GO Term Finder looks for significant GO terms shared among groups of genes in your list of input genes (see table below). To determine the statistical significance of a particular GO term associated with a group of genes in the list, GO Term Finder calculates the p-value - the probability or chance of seeing at least x number of genes out of the total n genes in the list annotated to a particular GO term, given that y number of genes out of the total N genes within the genome known to have that GO term annotation (i.e. given the background distribution). The closer the p-value is to zero, the more significant the particular GO term associated with the group of genes is (i.e. the less likely the observed annotation of the particular GO term to a group of genes occurs by chance).

The p-value of a GO term associated with a group of genes in your gene list is affected by the total number of genes estimated for an organism. The higher the total number of genes estimated for the organism, the closer the p-value is to zero and the more significant the particular GO term annotation to the group of genes in the list (see table above, compare respectively rows 1, 2 and 3 with rows 4, 5 and 6). For example, as shown in the table above, when searching the function ontology with a p-value cutoff of 0.01, no significant 'carrier activity' GO term was found for the list of 9 mouse genes for the specified 15,000 total mouse genes (row 6, due to a p-value above the p-value cutoff of 0.01)), while 3 genes out of the 9 genes in the list annotated to the 'carrier activity' GO term were found for the estimated 33,884 total mouse genes (row 3) with a p-value = 0.00265, which is still below the p-value cutoff of 0.01. Thus, though the same number of mouse genes (410) within the mouse genome annotated to the 'carrier activity' GO term, the higher total number of genes (33,884 versus 15,000) estimated for the mouse lowers the frequency the term used to annotate genes in the entire mouse genome, thereby yields the lower p-value for the group of genes in the list annotated to the 'carrier activity' GO term.

The p-value of a GO term associated with a group of genes in your gene list is also affected by the number of genes within an organism having that GO term annotation. The higher the number of genes within the organism with a particular GO term annotation that a group of genes in the list have, the further the p-value is to zero and the less significant the particular GO term is associated with the group of genes in the list. For example, as shown in the table above, though the same 3 mouse genes in the list are annotated to the 'calcium- transporting ATPase activity' (row 1) and 'carrier activity' (row 3) GO terms, the 'calcium-transporitng ATPase activity' GO term associated with the 3 mouse genes is more significant (i.e. lower p-value) than the 'carrier activity' GO term associated with those same 3 mouse genes, due to higher number of genes within the mouse genome annotated to 'carrier activity' GO term.

For more information on how GO Term Finder determines the statistical significance of GO terms annotation, please see the Description of GO Term Finder Algorithm at SGD or How GO Term Finder Calculates P-values (also available in PDF ).

Gene Association File Table lists the total annotated gene products and total estimated gene products for each organism. If the total estimated gene number of an organism is known, the GO Term Finder program's default total gene number for the organism is the organism's total estimate gene number. If not, the GO Term Finder program will use the total number of annotated genes existed in the organism's gene association file as the default total gene number.

If you prefer to use a different total gene number for an organism in the background distribution calculation of GO terms, you can type the number of gene products you estimate for the organism in the provided text box to override the program's default total gene number for the organism. However, if the gene number you entered is smaller than the total number of annotated genes existed in the organism's gene association file, the GO Term Finder program will not use the gene number you entered but uses the program's default total gene number for the organism.

Instead of providing a number, you can upload a background distribution of gene products. In this case, the total number of genes will be the number in the background distribution. This option is useful if you need to find significant terms within a smaller context than that of the entire population of genes with annotation.
 

The FDR is calculated by running 50 sumulations with random genes, and counting the average number of times a p-value as good as or better than a p-value generated from the real data is seen. This is used as the numerator. The denominator is the number of p-values in the real data that are as good as or better than it.

Thus, instead of setting your cutoff based on p-value, the FDR allows you to choose a cutoff that has an acceptable level of false discovery. FDR is the percentage of the GO terms with p-values as good as or better than a particular GO term with this FDR would be expected to be false positives. False positives are the expected number of false positives if that particular annotated GO term is chosen as the cutoff.
 

With this option checked, terms that are related by regulation (and possibly in no other way) are also included in the search, in just the same way as the traditional links:

is_a:
relationship: part_of

These links are always followed.

Gene Association File Table lists the organism default gene URLs used by the GO Term Finder program.

For example, 'https://www.yeastgenome.org/locus/xxxx' is the GO Term Finder program's default gene URL for Saccharomyces cerevisiae, where xxxx is a SGD_ID, SGD gene name, or SGD systematic ORF name (e.g. https://www.yeastgenome.org/locus/YPL250C).

You can also use the provided text box to enter the gene or protein URL you know displaying the type of information about a gene or protein you prefer over the type of information displaying by the GO Term Finder program's default URL. For example, 'http://www.ensembl.org/Homo_sapiens/geneview?gene=xxxx' is the GO Term Finder program's default gene URL for human protein, where xxxx is a UniProt_ID or UniProt_Accession (e.g. http://www.ensembl.org/Homo_sapiens/geneview?gene=SX30_HUMAN). If you prefer to use the UniProt (the Universal Protein Resource) URL 'http://www.uniprot.org/cgi-bin/upEntry?id=' to display information about a protein (e.g. http://www.uniprot.org/cgi-bin/upEntry?id=SX30_HUMAN), you can type the UniProt URL in the provided text box to override the program's default URL.
 

multitest/NODE1X.list
multitest/NODE1X.pcl
multitest/NODE2X.txt
multitest/run2/NODE1X.list
multitest/run2/NODE1X.pcl