Disease relevance of Genomics

• To elucidate the genomics of cellular responses to cancer treatment, we analyzed the expression of over 9,600 human genes in acute lymphoblastic leukemia cells before and after in vivo treatment with methotrexate and mercaptopurine given alone or in combination [1].
• Evolutionary genomics of Staphylococcus aureus: insights into the origin of methicillin-resistant strains and the toxic shock syndrome epidemic [2].
• Identification of eIF2Bgamma and eIF2gamma as cofactors of hepatitis C virus internal ribosome entry site-mediated translation using a functional genomics approach [3].
• These tools have been applied to a range of neurodegenerative disorders and are discussed and integrated in part II (Functional Genomics meets neurodegenerative disorders. Part II: application and data integration) [4].
• The structure of SlyA from Enterococcus faecalis, determined as a part of an ongoing structural genomics initiative (www.mcsg.anl.gov), revealed the same winged helix DNA-binding motif that was recently found in the MarR repressor from Escherichia coli and the MexR repressor from Pseudomonas aeruginosa, a sequence homologue of MarR [5].

Psychiatry related information on Genomics

• Effects of tyrosine hydroxylase mutants on locomotor activity in Drosophila: a study in functional genomics [6].
• Functional genomics studies in Alzheimer's disease reveal that age of onset, brain atrophy, cerebrovascular haemodynamics, brain bioelectrical activity, cognitive decline, apoptosis, immune function and amyloid deposition are associated with Alzheimer's disease-related genes [7].

High impact information on Genomics

• Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics' [8].
• Comparative genomics identifies a flagellar and basal body proteome that includes the BBS5 human disease gene [9].
• Using comparative genomics to screen for such a factor among evolutionarily conserved sequences between mouse and human, we have identified a novel transcript, H4F5, which lies closer to SMN1 than any previously identified gene in the region [10].
• Wellcome discusses structural genomics effort with industry...but data release remains an open question [11].
• Genetic testing and Alzheimer disease: has the time come? Alzheimer Disease Working Group of the Stanford Program in Genomics, Ethics & Society [12].

Chemical compound and disease context of Genomics

• Functional genomics identifies a mechanism for estrogen activation of the retinoic acid receptor alpha1 gene in breast cancer cells [13].
• A structural genomics comparison of purine nucleoside phosphorylases (PNPs) indicated that the enzyme encoded by Mycobacterium tuberculosis (TB-PNP) resembles the mammalian trimeric structure rather than the bacterial hexameric PNPs [14].
• The release of a complete Bifidobacterium longum genome sequence and the recent initiative to sequence additional strains are expected to open up a new era of comparative genomics in bifidobacterial biology [15].
• A series of experiments reported in the literature using fluxomics as an efficient functional genomics tool revealed that the L-lysine production of the Corynebacterium glutamicum strain MH20-22B correlates with the extent of intracellular NADPH supply [16].

Biological context of Genomics

• Comparative genomics. Gene expression differs in human and chimp brains [17].
• Immunology. Chip shots--will functional genomics get functional [18]?
• Recent advances in comparative genomics and bioinformatics have made it possible to elucidate when and why yeasts produce ethanol in high concentrations, and how this remarkable trait originated and developed during their evolutionary history [19].
• An integrated functional genomics screening program reveals a role for BMP-9 in glucose homeostasis [20].
• In the present study, an "inverse genomics" approach based on a randomized ribozyme gene library was applied to identify cellular genes regulating BRCA1 expression [21].

Anatomical context of Genomics

• We present here a detailed analysis of a rat polypeptide termed Nup50 (formerly NPAP60) that was previously found to be associated with the nuclear pore complex (F. Fan et al., Genomics 40:444-453, 1997) [22].
• (Burkhardt, E., Adham, I. M., Brosig, B., Gastmann, A., Mattei, M. G., and Engel, W. (1994) Genomics 20, 13-19) Leydig cells contain the message for a protein of the insulin/relaxin family which was named Leydig cell insulin-like protein (LEY I-L) [23].
• Using a functional genomics approach, we observed that IL-1beta induced in astrocytes a group of genes considered to be IFN-stimulated genes (ISG), suggesting that IL-1beta may also signal via IRF3 in these cells [24].
• A genomics approach to the detection of positive selection in cattle: adaptive evolution of the T-cell and natural killer cell-surface protein CD2 [25].
• A functional genomics approach for the identification of putative tumor suppressor genes: Dickkopf-1 as suppressor of HeLa cell transformation [26].

Associations of Genomics with chemical compounds

• LION and Degussa apply genomics to fermentation [27].
• The angiotensin-converting enzyme gene family: genomics and pharmacology [28].
• Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis [29].
• [Naylor, S.L., Marshall, A., Hensel, C., Martinez, P.F., Holley, B. & Sakaguchi, A.Y. (1989) Genomics 4, 355-361]; the DNF15S2 locus suffers deletions in small cell lung carcinoma associated with a reduction or loss of acylase activity (EC 3.5.1.14) [30].
• Comparative evolutionary genomics of androgen-binding protein genes [31].

Gene context of Genomics

• A functional genomics strategy reveals Rora as a component of the mammalian circadian clock [32].
• Identification of proangiogenic genes and pathways by high-throughput functional genomics: TBK1 and the IRF3 pathway [33].
• We used a functional genomics approach to identify a gene required for meiotic recombination, YGL183c or MND1 [34].
• To broaden our understanding of the function of the La homologous protein (Lhp1) in Saccharomyces cerevisiae, we have taken a genomics approach [35].
• Ragoussis and co-workers (Genomics 4:301) previously described a class I HLA gene (now designated HLA-J) that maps to within 50 kb of HLA-A [36].

Analytical, diagnostic and therapeutic context of Genomics

• Sixteen markers, including 11 whose isolation is described here and in the accompanying paper (A. Schedl et al., 1992, Genomics 14, 288-297), were ordered on a panel of albino-deletion DNAs and their distribution was examined by pulsed-field gel electrophoresis [37].
• A list of candidate X-linked POF genes is emerging from molecular studies of X chromosome abnormalities, data from the Human Genome Project and related functional genomics projects, and the results of gene targeting experiments in mice [38].
• Differential library screening of an albumen gland cDNA library, Western blot analysis, protein expression, immunolocalization studies, comparative genomics, and secretion assays identified a major Aplysia californica albumen gland protein ('capsulin') that is localized to egg capsules and to the sheaths of the egg cordon [39].
• The availability of multiple genomic sequences and more extensive use of genomics and proteomics technologies should allow a comprehensive dissection of the complex of host-adaptation and virulence in Y. pestis [40].
• Dr Winkelmann is the Head of the Cooperation Unit for Pharmacogenomics and Applied Genomics in Heidelberg, which was founded in 2001 by the Department of Internal Medicine VI and the Coordination Centre for Clinical Trials at the University of Heidelberg [41].

References