Kiwi

For more information about Kiwi, including documentation and tutorial, go to www.sysbio.se/kiwi. There you can also get the Python implementation of Kiwi and install it on your own system.

Select input type


[?]
Geneset-geneset interaction file (GSN) in .txt or .sif format
[?]
Geneset statistics result file (GSS) in .txt format
[?]
Gene level statistics file (GLS) in .txt format
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Gene-geneset file (GSC) in .txt format
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Network analysis parameter
P-value cutoff [?]
Use adjusted p-values [?]
Max no of genes in a gene-set [?]
Max degree of gene set [?]
Max shortest path length [?]
Show all edges [?]
Lump identical gene-sets [?]
Plotting parameters
Scaling factor for node size
[?]
Scaling of edge widths
[?]
Label sizes
[?]
Heatmap type [?]
Translate gene ids (Optional)
from: [?]
to: [?]
Species: [?]
Email (Optional)
Enter your email to receive your results [?]

Run


Contact

Enter your E-mail Id for getting the result in your mail.

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Use adjusted p-values

Use adjusted p-values (if provided as a separate column in GSS).This flag controls if p-values adjusted for multiple testing should be used.

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cft

This flag reports the annotation source for the genes in the GSA run (e.g. Ensembl). It should match the annotation sources listed in mygene.info (e.g. ensembl.gene).

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csp

This flag reports the species for the gene annotation (e.g. Homo sapiens). It should match the species listed in mygene.info (e.g. human).

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ctt

This flag controls the maximum degree of a geneset in the interaction network after which it is discarded from the results. It can be used to exclude very connected genesets (like This flag reports the annotation desired to plot the gene names in the heatmap (e.g. HUGO). It should match the annotation sources listed in mygene.info (e.g. symbol). in a metabolic network) from the plots.

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Max degree of a gene-set

This flag controls the maximum degree of a geneset in the interaction network after which it is discarded from the results. It can be used to exclude very connected genesets (like ATP in a metabolic network) from the plots.

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Kiwi

The Kiwi module combines geneset analyses with biological networks to visualize the interactions between genesets that are significant in a given biological system.

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Scaling of edge widths

This flag control the scaling of edge widths with one increment in the shortest path length between two connected genesets.

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Gene-geneset file (GSC)

The geneset collection (geneset-gene) file path. It is a two column table with genesets - genes associations in each row and no header.

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Gene level statistics file (GLS)

The gene-level statistics file path. It is a three column table with gene - p-value - fold-change in each row. The genes must be as first column, while p values and fold-changes must be identified in the headers as p-value and FC.

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Geneset-geneset interaction file (GSN)

It is a 2 column table where each row contains two interacting genesets, each one per column, with no header.

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Geneset statistics result file (GSS)

It is, in its minimum implementation, a 2 or more column table where each row must contain as first column the genesets and in any column a statistics value for its significance. The header must identify the first column as Name and the geneset statistics column as p-value. If -ad is set to True, adjusted p-value are expected to be found in a column identified by the header as p-adj. Alternatively, a full geneset result file generated using piano can be supplemented. If generated using the function writeFilesForKiwi.R in piano, the file is parsed automatically.

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Max no of genes in a gene-set

This flag control the maximum number of genes for a geneset after which it is discarded from the results. It can be used to exclude high gene count genesets, whose interpretability would be difficult and possibly messy to display in the heatmap.

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Heatmap type

This flag sets the color of the entries in the heatmap to black or white when set to .binary. or to a blue-to-red colormap according to the fold-change when set to .values..

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General Instructions

Click [?] to display instructions here, or navigate through the links below.

Tool description
Input instructions
Output description

Example files to download

geneset-geneset interaction file
geneset statistics result file
gene level statistics file
gene-geneset file

Click load minimal input and hit Run

Click load additional input and hit Run

Input Instructions

Kiwi accepts 4 inputs.
gsn [required]: The geneset-geneset interaction file.
gss [required]: The geneset statistics result file.
gsc [default = ..]: The geneset collection (geneset-gene) file.
gls [default = ..]: The gene-level statistics file.

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Input Type

To run Kiwi, the following data files are required:
Minimal input
A geneset-geneset interaction file (here on referred to as GSN file); A geneset statistics result file (here on referred to as GSS file). Warning If either the GSN or GSS files are missing or cannot be accessed, Kiwi will halt execution and produce an error.
Additional input
For a full experience, the following files are also recommended: A gene level statistics file (here on referred to as GLS file); A gene-geneset file (here on referred to as GSC file); If provided, the GLS file will output a heatmap that shows which genes contributed to the significance of a geneset.

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Label sizes

This flag sets the label sizes in the plots.

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lmp

Lump genesets that share an identical gene list. This flag controls if only one geneset (randomly chosen) among all genesets that share an identical list of genes should be kept in the geneset-geneset interaction network. If set to True, all but one geneset among those that share an identical gene lsit will be removed from the interaction network. In the plot, a geneset that lumps other genesets shows a label that describes the number of lumped genesets after a star (“*”). If set to False, all genesets are treated as independent entities in the network even if they share an identical gene list.

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Scaling factor for node size

This flag defines the node size of genesets with the highest p value to be plotted (in the extreme scenario, this equals pCutoff).

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Output file description

Kiwi generates Network plot and Heat map based on the selected inputs. The network is also available as a GraphML file that can be imported in Cytoscape for more advanced layouting.

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P-value cutoff

This flag controls the maximum threshold for the significance of a geneset, after which it is discarded from the results.

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No of permutations

This flag is used if gene-set p-values were calculated using a permutation test.This flag states the number of permutations used if geneset p-values were calculated using permutation tests rather than null hypothesis significance tests. This allows for better estimation of the node size of genesets whose p values are exactly zero.

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Show all edges.

This flag controls if all but the best edges (defined by having the shortest path length) for each node should be removed before plotting. If set to True, all edges (passing the spl cutoff) will be drawn. If set to False, only the best edges for each node will be included.

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Max shortest path length

This flag controls the maximum shortest path length between two genesets in the interaction network after which no edge would connect them. This can be interpreted as the threshold after which two genesets are considered unrelated.

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Online tools powered by kiwi

Citations
1) Väremo L*, Gatto F*, Nielsen J (2014) Kiwi: a tool for integration and visualization of network topology and gene-set analysis BMC Bioinformatics 15:408 (download)
A * indicates that these authors contributed equally to the work.