Overview of Help-Pages

Genomatix List Comparison

[Introduction] [Parameters] [Output]


This task compares up to 10 lists of elements, computing the union and intersection between identifiers from the lists and plotting a Venn diagram if possible.
A list can consist e.g. of sequence names, gene names, GeneIds or accession numbers. Additionally, there can be associated values for each input (e.g. expression values for GeneIds), which will be carried into the result lists.

The result page lists the number of elements and the first few elements from the following result sets: The first few elements of each result set are listed, and the full results can be exported to Excel or in tab-separated format (*.tsv).
The exported lists also contain the associated values for each element from each input list, if available.

For plotting Venn diagrams the R package VennDiagram is used. It is described in

Hanbo Chen and Paul C Boutros (2011)
VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R
BMC Bioinformatics 2011, 12:35


List Input
Number of Lists Select the number of lists you want to compare. Up to 10 lists can be analysed.
If two, three or four lists are analysed, the output will include a Venn diagram. For each list you will have to paste the values or supply a file (see below).
List <number> Each list can be supplied in two different ways:
  1. The elements can be entered with copy & paste into the text field; optional associated values can be given in an extra textfield. To be associated correctly to the main list-values they must be the same number and order as the list elements.
    Elements in these text fields can be separated by blanks, newlines or commas.
  2. A file containing the list (and optional additional values) can be uploaded as a tab-separated file.
    Note that only the values in the first column are used for comparison with the other lists, the other columns are used as associated values. The number of columns to be used can be set (e.g. if "3 columns" are selected, the first column contains the elements used for comparison, the next 2 columns are carried along to the output).
Case Sensitivity Check this option, if uppercase and lowercase letters should be distinguished in the comparison (default is case-insensitive comparison, i.e. element "act" will be the same as "ACT").
Header Lines Check this option, if the first (only one!) line of each uploaded file shall be removed before the analysis starts. This is to remove potential header lines containing e.g. descriptions of columns.
Compute Probability This option is only available, if exactly two lists are compared.

Usually your input lists are subsets of a large list of entities (the "population", in statistical terms), e.g. genes or promoters. Based on the lengths m and n of the input lists (counting only unique elements!), the cardinality i of the intersection of the two lists and the cardinality N of the population (a positive interger, which you must enter into the textfield), two probability values are computed:

  • the probability that two lists of m resp. n elements picked randomly from the population have exactly i elements in common, and
  • the probability that two lists of m resp. n elements picked randomly from the population have at least i elements in common
In the output, the probabilities are printed both as percent values and in scientific notation.
If you do not enter a value into the textfield, the probabilities are not computed.


The output consists of The exported lists contain the associated values from each input list for each element.
If no associated values were suplied, the union and intersection lists show from which input list they originated ("1" for present, "-" for not present).


Example Input:

List1Associated values for List1List2Associated values for List2

Example Output:

Venn diagram

(click to enlarge)

Union / Intersection
7 elements Abcg8, Abhd2, Ace2, Actl7a, Actn3, Adam15, Adam1a
2 elements Ace2, Actl7a
Probability values probability that 2 random subsets
(having 5 resp. 4 elements)
picked from a set of 20 elements, have an intersection
of exactly 2 elements is 21.6718% ( 0.2167182663e0 )
of at least 2 elements is 24.8710% ( 0.2487100103e0)
Single Lists
List1 (Input List1) 4 elements Abcg8, Abhd2, Ace2, Actl7a
4 elements Abcg8, Abhd2, Ace2, Actl7a
0 elements -
2 elements Abcg8, Abhd2
List2 (Input List2) 5 elements Ace2, Actl7a, Actn3, Adam15, Adam1a
5 elements Ace2, Actl7a, Actn3, Adam15, Adam1a
0 elements -
3 elements Actn3, Adam15, Adam1a
Export selected list as

When exporting the intersection of both lists to Excel the output looks like this:

Elementvalue(s) from List1value(s) from List2

If no associated values were supplied, the union of both lists would look like this:

Elementdefined in List1defined in List2