Resource Report

URL: http://cgap.nci.nih.gov/SAGE/AnatomicViewer

Proper Citation: SAGE GENIE (RRID:SCR_000796)

Description: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9, 2022. The SAGE Genie website provides highly intuitive, visual displays of human and mouse gene expression, based on a unique analytical process (Boon et al.) that reliably matches SAGE tags, 10 or 17 nucleotides in length, to known genes. Recently, with the construction and incorporation of a reference database of SNP-associated alternative tags into SAGE Genie (Silva et al.), the interpretation of tag to human gene mapping has been enhanced. Human SAGE Genie Tools The SAGE Anatomic Viewer visually displays the relative expression of a given gene in normal and malignant tissues of the human body. In addition, there is access to: o The Digital Northern, which shows the relative expression of the gene in each library. o The Ludwig Transcript (LT) Viewer, which visually represents a particular transcript with up to four possible virtual SAGE tag locations (starting from the 3' end) and locations of internally primed or alternatively polyadenylated transcripts. o Expanded access to brain, hES cells, and breast cell subtypes. * The SAGE Digital Gene Expression Displayer distinguishes significant differences in gene expression profiles between two pools of SAGE libraries. * The SAGE Experimental Viewer provides DGED results for pre-set pairs of libraries, one under control and the other under experimental conditions. * The SAGE Absolute Level Lister lists all SAGE libraries and links to the distribution of transcript expression levels in any given library. * The SAGE Library Finder tool searches for one or more tissue-specific libraries from the SAGE collection. * SAGE Genie Downloads provide files of genes, tags, datasets, mappings, and more. * SAGE Genomics Finder tool searches for genomics info for tags. * DKView tool for viewing Digital Karyotyping data. * DK Microbe tool searches for exact matches of 17 base-pair digital karyotyping tags in bacterial and viral genomes. * SAGE Tag Extraction tool to extract tags from sequence files. Mouse SAGE Genie Tools * The mSAGE Expression Matrix visually displays the relative expression of a given gene through stages of mouse development. In addition, there is access to: o The Digital Northern, which shows the relative expression of the gene in each library. o The Ludwig Transcript (LT) Viewer, which visually represents a particular transcript with up to four possible virtual SAGE tag locations (starting from the 3' end) and locations of internally primed or alternatively polyadenylated transcripts. * The mSAGE Absolute Level Lister lists all mouse SAGE libraries, organized by either tissue (normal or malignant) or developmental stage, and links to the distribution of transcript expression levels in any given library. * The mSAGE Digital Gene Expression Displayer distinguishes significant differences in gene expression profiles between two pools of mouse SAGE libraries. * The mSAGE Experimental Viewer automatically sets up the DGED with mouse libraries, prepared as stand alone experiments, for gene expression comparison. * The mSAGE Library Finder tool searches for one or more tissue-specific mouse libraries from the SAGE collection. * mSAGE Genie Downloads provide files of mouse genes, tags, datasets, mappings, and more. * SAGE Genomics Finder tool searches for genomics info for tags. * SAGE Tag Extraction tool to extract tags from sequence files. Notes: The majority of human libraries are short whereas the majority of mouse libraries are long. Several mouse developmental libraries are prepared by the SAGELite method. SAGELite is an extension of the long Sage protocol that includes a PCR-based amplification stage to allow the use of 10ng to 100ng of total RNA to produce a Sage library. However, it has been observed that a significant bias incurred by this amplification process. SAGE Genie was produced as part of the NCI CGAP SAGE project with collaborators from Johns Hopkins University, the Ludwig Institute for Cancer Research, Sao Paulo Branch, the University of Texas MD Anderson Cancer Center, and the Genome Sciences Center of the BCCRC.

Synonyms: SAGE GENIE

Resource Type: data or information resource, database

Defining Citation: PMID:12119410

Keywords: molecular neuroanatomy resource