Science Park - Research Division

Gene Expression
& Gene Targeting Tools

We provide web-based data storage and analysis tools for several of the global gene expression techniques employed at Science Park— cDNA and oligonucleotide microarrays, 2D-PAGE, Serial Analysis of Gene Expression, and Rapid Analysis of Gene Expression. In addition we've developed a search engine to find potential triplex-forming oligonucleotide target sequences in the human and mouse genomes.

			Triplex-forming Oligonucleotide Search Engine
			The Triplex-forming Oligonucleotide Target Sequence Search Engine searches gene sequences for potential TFO target sequences matching user-specified criteria, including length and base composition. The engine gives the user the option to choose whether to search a raw genomic sequence or a repeat-masked sequence. Search results list the TFO target sequences found along with descriptive information about them, including length, percent G, position on the chromosome, gene region in which they were found, matches to known repeat sequences, and PubMed identifiers for articles reporting validated TFO target sequences. The search results are enriched with links to NCBI resources: Entrez Gene, GenBank, BLAST, and PubMed.
			2D PAGE Data Resource
			Currently under development, the 2D PAGE Data Resource will provide public reference maps of mouse skin proteins as well as a private warehouse for 2D gel images, mass spectrometry identification data, and quantification data. The tool will also improve the protein identification process by maintaining a database of experimentally determined peptide fingerprints for protein identification in lieu of using theoretical data. More...
			BASE Microarray Database and Analysis Tool  (login required)
			For storage and analysis of cDNA and oligonucleotide microarray data we provide a local installation of the MIAME-compliant open source BioArray Software Environment (BASE) developed at Lund University in Sweden. In addition to data storage, BASE includes tools for data normalization, filtering, annotation, and analysis. The flexible plug-in architecture of BASE allows addition of analysis tools as they are developed. More...
			SAGE Library Tool  (login required)
			The SAGE library tool allows users of the Serial Analysis of Gene Expression technique to store, compare, search, annotate, and analyze SAGE libraries. Users can perform on-line library comparisons and annotation as well as generate reports for download. The tool utilizes NCI SAGE Genie and NCBI SAGEmap tag to gene mapping in addition to NCBI LocusLink, NCBI UniGene, and Gene Ontology Consortium annotation. More...
			RAGE Laboratory Information System  (login required)
			The RAGE LIMS supports the Rapid Analysis of Gene Expression technique developed at Science Park. The RAGE process uses PCR amplification of pre-determined cDNA fragments representing specific genes and capillary electrophoresis for analysis of the fragments. Using the RAGE LIMS laboratory personnel can manage experiments and analyze fragments directly from sequencer data files. More...
	Our gene expression and gene targeting tools are funded by the NIEHS Center for Research on Environmental Disease and the National Cancer Institue.
	Last update: Saturday, 09-Feb-2008 07:42:08 CST