GoMiner Wrapper

Step 1:
Select total file	Input should be a text file with '.txt' extension. if no file is specified.
OR
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)
Choose data source from list
OR
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)
Choose organism from list
OR
Specify semicolon separated NCBI Tax ID's For example, human and mouse would be given as 9606;10090

Step 5: Select Evidence Code(s)
Choose evidence level from list
OR
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 Bioinformatics Group, Developmental Therapeutics Branch (DTB), Developmental Therapeutics Program (DTP), Center for Cancer Research (CCR), National Cancer Institute (NCI). We would like to hear from you. You can reach the team via email.

GoMiner was originally developed jointly by the Genomics and Bioinformatics Group (GBG) of LMP, NCI, NIH and the Medical Informatics and Bioimaging group of BME, Georgia Tech/Emory University. It is now maintained and under continuing development by GBG.

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