Genomics profiling

Chamber J et al. DNA microarrays of the complex human cytomegalovirus genome profiling kinetic class with drug sensitivity of viral gene expression. J Virol 1999 73 5757-5766... 

Figure 3.3 Comparison of array CGH among DNA extracted from fresh tissue, FFPE tissue by heating protocol or nonheating protocol for two human tissue samples of metastatic carcinoma in lymph node (a-c), and undifferentiated non-small cell carcinoma (d-f). Array CGH hybridization genomic profiles show ratio values representing relative copy number of single BACs. A good result is scored as 1.0 that indicates a low standard deviation for gains (>0.2), normal (0.0), or losses (<-0.2). In these two cases, fresh samples show best score as 2, both FFPE tissue samples show identical score of 3. Each spot represents the average of three replicates. Clones are ordered by chromosomal position as numbers at the bottom (x axis) of each picture. The y axis is the log2 ratio of test reference intensity. Provided by Sandy DeVries from Dr. Frederic Waldman s Lab at UCSF.

There are fundamental differences in the information that can be collected by proteomic versus genomic profiling. The proteome (total set of proteins expressed... 

In summary, in silica needs to embrace the complexity of the several membrane permeation processes that occur in viva, in order to provide the drug developers with a pure in silica decision making tool, which can predict in vivo endpoints for specific genomic profiles, exclusively from a compound s molecular structure. 

Chemical genomics profiling of environmental chemical modulation of hmnan nuclear receptors. Environ Health Perspect 119 1142-1148... 

Gordon MA, Gil J, Lu B et al. Genomic profiling associated with recurrence in patients with rectal cancer treated with chemoradiation. Pharmacogenomics 2006 7 67-88. 

G Giaever, D Shoemaker, TW Jones, H Liang, EA Winzler, A Astromoff, RW Davis. Genomic profiling of drug sensitivities via induced haploinsufficiency. Nature Genet 21 278-283, 1999. 

Weiss MM, Kuipers EJ, Postma C, Snijders AM, Siccama I, Pinkel D, Westerga J, Meuwissen SG, Albertson DG, Meijer GA, Genomic profiling of gastric cancer predicts lymph node status and survival, Oncogene, 22 1872-1879, 2003. 

The underlying premise of microarray analyses is oligonucleotide hybridizations that are used to gain genomic profiles of individual samples. These profiles can be... 

Chemical genomic profiling - using microarrays to determine the effects of highly specific drug-mediated kinase inhibition of gene expression. 

Fig. 2.4 PFGE profiles genomic DNA from indigenous O. oeni strains isolated from a wine after 3 days of inoculation with O. oeni M42. The genomic profile of strain M42 is shown in line 15 as a reference. Molecular weight standard phage X concatemers (From Moreno-Arribas et al. 2008b, with permission)...

The introduction of novel procedures into an integral genomic medicine protocol for CNS disorders and dementia is an imperative requirement in drug development and in clinical practice in order to improve diagnostic accuracy and to optimize therapeutics. Personalized strategies, adapted to the complexity of each case, are essential to depict a clinical profile based on specific biomarkers correlating with individual genomic profiles [7, 15]. 

Haggarty, S.J., Clemons, P.A. and Schreiber, S.L. (2003) Chemical genomic profiling of biological networks using graph theory and combinations of small molecule perturbations. /. Am. Chem. Soc., 125, 10543-10545. 

Coindre JM, Hostein I, Maire G, et al. Inflammatory malignant fibrous histiocytomas and dedifferentiated liposarcomas Histological review, genomic profile, and MDM2 and CDK4 status favor a single entity. J Pathol. 2004 203 822-830. 

Lapointe J, Li C, Giacomini CP, Salari K, et al. Genomic profiling reveals alternative genetic pathways of prostate Urmorigen-esis. Cancer Res. 2007 67 8504. 

Fig. 6-23 Chemical-genomic profiling (data node networks derived from the mapping of from Ref. 82). (a) 276 unique combinations a matrix of 24 x 24 combinations of small and 24 single treatments of small-molecule molecules against a set of 10 strains of the...

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