GOAPhAR Help

1. What is GOAPhAR? GOAPhAR is abbreviated for Gene Ontology, Annotations and Pathways for Array Research. It is a web-based tool that gives information about gene identifiers with respect to their Gene Annotation, Protein Annotation, Protein Interactions, Biological Pathways andGene Ontology associations. It also provides the associated identifiers from other domains, presence of available microarray datasets, statistical validity of clusters of microarray data and description from affymetrix.

2. What can GOAPhAR provide in terms of analysis? GOAPhAR provides annotation to the genes, proteins, chromosomal location, protein structure, biological pathways the gene is involved in, available microarray experimental data about the gene, links (IHOP) to available literature about protein interactions. A full list of functionality can be seen here.

3. What the major aspects of GOAPhAR? GOAPhAR provides links to many databases that provide information about the genes. The annotation links are classified as Gene Annotations, Protein Annotations, Gene Ontology, Protein Interactions. It further provides a tool to assess the quality of clusterings of microarray data in 'Statistical Validity'.

4. What are the sources of information in GOAPhAR? Sources of Information

5. What kind of gene identifiers and genomes does GOAPhAR accept? Currently GOAPhAR accepts Affymetrix, GenBank and Unigene identifiers from Human, Rat and Mouse genomes.

6. What is the input format for data in GOAPhAR? The genes can be uploaded as a text file or a list of identifiers can be pasted into the text box provided. The gene identifiers should be delimited by a new line. The Type of Identifier (Affymetrix,GenBank,Unigene) and Genome (Human,Mouse,Rat) must be specified.

A list of identifiers,
Example:
1007_s_at
1053_at
117_at
121_at
1255_g_at
1294_at
1316_at

Text File,
Example

For Statistical validity, the format should be a text file that contains the identifier, cluster number and parameter of interest (fold change,expression). These entries must be tab delimited. Example

7. Can the results be downloaded? Except for the Protein-Interactions and Statistical Validity, all the results can be downloaded in a text file. The format is a tab-delimited text file, which can be saved as myfilename.xls and viewed in excel sheet. The Statistical Validity results can be copied from the website.

8. Why do I see duplication of Affymetrix/Genbank/Unigene Identifiers in Gene Annotation and Biological Pathways tables? Many of the genes have synonyms, which are mapped to pathway maps. To avoid the risk of missing some pathway maps due to 'gene synonyms' we have made the gene name as the primary key for displaying the data.

9. Why are my genes not highlighted on Biocarta/GenMAPP/CellML/SPAD/Panther maps? The genes are currently highlighted in KEGG maps. The identifiers of other pathways databases do not allow for the highlighting of genes in the pathway maps.

10. Can there be a scenario where some of the genes are not annotated? It can happen due to one or more of the following reasons
a. GOAPhAR might not have updated information
b. Many identifiers are ESTs, which might not have much information about them.
c. Some of the open databases might not have updated information.

11. What do I do if insufficient information is retrived from GOAPhAR? We strongly recommend the use of NCBI to query in case of unsatisfactory results from GOAPhAR. We believe NCBI has the most information about a gene/est.

12. Is there a maximum limit on the number of genes that can be queried? There is no limit on the number of genes in a list, but there can be a significant delay in response time if more than a 1000 genes are queried. Responses for a gene list of up to 50 are very fast and take less than 2 seconds with a fast internet connection. However, Protein Interaction application in GOAPhAR takes substantial amout of time as it tries to find evidence for interactions.

13. Who can use GOAPhAR? Currently it is free for all academic users.

14. Who do I contact if there is an error in functionality or missing links? Sachin mathur (smathur@kumc.edu)

15. What are the system requirements to run GOAPhAR? The computer should have IE browser 5.5 and up, firefox 2.0 or Netscape 7.0 and up.

16. Are there any recommended ways to view results from GOAPhAR? The text file can be downloaded and saved on the computer. The results can be viewed as a spreadsheet by opening the text file through Microsoft Excel.

17. How do I make use of the statistical validity package? Currently the statistical validity package works on only one dimensional data i.e., if the dataset has 8 microarrays with 2 conditions (4 replicates of each condition), one dimensional data can be obtained by taking the fold change between the conditions. This data can then be clustered using clustering algorithms like Self Organizing Maps, K-Means by using packages like Eisen-Cluster. The result obtained must be formatted into the required file format and used as input in the cluster validity package.
We are currently working on making this multi-dimensional to obviate the need to reduce the data to one dimension.