Microarray technology and gene expression analysis for the study of angiogenesis

Bibliography

• CARMELIET P: Mechanisms of angiogenesis and arteriogenesis. Nat. Med. (2000) 6:389–395.
   PubMed Web of Science ®Google Scholar
• CARMELIET P, JAIN RK: Angiogenesis in cancer and other diseases. Nature (2000) 407:249–257.
   PubMed Web of Science ®Google Scholar
• SHIMA DT, MAILHOS C: Vascular developmental biology: getting nervous. Curt: Opin. Genet. Dev. (2000) 10:536–542.
   PubMed Web of Science ®Google Scholar
• HOUGH CD, SHERMAN-BAUST CA, PIZER ES et al.: Large scale serial analysis of gene expression reveals genes differentially expressed in ovarian cancer. Cancer Res. (2000) 60:6281–6287.
   PubMed Web of Science ®Google Scholar
• ALIZADEH A, EISEN M, DAVIS RE et al: Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature (2000) 403:503–511.
   PubMed Web of Science ®Google Scholar
• BITTNER M, MELTZER P, CHEN Y et al.: Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature (2000) 406(6795):536–540.
   PubMed Web of Science ®Google Scholar
• GOLUB TR, SLONIM DK, TAMAYO P et al.: Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science (1999) 268(5439):531–537.
   Google Scholar
• EISEN MB, SPELLMAN PT, BROWN PO, BOTSTEIN D: Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA (1998) 95:14863–14868.
   PubMed Web of Science ®Google Scholar
• HUGHES TR, MARTON MJ, JONES ARet al.: Functional discovery via a compendium of expression profiles. Cell (2000) 102:109–126.
   Google Scholar
• BUTTE AJ, TAMAYO P, SLONIM D, GOLUB TR, KOHANE IS: Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proc. Natl. Acad. Sci. USA (2000) 97:12182–12186.
   PubMed Web of Science ®Google Scholar
• MARTON M, DERISI J, BENNETT H et al.: Drug target validation and identification of secondary drug target effects using DNA microarrays. Nat. Med. (1998) 4:1293–1301.
   PubMed Web of Science ®Google Scholar
• SHERF U, ROSS DT, WALTHAM M et al.: A gene expression database for the molecular pharmacology of cancer. Nat. Genet,. (2000) 24:236–244.
   PubMed Web of Science ®Google Scholar
• BEHR MA, WILSON MA, GILL WP et al: Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science (1999) 284(5419):1520–1523.
   PubMed Web of Science ®Google Scholar
• MILES MF: Microarrays: lost in a storm of data? Nat. Rev Neurosci (2001) 2:441–443.
   Google Scholar
• LEE MLT, KUO FC, WHITMORE GA, SKLAR J: Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc. Nati Acad. Sci. USA (2000) 97:9834–9839.
   PubMed Web of Science ®Google Scholar
• BARTOSIEWICZ M, TROUNSTINE M, BARKER D, JOHNSTON R, BUCKPITT A: Development of a toxicological gene array and quantitative assessment of this technology. Arch. Biochein. Biophys. (2000) 376:66–73.
   PubMed Web of Science ®Google Scholar
• GESCHWIND DH: Sharing gene expression data: an array of options. Nat. Rev Neurosci. (2001) 2:435–438.
   PubMed Web of Science ®Google Scholar
• LIOTTA L, PETRICOIN E: Molecular profiling of human cancer. Nat. Rev Genet (2000) 1:48–56.
   PubMed Web of Science ®Google Scholar
• GOLDSWORTHY SM, STOCKTON PS, TREMPUS CS et al.: Effects of fixation on RNA extraction and amplification from laser capture microdissected tissue. Mo/. Carcinog. (1999) 25:86–91.
   PubMed Web of Science ®Google Scholar
• ••Article of considerable interest.
   Google Scholar
• HUANG J, QI R, QUACKENBUSH J, DAUWAY E, LAZARIDIS E, YEATMAN T: Effects of ischemia on gene expression." Surg. Res. (2001) 99:222–227.
   PubMed Web of Science ®Google Scholar
• ••Article of considerable interest.
   Google Scholar
• OHNMACHT GA, WANG E, MOCELLIN, S et al.: Short-term kinetics of antigen expression in response to vaccination. brununol. (2001) 167:1809–1820.
   Google Scholar
• EMMERT-BUCK MR, BONNER RF, SMITH PD et al: Laser capture microdissection. Science (1996) 274:998–1001.
   PubMed Web of Science ®Google Scholar
• LUO L, SALUNGA RC, GUO H et al: Gene expression profiles of laser-captured adjacent neuronal subtypes. Nat. Med. (1999) 5:117–122.
   PubMed Web of Science ®Google Scholar
• OYAMA H, ZANG X, KOHNO Y et al: Laser capture microdissection-generated target sample for high-density oligonucleotide array hybridization. Biotechniques (2000) 29:530–536.
