Genomic Resources
The program uses an array of bioinformatics and genomics resources, which include
publicly available, in-house developed and proprietary ones. A list of some of the
bioinformatic and genomic resources are provided below. The list will be continuously
updated to add more resources. LSUHSC investigators are welcome to use these resources
independently or with support from BIG staff. However, all investigators using these
resources listed on this website must acknowledge and cite the original sources appropriately.
Gene Expression Omnibus (GEO): is a public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles. The database can be accessed through this website. http://www.ncbi.nlm.nih.gov/geo/
ArrayExpress: It is one of the repositories recommended by major scientific journals to archive functional genomics data to support reproducible research. Experiments are submitted directly to ArrayExpress or are imported from the NCBI Gene Expression Omnibus database. For high-throughput sequencing based experiments the raw data is brokered to the European Nucleotide Archive, while the experiment descriptions and processed data are archived in ArrayExpress. Tools are provided to help users query and download experiments and curated gene expression profiles. The database can be accessed through this website. https://www.ebi.ac.uk/arrayexpress/
Sequence Read Archive (SRA): The database makes biological sequence data available to the research community to enhance reproducibility and allow for new discoveries by comparing data sets. The SRA stores raw sequencing data and alignment information from high-throughput sequencing platforms, including Roche 454 GS System®, Illumina Genome Analyzer®, Applied Biosystems SOLiD System®, Helicos Heliscope®, Complete Genomics®, and Pacific Biosciences SMRT®. http://www.ncbi.nlm.nih.gov/sra
dbGaP: The database of Genotypes and Phenotypes (dbGaP) was developed to archive and distribute the data and results from studies that have investigated the interaction of genotype and phenotype in Humans. http://www.ncbi.nlm.nih.gov/gap
The Cancer Genome Atlas: is a comprehensive and coordinated effort to accelerate our understanding of the molecular basis of cancer through the application of genome analysis technologies, including large-scale genome sequencing. TCGA is a joint effort of the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI), two of the 27 Institutes and Centers of the National Institutes of Health, U.S. Department of Health and Human Services. For more details and how access the TCGA visit the following website: http://cancergenome.nih.gov/
IHEC: The International Human Epigenome Consortium (IHEC) is a global consortium with the primary goal of providing free access to high-resolution reference human epigenome maps for normal and disease cell types to the research community. The epigenome reference maps will be of great utility to LSUHSC researchers in basic and applied research. For detailed information and access, please visit the following website: http://ihec-epigenomes.org/
The NIH Roadmap Epigenomics Mapping Consortium: The project was launched with the goal of producing a public resource of human epigenomic data to catalyze basic biology and disease-oriented research. This resource can be used by the LSHSC research community in support of their research. For details and access visit the following website: http://www.roadmapepigenomics.org/
ENCODE: The encode, Encyclopedia Of DNA Elements project was launched by the National Human Genome Research Institute (NHGRI) as a public research consortium in September 2003, to carry out a project to identify all functional elements in the human genome sequence. The project can be used as references for scientists conducting function genomics. The database can be accessed at this website https://www.genome.gov/encode/
The GWAS Catalog: This is a public genomics resource provided jointly by the National Human Genome Research Institute (NHGRI) and the European Bioinformatics Institute (EMBL-EBI). The catalogue contains genetic variants and genes associated with common human diseases and is an excellent resource for geneticists. The catalogue can be accessed through the following websites: http://www.ebi.ac.uk/gwas/docs/about or https://www.genome.gov/gwastudies/
The International HapMap Project: This is a multi-country effort to identify and catalog genetic similarities and differences in human beings. This is a great resource for LSUHSC researchers interested in understanding genomic variation. The resource can be accessed on the following website: https://hapmap.ncbi.nlm.nih.gov/
TARGET: (Therapeutically Applicable Research to Generate Effective Treatments) An excellent genomic resource supported by NIH and children's oncology group. TARGET applies a comprehensive genomic approach to determine molecular changes that drive childhood cancers. The Bioinformatics and Computational Medicine Program uses the resource for genomic studies on childhood cancers. The resource is accessible through the following websites: https://ocg.cancer.gov/programs/target