GoMiner Wrapper

This is the web interface for High-Throughput GoMiner™. You need to upload two files to the server, a total file with all of the genes in your experiment, and one of two types of changed files. Detailed descriptions of the input files are available. You will receive an email message with instructions on how to download your results once they are complete. Documentation for both the output files generated and possible error codes are also online.

Step 1:

Select total file

Input should be a text file with '.txt' extension. if no file is specified

Select Auto-Generate option

Auto-Generate (Increases Computation Time Significantly)

Step 2: Select the changed file

Accepts zip file with '.zip' or text file with '.txt' extension

Step 3: Select DataSource(s)

From list

Data sources:

Enter list

Specify semicolon separated list of data sources:

You find possible values at the Gene Ontology web site; look at the abbreviate and synonym fields.
For example, UniProtKB and Mouse Consortium would be UniProKB;MGI

Step 4: Select Organism(s)

From list

Organisms:

Enter list

Specify semicolon separated NCBI Tax ID's:

For example, human and mouse would be given as 9606;10090

Step 5: Select Evidence Code(s)

From list

Evidence levels:

Enter list

Specify semicolon separated GO Evidence Code:

For example, "Inferred by Curator" and "Inferred from Direct Assay" would be given as IC;IDA

Step 6: Select Lookup Settings

Cross Reference

Synonym

Step 7: Select Statistical Constraints for Summary Reports

P-Value

FDR

Both

The p-value and/or FDR determine which categories are counted in the .report file and which categories are displayed in the CIM.

Step 8: Select number of randomizations

Step 9: Smallest Category Size for Category Statistics

Limits the categories that will be included in the CIM and summary reports. Categories whose size (i.e., the number of genes) is less than this threshold will be omitted from category statistic calculations, and randomized categories below this threshold will be omitted from FDR calculations.

Step 10: CIM

No CIM

Basic CIM

Additional CIMs (Uses Moderately Increased Hard Drive Storage)

Largest Category Size (i.e., the number of genes) to Include in CIM

Step 11: Select Root Category for evaluating enrichment ratios, Fisher's Exact and the FDR's.

All/Gene ontology

Biological process

Cellular component

Molecular function

Step 12: Your E-mail Address

Step 13: Submit your query

GoMiner™ is a development of the Genomics and Pharmacology Facility, Developmental Therapeutics Branch (DTB), Center for Cancer Research (CCR), National Cancer Institute (NCI).

Please email us with any problems, questions or feedback on the tool.

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