Pathway Genomics

R. Caspi, H. Foerster, C. A. Fulcher, P. Kaipa, M. Krummenacker, M. Latendresse, S. Paley, S. Y. Rhee, A. G. Shearer, C. Tissier, T. C. Walk, P Zhang, and P D. Karp, The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 36(Database issue), D623 D631 (2008). 

Yang HH, Hu Y, Buetow KH et al. A eomputational approach to measuring coherence of gene expression in pathways. Genomics 2004 84 211-217. 

Shapir, N., E.F. Mongodin, M.J. Sadowsky, S.C. Daugherty, K.E. Nelson, and L.P. Wackett (2007). Evolution of catabolic pathways Genomic insights into microbial s-hiazine metabolism. J. Bacteriol., 189 674-682. 

BioCyc SRI International Describes the genome and metabolic pathways of a single organism—total 1690 pathway/genome databases (http // biocyc.org/)... 

SRI International Pathway Tools software supports creation, editing, querying, visualization, analysis, and publishing of Pathway/Genome Database (http // bioinformatics.ai.sri.com/ptools/)... 

Karp PD, Ouzounis CA, Moore-Kochlacs C et al (2005) Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res 33 6083-6089... 

Most recently, in silico methods have been apphed to the systems biology of metabolic pathways. An analysis of the human genome assigns 2709 human enzymes to 896 bioreactions 622 of the enzymes are assigned roles in 135 predicted metabolic pathways. The predicted pathways closely match the known nutritional requirements of humans. This analysis identifies probable omissions in the human genome annotation in the form of 203 pathway holes (missing enzymes within the predicted pathways). The predicted human metabolic map is described by a Pathway/Genome Database called HumanCyc, which is available at http //HumanCyc.org/. 

Romero PR, Karp P. Nutrient-related analysis of pathway/genome databases. Pac Symp Biocomput. 2001 471-482. 

BioCyc. URL http //biocyc.org/. Pathway/genome databases of single organisms MetaCyc has literature derived metabolic pathway data from many organisms. 

H.C. Huang, P.S. Klein, The Frizzled family receptors for multiple signal transduction pathways, Genome Biol. 2004, 5, 234.1-2234.7. 

P. D. Karp, M. Krummenacker, S. Paley and J. Wagg, Integrated pathway-genome databases and their role in drug discovery, TIBTECH, 17 (1999), 275-281. 

Metabolic signaling databases contain detailed information on metabolic pathways. These DBs have well-established data structures but have nonuniform ontologies. BioCyc is a collection of pathway/genome databases for many bacteria and up to 14 species of other organisms. Enzyme catalyzed... 

In the last step of the gene expression pathway, genomic information encoded in messenger RNAs is translated into protein by a ribonucleoprotein called the ribosome. The prokaryotic ribosome (MW approximately 2.6 x 10 daltons) is about 2/3 RNA and 1/3 protein and consists of 2 subunits the larger of which is approximately twice the molecular weight of the smaller. The small subunit mediates the interaction between the mRNA codon and the tRNA anticodon, an interaction on which the fidelity of translation depends. The large subunit, which sediments at SOS in prokaryotes, includes the activity that catalyzes peptide bond formation - peptidyl transferase. 

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