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Artificial intelligence publications October 1, 2010 Article

Beyond the Genome (BTG) Is a (PGDB) Pathway Genome Database: Humancyc

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Trupp, M., Altman, T., Fulcher, C.A. et al. Beyond the genome (BTG) is a (PGDB) pathway genome database: HumanCyc. Genome Biol 11 (Suppl 1), O12 (2010). https://doi.org/10.1186/gb-2010-11-s1-o12

Introduction

HumanCyc is a manually curated database of enzymatic reactions and metabolic pathways that can be used as a versatile reference resource or as a tool for analyzing ‘omics’ data sets in the context of metabolic pathways. The HumanCyc database was generated from the annotated genome using the Pathway Tools [1] software package written by SRI International (SRI). The software assists users in analyzing genomic data by predicting the metabolic network of an organism, presenting pathway and genome data in user-friendly and intuitive displays, and providing tools for missing enzyme identification, ‘omics’ data analyses and comparative studies.

The HumanCyc website (http://humancyc.org/) and the downloadable HumanCyc software support a variety of query, visualization and analysis tools. Users can find and display existing metabolites, pathways and enzymes. Users can also define groups of metabolites or proteins and perform enrichment analysis of an ‘omics’ data set to determine over- represented substrates, pathways or enzymes. It is possible to color code a ‘zoomable’ human metabolic network diagram with metabolomic, proteomic or transcriptomic data for visual analysis of patterns in data sets. The software colors entities in the diagram to reflect their measured levels in user-uploaded ‘omics’ data sets.

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