YEASTRACT logo
 
Tutorial

Web Services new web services

DISCOVERER

Regulatory Associations:
- Search for TFs
- Search for Genes
- Search for Associations

Group genes:
- Group by TF
- Group by GO

Pattern Matching:
- Search by DNA Motif
- Find TF Binding Site(s)
- Search Motifs on Motifs

Utilities:
- ORF List ⇔ Gene List
- IUPAC Code Generation
Generate Regulation Matrix

Retrieve:
- TF-Consensus List
- Evidence Code List
- Upstream Sequence
- Flat files

About Yeastract:
- Contact Us
- Cite YEASTRACT
- Acknowledgments
- Credits


Support & suggestions:

KDBIO/INESC-ID IST

Group Genes by GO - Help

BSRG/IST

Index

  1. Summary
  2. Input
  3. Options
  4. Output



1. Summary

This utility groups a given set of genes according to the GO terms assigned to them by the SGD.

Back to top


2. Input

The input required is a list of genes and/or ORF names.

Back to top


3. Options

Grouping can be done by the three gene ontologies: Biological Process, Molecular Function or Cellular Component. The specificity of the grouping can be enhanced by increasing the level of the GO hierarchy (that ranges from 2 to 6, 6 being the most specific).
Furthermore, the user may restrict its search to the regulatory associations identified based on direct or indirect evidences. Direct Evidence was considered to be provided through experiments such as Chromatine ImmunoPrecipitation (ChIP), ChIP-on-chip and Electrophoretic Mobility Shift Assay (EMSA), that prove the direct binding of the TF to the target gene's promoter region, or such as the analysis of the effect on target-gene expression of the site-directed mutation of the TF binding site in its promoter region, which strongly suggests that the TF interacts with that specific target promoter. The classification Indirect Evidence was attributed to experiments such as the comparative analysis of gene expression changes occurring in response to the deletion, mutation or over-expression of a given TF. The complete enumeration of the experimental approaches considered to provide direct or indirect evidences is provided in Table Evidence code list.

Back to top


4. Output

This query returns a table organized by GO terms, ordered by the percentage of the genes (from the input list) associated with each GO term. For each GO term the table contains the names of the genes associated with it.

Back to top
Back to top top w3c xhtml validator w3c css validator w3c xhtml+rdfa validator