Category Cross-Omics>Knowledge Bases/Databases/Tools

Abstract HumanCyc is a bioinformatics database that describes the human 'metabolic pathways' and the human genome.

By presenting metabolic pathways as an organizing framework for the human genome, HumanCyc provides the user with an extended dimension for functional analysis of H. sapiens at the genomic level.

The current version of HumanCyc was constructed using Build 31 of the human genome.

Database Generation -- Data on the human genome from Ensembl, LocusLink and GenBank were carefully parsed via perl scripts, and then merged, in order to create a minimally redundant human gene set to serve as an input to SRI's PathoLogic software (see G6G Abstract Number 20235), which generated the database and predicted H. sapiens metabolic pathways from functional information contained in the genome's annotation.

SRI did Not re-annotate the genome, but worked with the ‘gene function’ assignments in Ensembl, LocusLink, and GenBank.

The resulting pathway/genome database (PGDB) includes information on 28,783 genes, their products and the metabolic reactions and pathways they catalyze.

Also included are many links to other databases and publications.

HumanCyc was generated by combining the gene sets from the Ensembl and LocusLink databases.

LocusLink gene entries were merged into Ensembl genes when appropriate based on equivalence of gene names and links to other databases, in order to obtain as non-redundant a gene set as possible.

SRI also imported comments from the LocusLink database into HumanCyc gene and protein entries. All imported comments end with a citation to LocusLink to indicate their source.

HumanCyc Curation -- SRI has undertaken a limited curation effort for HumanCyc that includes an assessment and correction of the computationally generated metabolic network, and some curation of metabolic pathways and enzymes.

HumanCyc is very much a work in progress, is incomplete in many respects, and may contain errors.

Note: HumanCyc does Not contain signaling pathways. Some data, like alternative splicing and tissue specificity are Not yet supported, whereas other types of information, such as transporters and cellular compartments, although supported by the software, have yet to be added.

H. sapiens Genome -- HumanCyc contains the complete genome sequence of H. sapiens, as presented in Build 31 and describes the nucleotide position and function of every H. sapiens gene, as well as their products and predicted metabolic network.

HumanCyc is linked to many biological databases:

1) Genomic: Ensembl; GenBank (Entrez); LocusLink; RefSeq; Unigene; GeneCards; UCSC Human Genome DB.

2) Protein: SwissProt; RefSeq; Entrez.

3) Disease: OMIM.

4) Other: GO (Gene Ontology); PubMed.

System Requirements

See G6G Abstract Number 20230 or BioCyc


Manufacturer Web Site HumanCyc

Price Free for academic institutions. Fee required for commercial use. Licence required.

G6G Abstract Number 20234

G6G Manufacturer Number 102506