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SaddleSum
WEB SERVICE
Query Form
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Standalone Program and Cytoscape Plugin
DOCUMENTATION
Overview
Standalone Program
Web Service
Cytoscape Plugin
Additional Information
SaddleSum QUERY FORM
Term Database and Weights
Term Database:
GO + KEGG: Arabidopsis thaliana
GO + KEGG: Caenorhabditis elegans
GO + KEGG: Danio rerio
GO + KEGG: Drosophila melanogaster
GO + KEGG: Homo sapiens
GO + KEGG: Mus musculus
GO + KEGG: Plasmodium falciparum
GO + KEGG: Rattus norvegicus
GO + KEGG: Saccharomyces cerevisiae
[?]
Enter the term database apropriate for your query.
Weights: enter here
[?]
Enter the measured entities (genes) with their weights. Each line should contain two columns separated by spaces or a tab, with the first column being the gene ID and the second the numerical weight associated with that ID.
Entities can be entered as NCBI Gene IDs or canonical gene symbols appropriate for the selected species. Note that the weights entered through the form are ignored if a file is uploaded.
or submit a file
[?]
Upload a file with the measured entities (genes) with their weights. Each line should contain two columns separated by spaces or a tab, with the first column being the gene ID and the second the numerical weight associated with that ID.
Entities can be entered as NCBI Gene IDs or canonical gene symbols appropriate for the selected species. Note that the weights entered through the form are ignored if a file is uploaded.
Each line should contain a gene identifier and its weight, separated by space or a tab.
Statistical Parameters
E-value cutoff:
[?]
Set the largest E-value for a term to be considered significant.
Minimum term size:
[?]
Set the minimum number of entities for a term to be considered. Only entites with supplied weights count towards the term size.
Effective termdb size:
[?]
Set the effective term database size for applying Bonferroni correction (i.e. calculating E-values) to P-values output by the algorithm. If the value set is 0 (default), the total number of terms considered is used.
Statistics:
Lugananni-Rice (sum of weights)
One-sided Fisher's Exact test
[?]
Set statistical method used to evaluate term enrichment statistics.
Lugananni-Rice
is the default SaddleSum method, while
One-sided Fisher's Exact test
is a widely used alternative that requires a cutoff (see below) to be set.
Weight Processing Parameters
Transformation:
No transformation
Flip signs
Take absolute value
[?]
Apply a transformation to each of the provided weights prior to other applying other processing options (see below) and calculating enrichment statistics.
Apply cutoff:
No cutoff
By rank
By weight
[?]
Choose a type of cutoff to apply. The value of cutoff should be entered in the next field.
By rank
sets all weights ranked lower than the chosen value to 0. If there are several weights tied at the cutoff, keep all of them.
By weight
sets all weights smaller than the chosen value to 0.
Cutoff value:
[?]
Enter the cutoff value. The interpretation of the value depends on the cutoff type chosen above.
Discretize weights:
[?]
Discretize weights. Set all weights greater than 0 to 1 and all those smaller than 0 to 0.
Output Parameters
Output Format:
HTML with embedded image
Plain text (without image)
TAB-delimited (without image, full results)
[?]
Choose output format for the results.
Image Format:
SVG in Navigator
SVG
[?]
Choose the format of the image showing the hierarchy of significant terms. The 'SVG in Navigator' format is best for viewing the image online while 'SVG' can be used to save the image.
Color Map:
Blues8
Reds8
Greys8
Greens8
Oranges8
YlGn8
YlGnBu8
GnBu8
RdPu8
PuRd8
BrBG8
[?]
Choose the color palette to color the nodes.
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Maintained by Mehdi Bagheri Hamaneh. Last update: June 17, 2025.