About GeneACT
GeneACT is a web-based cis-acting element browser that provides graphic visualization and extraction of common regulatory sequence elements in the promoters and 3.-UTRs that are evolutionarily conserved across multiple mammalian species. GeneACT is written mainly in Java and Java Server Page (JSP). We make use of an Apache Tomcat server to host our website and a PostgreSQL server to store the genomic and preprocessed data. We make use of Scalable Vector Graphics (SVG) to dynamically illustrate the regulatory regions of mammalian genomes. All raw data files are downloaded from NCBI ftp sites and the ftp locations are as follow:
Genome Assembly:
ftp://ftp.ncbi.nih.gov/genomes/
TFD dataset:
ftp://ftp.ncbi.nih.gov/repository/TFD/
HomoloGene dataset:
ftp://ftp.ncbi.nih.gov/pub/HomoloGene/
The mapping of the genes to the sequences is provided by the NCBI map viewer, which can also be found in the Genome Assembly directory on the NCBI FTP site. As new genome assemblies become available, we will update our genome definition as well as our homologene definition accordingly.
In more detail, we got the genome assemblies from NCBI and stored all the sequences in the database. We obtained information about the genes, such as the chromosomal location of the introns, exons and coding sequences of all genes from NCBI map viewer. To obtain the orthlogs information, we made use of NCBI homologene as the source to relate the genes in each mammalian species. We dropped all the genes that are not in the homologene database in any one of the three genomes, resulting in 13542 genes totally in our database. Transcription factor binding sites information was also obtained from the NCBI ftp site. All these information were parsed into the database (All data files are available upon request). For microRNAs, we obtained all the miRNA sequences from miRbase. 3.UTRs of all of the 13542 genes from each genome are extracted from our database. These UTRs were then searched for potential miRNA targets using the miRanda Algorithm. Only the targets that are found in each of the three genomes were considered and these results were parsed into our database. Making use of the information in the database, we preprocessed all the binding sites that are found upstream of the start codon (up to 10000bp) of each gene that go across all three genomes for the DBSS analysis. For TFD information downloaded from the NCBI, we manually curated the binding sites information and discarded the redundant binding sites found in the database.
To allow easy access to the information in the database and the tools available, we created a website (http://promoter.colorado.edu/geneact).
This website contains 4 tools, Potential Binding Site Search (PBSS), Differential Binding Site Search (DBSS), Genomic Sequence Retrieval and Transcription Factor Database Search. Via these webpages, we collect user input and return the requested results to the user. For Transcription Factor Database Search, a request of adding new binding sites into the database will be reviewed by our curators and the binding site will be used in the next round of preprocessing for the DBSS analysis.
For information about the tools available, please visit our help pages. Source codes are available here.
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