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  EmbryoGENE sponsored tools
  • FlexArray - Software for the statistical analysis of one-color and two-color microarray experiments. EmbryoGENE has produced a user guide for the use of FlexArray
  • ELMA: EmbryoGENE LIMS And Microarray Analysis - Official repository for the results of all of EmbryoGENE's microarray experiments. Also does quality control of hibridization results and basic statistical analysis.

  Enrichment analysis tools
  • DAVID: Database for Annotation, Visualization and Integrated Discovery - Comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.
  • GSEA: Gene Set Enrichment Analysis - Determines whether a set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes).
  • FuncAssociate 2.0- Web application that discovers properties enriched in lists of genes or proteins that emerge from large-scale experimentation.
  • GoMiner - Leverages the Gene Ontology (GO) to identify the biological processes, functions and components represented in gene lists.

  • AnimalQTLdb: Animal Quantitative Trait Locus database - Publicly available QTL data on livestock animal species.
  • Snat: Bovine SNP Annotation Tool - Integrated database of bovine SNP data.
  • GEO: Gene Expression Omnibus - Database repository of high throughput gene expression data and hybridization arrays, chips, microarrays.
  • GO: Gene Ontology - Standardized representation of gene and gene product attributes across species and databases.
  • KEGG: Kyoto Encyclopedia of Genes and Genomes - Integrated database resources, including pathways, ontologies, chemical compounds, etc.
  • Biomart - Advanced queries on multiple databases.

  Microarray Analysis tools
  • NIA Array Analysis - Web-based tool for principal component and significance analysis of microarray data.
  • WebArray - Web platform for analysis of microarray data. Two-color data and Affymetrix data are supported.
  • Babelomics - Formerly GEPAS. Babelomics is an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling.
  • TM4 - Suite of microarray tools consisting of four major applications: Microarray Data Manager (MADAM), TIGR_Spotfinder, Microarray Data Analysis System (MIDAS), and Multiexperiment Viewer (MeV).

  Other tools
  • Galaxy - Open, web-based platform for building custom data intensive analysis pipelines that can be shared and reproduced.
  • Venny - Interactive tool for comparing lists with Venn Diagrams.
  • BioVenn - Web application for the comparison and visualization of biological lists using area-proportional Venn diagrams
  • Primer3 - Pick primers from a DNA sequence.
  • NCBI/ Primer-BLAST - Finding primers specific to your PCR template (using Primer3 and BLAST).
  • Dropbox - Easy sharing of data files between colleagues of locations.
  • Cytoscape - An Open Source Platform for Complex Network Analysis and Visualization. Supports plugins:
    • BiNGO - Cytoscape plugin to assess overrepresentation of Gene Ontology categories in biological networks
    • Enrichment map - Cytoscape plugin for functional enrichment visualization.
    • Agilent literature search - Creates a CyNetwork based on searching the scientific literature

  Other bovine genome browsers