SysZNF: the C2H2 zinc finger gene database

Abstract

C2H2 zinc finger (C2H2-ZNF) genes are one of the largest and most complex gene super-families in metazoan genomes, with hundreds of members in the human and mouse genome. The ongoing investigation of this huge gene family requires computational support to catalog genotype phenotype comparisons of C2H2-ZNF genes between related species and finally to extend the worldwide knowledge on the evolution of C2H2-ZNF genes in general. Here, we systematically collected all the C2H2-ZNF genes in the human and mouse genome and constructed a database named SysZNF to deposit available datasets related to these genes. In the database, each C2H2-ZNF gene entry consists of physical location, gene model (including different transcript forms), Affymetrix gene expression probes, protein domain structures, homologs (and synteny between human and mouse), PubMed references as well as links to relevant public databases. The clustered organization of the C2H2-ZNF genes is highlighted. The database can be searched using text strings or sequence information. The data are also available for batch download from the web site. Moreover, the graphical gene model/protein view system, sequence retrieval system and some other tools embedded in SysZNF facilitate the research on the C2H2 type ZNF genes under an integrative view. The database can be accessed from the URL http://epgd.biosino.org/SysZNF.

Figure 1.

Browsing and searching in SysZNF. (A) Browsing SysZNF through chromosomes or by domains. (B) Text strings, SQL and bio-sequences searching. The gene symbol, protein domain name and physical location can be used as search fields in the ‘ADVANCED SEARCH’. Only the ‘search’ statement could be used in the ‘ONLINE SQL SEARCH’. Both protein and nucleic acids sequences can serve as input in the BLAST search page. The user can also access the result of BLAST by email.

Figure 2.

Screenshot of a C2H2-ZNF gene entry. (A) Physical coordinates, gene model and domain structures. (B) A C2H2-ZNF gene cluster. (C) Putative homologs and synteny regions. (D) A detailed synteny region between the human and mouse. (E) Literatures and cross-references related to the gene in this entry. The toothed margin of this screenshot denotes that it is only part of the whole gene entry page.

Figure 3.

Some embedded tools. (A) Genome sequence retrieval system. (B) FunnyFingerSelector, a tool to combine individual fingers and predict the DNA binding sites of the resulting ZNF array. (C) FunnyCluster, a tool to infer physical distance-based clusters of C2H2-ZNF genes in SysZNF according to any user defined interval distance.