gaasenbeek M., Mesirov J.P., Coller H., Loh M.L., Downing J.R., Caligiuri M.A., Bloomfield C.D., and Lander E.S. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286 5439 (1999) 531-537
10. Kostka D., and Spang R. Finding disease specific alterations in the co-expression of genes. Bioinformatics 20 Suppl 1 (2004) 194-199
11. McChesney P.A., Aiyar S.E., Lee O.J., Zaika A., Moskaluk C., Li R., and El-Rifai W. Cofactor of BRCA1: a novel transcription factor regulator in upper gastrointestinal adenocarcinomas. Cancer Res. 66 3 (2006) 1346-1353
12. Zhang J.S., Wang L., Huang H., Nelson M., and Smith D.I. Keratin 23 (K23), a novel acidic keratin, is highly induced by histone deacetylase inhibitors during differentiation of pancreatic cancer cells. Genes Chromosomes Cancer 30 2 (2001) 123-135
13. Huang X., Godfrey T.E., Gooding W.E., McCarty K.S., and Gollin S.M. Comprehensive genome and transcriptome analysis of the 11q13 amplicon in human oral cancer and synteny to the 7F5 amplicon in murine oral carcinoma. Genes Chromosomes Cancer 45 11 (2006) 1058-1069
14. Cho N.Y., Kim B.H., Choi M., Yoo E.J., Moon K.C., Cho Y.M., Kim D., and Kang G.H. Hypermethylation of CPG island loci and hypomethylation of line-1 and Alu repeats in prostate adenocarcinoma and their relationship to clinic opathological features. J. Pathol. 211 3 (2007) 269-277
15. Kitazawa S., Kitazawa R., Obayashi C., and Yamamoto T. Desmoid tumor with ossification in chest wall: possible involvement of bambi promoter hypermethylation in metaplastic bone formation. J. Bone Miner. Res. 20 8 (2005) 1472-1477
16. Shames D.S., Girard L., Gao B., Sato M., Lewis C.M., Shivapurkar N., Jiang A., Perou C.M., Kim Y.H., Pollack J.R., Fong K.M., Lam C.L., Wong M., Shyr Y., Nanda R., Olopade O.I., Gerald W., Euhus D.M., Shay J.W., Gazdar A.F., and Minna J.D. A genome-wide screen for promoter methylation in lung cancer identifies novel methylation markers for multiple malignancies. PLoS Med. 3 12 (2006) e486
17. Shu J., Jelinek J., Chang H., Shen L., Qin T., Chung W., Oki Y., and Issa J.P.J. Silencing of bidirectional promoters by DNA methylation in tumorigenesis. Cancer Res. 66 10 (2006) 5077-5084
18. Sherman T.S., Huang D.W., Tan Q., Guo Y., Bour S., Liu D., Stephens R., Baseler M.W., Lane H.C., and Lempicki R.A. David knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis. BMC Bioinformatics 8 1 (2007) 426
19. Farh K.K.H., Grimson A., Jan C., Lewis B.P., K Johnston W., Lim L.P., Burge C.B., and Bartel D.P. The widespread impact of mammalian micrornas on mRNA repression and evolution. Science 310 5755 (2005) 1817-1821
20. Vardhanabhuti S., Wang J., and Hannenhalli S. Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation. Nucleic Acid Res. 35 10 (2007) 3203-3213