LCGbase:a Comprehensive Database For Lineage-based Co-regulated Genes

Different lineage (such as vertebrates and arthropods) and animal genes, well-organized and orderly integration into the dynamic chromosome structures that physical development and cell differentiation on behalf of a major regulatory mechanism, comparative genomics indicate that genes are not distributed randomly.lt is associated with the chromosome structures and the regulation of sequence.Bidirectional gene pair is defined as two adjacent genes which are divergently transcribed on opposite strands of DNA.We use this bidirectional gene pairs the expand the windows on the strands to define the clusters, In between animals within the family and family to assess the genome, the genome is actually a cluster of most genes, which is at different stages of the progressive stable, with biological significance. Until now, many questions about gene organization, such as in a cluster (cluster) what is the smallest number of genes, what is leading to gene co-regulation (co-regulation) of the driver, have to be resolved. Here, we provide an easy to use LCGbase database (A Comprehensive Database for Lineage-based Co-regulated Genes), use one of the dynamic evolution of information on two different families of the animal kingdom:vertebrates and arthropods gene clustering and sorting. This is a LAMP platform using web database, can provide users with effective interactive query service. Our database has the advantage of three easy to understand:1、A representative of this database, including species of vertebrates and arthropods typical of all high-quality genomic components.2、The database of human-centric, the other family (such as primates, mammals, reptiles) in the genomes of all the genes mapped to the human genome, and from well-defined genes (gene cluster that is a minimum:by two adjacent genes constitute a two-way, parallel polymerization gene) gene cluster to produce more. In addition, users can search any neighboring genes and their detailed comments.3、A flexible definition of the database parameters, such as two adjacent genes of the distance between the transcription start site, can be extended to different species, the side-phase clusters of genes in the distance between the transcription start site.We also offer a number of the sequence alignment, gene semantic annotation, promoter recognition, gene expression, coordinated expression (co-expression) and coordination of control (coordinate expression and coordinate regulation) and useful tool for evolutionary analysis.The tool which named KaKs calculator2.0is used in evolutionary analysis,it use the gamma-series methods and a sliding windows technique. KaKs calculator2.0can be accessed in http://sourceforge.net/projects/kakscalculator2/with source code in GPL. The database not only provides a definition of the specified family and the way gene cluster designated species, but also for further research:gene co-regulation of gene expression (DNA methylation and histone marks) of the genetic control of gene cluster environment and species in the chromosomal evolution structure, providing a convenient. LCGbase have effectively online, site http://lcgbase.big.ac.cn/LCGbase/...