Transcript Expression Analysis

This section contains links to microarray methods, standards for microarray data, and analysis tools for expression data from other high-throughput technologies. Also contains tools for transcript expression in general.

Found 141 links

Displaying 15 links

ACIDDatabase Content

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The Array Clone Information Database (ACID) is a searchable resource for information about human, mouse, and rat cDNA clones. Each clone contains information about the assigned UniGene cluster(s), location in the full-length transcript, assigned gene ontology terms and position in the genome assembly.

links directory index: 18
TitlePublication YearGoogle Scholar Citation Count
ACID: a database for microarray clone information200418

Affymetrix NetAffx Analysis CenterDatabase Content

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Allows correlation of GeneChip array results with array design and annotation information; provides access to array content information, including probe sequences and gene annotations; free registration is required.

links directory index: 448
TitlePublication YearGoogle Scholar Citation Count
NetAffx: Affymetrix probesets and annotations2003448

AMIC@Tool Content

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The All Microarray Clustering @ once (AMIC@) web application provides users with a range of microarray gene expression data clustering algorithms. Algorithms can be run concurrently on the same data sets. Data can be visualized by heat maps and downloaded as a standard clustered data file for further analysis.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
AMIC@: All MIcroarray Clusterings @ once20089

ArrayAnalysis.orgTool Content

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ArrayAnalysis.org is a web server for quality control and pre-processing analysis of Affymetrix gene expression results by extending, integrating and harmonizing functionality of Bioconductor packages. The tool may also be downloaded for use in R.

links directory index: not available
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ArrayPipeTool Content

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ArrayPipe allows users to customize a processing pipeline for the analysis of microarray data. Includes methods for quality assessment of slides, data visualization, normalization, and detection of differentially expressed genes. Output consists of reports formatted as standard web pages and tab-delimited lists of calculated values.

ArrayProspectorTool Content

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ArrayProspector is a set of predicted functional associations between genes that have been inferred from microarray expression data from the Standford Microarray Database. Users can search for genes linked to query or for links between two genes.

ArrayTrackTool Content

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ArrayTrack™ provides an integrated solution for managing, analyzing, and interpreting microarray gene expression data. Specifically, ArrayTrack™ is MIAME (Minimum Information About A Microarray Experiment)-supportive for storing both microarray data and experiment parameters associated with a pharmacogenomics or toxicogenomics study.

BabelomicsTool Content

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Babelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Other tools include Biocarta pathways, Transfac and a tool de novo functional annotation of sequences.

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