Transcriptional regulation of protein complexes and biological pathways

Mammalian Genome

Volumn 14, Issue 9, 2003, Pages 611-619

  Hannenhalli, Sridhar ^a   Levy, Samuel ^a,b  

^a Informatics Research   (United States)

^b Ctr for the Advancement of Genomics   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT; GENE PRODUCT; GLUTAMATE RECEPTOR; N METHYL DEXTRO ASPARTIC ACID RECEPTOR; TRANSCRIPTION FACTOR; VITAMIN;

APOPTOSIS; ARTICLE; GENE CONTROL; GENE EXPRESSION; GENETIC TRANSCRIPTION; HUMAN; METABOLISM; NUCLEOTIDE SEQUENCE; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION;

APOPTOSIS; BINDING SITES; DNA; GENETIC COMPLEMENTATION TEST; HUMANS; MACROMOLECULAR SUBSTANCES; MODELS, GENETIC; PROTEINS; RECEPTORS, GLUTAMATE; RECEPTORS, N-METHYL-D-ASPARTATE; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 0041352070     PISSN: 09388990     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00335-002-2260-x     Document Type: Article

References (32)

1. Alexe G, Alexe S, Foldes S, Hammer PL (2000) Consensus algorithms for generation of all maximal bicliques. DIMACS Tech Report, pp 1-20
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215, 403-410
3. Bader GD, Donaldson I, Wolting C, Ouellette BF, Pawson T et al. (2001) BIND-the biomolecular interaction network database. Nucleic Acids Res 29, 242-245
4. Bickler PE, Donohoe PH, Buck LT (2000) Hypoxia-induced silencing of NMDA receptors in turtle neurons. J Neurosci 20, 3522-3528
5. Chen G, Goeddel DV (2002) TNF-R1 signaling: a beautiful pathway. Science 296, 1634-1635
6. Chiarugi V, Cinelli M, Magnelli L, Dello SP (2002) Apoptosis: molecular regulation of cell death and hematologic malignancies. Mol Biotechnol 20, 305-314
7. Cho RJ, Huang M, Campbell MJ, Dong H, Steinmetz L, et al. (2001) Transcriptional regulation and function during the human cell cycle. Nat Genet 27, 48-54
8. Feng Z, Chang RC, Bing G, Hudson P, Tiao Net al. (1999) Long-term increase of Sp-1 transcription factors in the hippocampus after kainic acid treatment. Brain Res Mol Brain Res 69, 144-148
9. Fessele S, Maier H, Zischek C, Nelson PJ, Werner T (2002) Regulatory context is a crucial part of gene function. Trends Genet 18, 60-63
10. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147
11. Ge H, Liu Z, Church GM, Vidal M (2001) Correlation between transcriptome and interactome mapping data from Saccharornyces cerevisiae. Nat Genet 29, 482-486
12. Gordon-Krajcer W, Salinska E, Lazarewicz JW (2002) N-methyl-D-aspartate receptor-mediated processing of beta-amyloid precursor protein in rat hippocampal slices: in vitro-superfusion study. Folia Neuropathol 40, 13-17
13. Halfon MS, Grad Y, Church GM, Michelson AM (2002) Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. Genome Res 12, 1019-1028
14. Hertz GZ, Stormo GD (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 15, 563-577
15. Husi H, Ward MA, Choudhary JS, Blackstock WP, Grant SG (2000) Proteomic analysis of NMDA receptor-adhesion protein signaling complexes. Nat Neurosci 3, 661-669
16. Jacobs O, Van Bree L, Mailleux P, Zhang F, Schiffmann SN et al. (1994) Homolateral cerebrocortical increase of immediate early gene and neurotransmitter messenger RNAs after minimal cortical lesion: blockade by N-methyl-D-aspartate antagonist. Neuroscience 59, 827-836
17. Kanehisa M, Goto S, Kawashima S, Nakaya A (2002) The KEGG databases at GenomeNet. Nucleic Acids Res 30, 42-46
18. Kinoshita K, Watanabe Y, Yamamura M, Matsuoka Y (1998) TRH receptor agonists ameliorate 3-acetylpyridine-induced ataxia through NMDA receptors in rats. Eur J Pharmacol 343, 129-133
19. Krainc D, Bai G, Okamoto S, Caries M, Kusiak JW et al. (1998) Synergistic activation of the N-methyl-D-aspartate receptor subunit 1 promoter by myocyte enhancer factor 2C and Sp1. J Biol Chem 273, 26218-26224
20. Levy S, Hannenhalli S (2002) Identification of transcription factor binding sites in the human genome. Mamm Genome 13, 510-514
21. Markstein M, Markstein P, Markstein V, Levine MS (2002) Genome-wide analysis of clustered dorsal binding sites identifies putative target genes in the Drosophila embryo. Proc Natl Acad Sci USA 99, 763-768
22. Mostafa SS, Papoutsakis ET, Miller WM (2001) Oxygen tension modulates the expression of cytokine receptors, transcription factors, and lineage-specific markers in cultured human megakaryocytes. Exp Hematol 29, 873-883
23. Pieri I, Klein M, Bayertz C, Gerspach J, van der Ploeg A et al. (1999) Regulation of the murine NMDA-receptor-subunit NR2C promoter by Sp1 and fushi tarazu factorl (FTZ-F1) homologues. Eur J Neurosci 11, 2083-2092
24. Platenik J, Kuramoto N, Yoneda Y (2000) Molecular mechanisms associated with long-term consolidation of the NMDA signals. Life Sci 67, 335-364
25. Ptashne M, Gann A (1998) Imposing specificity by localization: mechanism and evolvability. Curr Biol 8, R812-R822
26. Sevoz-Couche C, Maisonneuve B, Hamon M, Laguzzi R (2002) Glutamate and NO mediation of the pressor response to 5-HT3 receptor stimulation in the nucleus tractus solitarii. Neuroreport 13, 837-841
27. Sorensen SD, Macek TA, Cai Z, Saugstad JA, Conn PJ (2002) Dissociation of protein kinase-mediated regulation of metabotropic glutamate receptor 7 (mGluR7) interactions with calmodulin and regulation of mGluR7 function. Mol Pharmacol 61, 1303-1312
28. Sosa R, Hoffpauir B, Rankin ML, Bruch RC, Gleason L (2002) Metabotropic glutamate receptor 5 and calcium signaling in retinal amacrine cells. J Neurochem 81, 973-983
29. Staudt LM, Brown PO (2000) Genomic views of the immune system. Annu Rev Immunol 18, 829-859
30. Washbourne P, Bennett JE, McAllister AK (2002) Rapid recruitment of NMDA receptor transport packets to nascent synapses. Nat Neurosci 5, 751-759
31. Wingender E, Chen X, Fricke E, Geffers R, Hehl R et al. (2001) The TRANSFAC system on gene expression regulation. Nucleic Acids Res 29, 281-283
32. Yee WM, Frim DM, Isacson O (1993) Relationships between stress protein induction and NMDA-mediated neuronal death in the entorhinal cortex. Exp Brain Res 94, 193-202