   PubMed Web of Science ®Google Scholar
• EBERWINE J: Amplification of mRNA populations using a RNA generated from immobilized oligo(dT)-T7 primed cDNA. Biotechniques, (1996) 20(4):584–591.
   PubMed Web of Science ®Google Scholar
• WANG E, MILLER LD, OHNMACT GA, LIU ET, MARINCOLA FM: High-fidelity mRNA amplification for gene profiling. Nat. Biotech. (2000) 18:457–459.
   PubMed Web of Science ®Google Scholar
• SCHENA, M, SHALON D, DAVIS RW, BROWN PO: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science (1995) 270:467–470.
   PubMed Web of Science ®Google Scholar
• LOCKHART DJ, DONG H, BYRNE MC et al: Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotech. (1996) 14:1675–1980.
   PubMed Web of Science ®Google Scholar
• LIPSHUTZ R, FODOR SP, GINGERAS TR et al.: High density synthetic oligonucleotide arrays. Nat. Genet. (1999) 21:S20–S24.
   Google Scholar
• GESCHWIND DH, OU J, EASTERDAY MC et al.: A genetic analysis of neural progenitor differentiation. Neuron (2001) 29:325–339.
   PubMed Web of Science ®Google Scholar
• WU TD: Analyzing gene expression data from DNA microarrays to identify candidate genes." Pathol. (2001) 195:53–65.
   PubMed Web of Science ®Google Scholar
• ••Valuable review on approaching microarraydata analysis.
   Google Scholar
• SHERLOCK G: Analysis of large-scale gene expression data. Brief Bioinform. (2001) 2:350–362.
   PubMedGoogle Scholar
• BRAZMA A, VILO J: Gene expression dataanalysis. Microbes Infect. (2001) 3:823–829.
   PubMed Web of Science ®Google Scholar
• CHEN Y, DOUGHERTY ER, BITTNER M: Ratio-based decisions and the quantitative analysis of cDNA microarray images. J. Bionted. Opt. (1997) 2:364–374.
   PubMedGoogle Scholar
• HEDENFALK I, DUGGAN D, CHEN Y et al: Gene-expression profiles in hereditary breast cancer. N Engl. J. Med. (2001) 344:539–548.
   PubMed Web of Science ®Google Scholar
• SHENA M, SHALON D, HELLER R, CHAI A, BROWN PO, DAVIS RW: Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc. Natl. Acad. Sci. USA (1996) 93:10614–10619.
   PubMed Web of Science ®Google Scholar
• TAVAZOIE S, HUGHES JD, CAMPBELL MJ, CHO RJ, CHURCH GM: Systematic determination of genetic network architecture. Nat. Genet. (1999) 22:281–285.
   PubMed Web of Science ®Google Scholar
• TAMAYO P, SLONIM D, MESIROV J et al: Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc. Natl. Acad. Sci. USA (1999) 96:2907–2912.
   PubMed Web of Science ®Google Scholar
• PLANET PJ, DESALLE R, SIDDALL M, BAEL T, INDRA NS, STANLEY SE: Systematic analysis of DNA microarray data: ordering and interpreting patterns of gene expression. Cenome Res. (2001) 11:1149–1155.
   Google Scholar
• LE NAOUR F, HOHENKIRK L, GROLLEAU A et al.: Profiling changes in gene expression during differentiation and maturation of monocyte-derived dendritic cells using both oligonucleotide microarrays and proteomics. Biol. Chem. (2001) 276(21):17920–17931.
   Web of Science ®Google Scholar
• CHEN BPC, LI Y, ZHAO Y et al: DNA microarray analysis of gene expression in endothelial cells in response to 24-h shear stress. Physiol Cenomics (2001) 7:55–63.
   PubMed Web of Science ®Google Scholar
• SVAREN J, EHRIG T, ABDULKADIR SA, EHRENGRUBER MU, WATSON MA, MILBRANDT J: EGR1 target genes in prostate carcinoma cells identified by microarray analysis. Biol. Chem (2000) 275(49):38524–38531.
   Web of Science ®Google Scholar
• CHEN JJVV, PECK K, HONG T et al.: Global analysis of gene expression in invasion by a lung cancer model. Cancer Res. (2001) 61:5223–5230.
   PubMed Web of Science ®Google Scholar
• XU H, RAAFAT EL, GEWELY M: p53-responsive genes and the potential for cancer diagnostics and therapeutics development. Biotechnol Ann. Rev (2001) 7:131–164.
   PubMedGoogle Scholar
• DONG G, LOUKINOVA E, CHEN Z et al.: Molecular profiling of transformed and metastatic murine squamous carcinoma cells by differential display and cDNA microarray reveals altered expression of multiple genes related to growth, apoptosis, angiogenesis, and the NF-kappa B signal pathway. Cancer Res. (2001) 61:4697–4808.
   Google Scholar
• KHANNA C, KHAN J, NGUYEN Pet al.:Metastasis-associated differences in gene expression in a murine model of osteosarcoma. Cancer Res. (2001) 61:3750–3759.
   Google Scholar
• •In this elegant study and excellent example on the use of microarrays, the authors identify several genes of interest, one of which is well validated at the mRNA and protein, level.
   Google Scholar
• TERUYAMA K, ABE M, NAKANO T, TAKAHASHI S, YAMADA S, SATO Y: Neurophilin-1 is a downstream target of transcription factor Ets-1 in human umbilical vein endothelial cells. FEBS Lett. (2001) 504(1-2):1–4.
   PubMed Web of Science ®Google Scholar
• ST. CROIX B, RAGO C, VELCULESCU V, et al.: Genes expressed in human tumor endothelium. Science (2000) 289:1197–1202.
   PubMed Web of Science ®Google Scholar
• AUERBACH R, KUBAI L, KNIGHTON D,, FOLKMAN J: A simple procedure for the long-term cultivation of chicken embryos. Dev. Biol. (1974) 41(2):391–394.
   PubMed Web of Science ®Google Scholar
• DONG QG, BERNASCONI S, LOSTAGLIO S et al: A general strategy for isolation of endothelial cells from murine tissues. Arter. Thromb. Vasc. Biol. (1997) 17:1599–1604.
   PubMed Web of Science ®Google Scholar
• RICHARD L, VELASCO P, DETMAR M:A simple immunomagnetic protocol for the selective isolation and long-term culture of human dermal microvascular endothelial cells. Exp. Cell Res. (1998) 240:1–6.
   PubMed Web of Science ®Google Scholar
• KRIEHUBER E, BREITENEDER-GELEFF S, GROEGER M: Isolation and characterization of dermal lymphatic and blood endothelial cells reveal stable and functionally specialized cell lineages. Exp. Med. (2001) 194(6):797–808.
   PubMed Web of Science ®Google Scholar
• SGROI DC, TENG S, ROBINSON G, LEVANGIE R, HUDSON JR, ELKAHLOUN AG: In vivo gene expression profile analysis of human breast cancer progression. Cancer Res. (1999) 59:5656–5661.
   PubMed Web of Science ®Google Scholar
• KITAHARA O, FURUKAWA Y, TANAKA T et al.: Alterations of gene expression during colorectal carcinogenesis revealed by cDNA microarrays after laser-capture microdissection of tumor tissues and normal epithelia. Cancer Res. (2001) 61:3544–3549.
   PubMed Web of Science ®Google Scholar
• ALE VIZOS I, MAHADEVAPPA M, ZHANG X et al.: Oral cancer in vivo gene expression profiling assisted by laser capture microdissection and microarray analysis. Oncogene (2001) 20:6196–6204.
   PubMed Web of Science ®Google Scholar
• NAGLE RB: New molecular approaches to tissue analysis. J. Histochem. Cytochem. (2001) 49(8):1063–1064.
   PubMed Web of Science ®Google Scholar
• LIOTTA LA, KOHN EC: The microenvironment of the tumour-host interface. Nature (2001) 411:375–379.
   PubMed Web of Science ®Google Scholar
• OLSON TA, MOHANRAJ D, CARSON LF, RAMAKRISHNAN S: Vascular permeability factor gene expression in normal and neoplastic human ovaries. Cancer Res. (1994) 54:276–280.
   PubMed Web of Science ®Google Scholar
• MARTOGLIO AM, TOM BD, STARKEY M et al.: Changes in tumorigenesis- and angiogenesis-related gene transcript abundance profiles in ovarian cancer detected by tailored high density cDNA arrays. Mol Med. (2000) 6:750–765.
   PubMed Web of Science ®Google Scholar
• RAY JM, STETLER-STEVENSON WG: The role of matrix metalloproteases and their inhibitors in tumour invasion, metastasis and angiogenesis. Eur. Respir. (1994) 7(11):2062–2072.
   PubMed Web of Science ®Google Scholar
• MORI M, SADAHIRA Y, KAWASAKI S, HAYASHI T, NOTOHARA K, AWAI M: Capillary growth from reversed rat aortic segments cultured in collagen gel. Acta Pathol fpn. (1988) 38(12):1503–1512.
   PubMedGoogle Scholar
• NICOSIA RE OTTINETTI A: Growth of microvessels in serum-free matrix culture of rat aorta. Lab. Invest. (1990) 63(1):115–122.
   PubMed Web of Science ®Google Scholar
• BERGER AC, ALEXANDER HR, TANG G et al.: Endothelial monocyte activating polypeptide II induces endothelial cell apoptosis and may inhibit tumor angiogenesis. Microvasc. Res. (2000) 60:70–80.
   PubMed Web of Science ®Google Scholar
• KRUGER EA, DURAY PH, TSOKOS MGet al.: Endostatin inhibits microvessel formation in the ex vivo rat aortic ring angiogenesis assay. Biochem. Biophys. Res. Commun. (2000) 268(1):183–191.
   Google Scholar