The
List Enrichment
process compares a set of curated lists (containing genes, proteins, or metabolites, for example) against a table of significance values, and then tests for significant enrichment using Fisher's exact test for
association
. It generates a report on the results in
.rtf
,
.pdf
, or
.html
format.
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A
Significance Input SAS Data Set
. This data set must contain a significance
variable
, typically a -log
10
p-value
. The
u95a_anov_amr.sas7bdat
data set serves as an example. and is shown below. This data set was derived following
ANOVA
analysis for the
Affymetrix Latin Square Data
set. The results of the
anova
were merged with annotation data for this experiment, downloaded from the
Affymetrix website
. This data set contains 88 columns listing annotation along with statistical information including probabilities, LSMeans,
standard deviations
, differences and their associated -
log
10
p
-values, and significance indices. Individual genes or
probes
are listed in rows.
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A
List Description File
. This tab-delimited
.txt
file specifies the files containing the ID lists to be compared with the
Significance Input SAS Data Set
. This table must have two columns with first-row headers
Name
and
File
.
Name
provides names that are to appear in the output file, and
File
contains the filenames with extensions of the files containing the list data. Each row of this table references a different list, and Fisher exact tests are computed for each. This file is a tab-delimited
.txt
file. However, comma-separated text (
.csv
) or Excel (
.xls
) are also acceptable formats. The
Example_List_Description_File.txt
file serves as an example, and is shown below.
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One or more
List Files
. These files contain the ID lists to be compared with the
Significance Input SAS Data Set
. Two
.txt
files,
Interleukin_Receptors.txt
and
Protein_Kinases.txt
, serve as list data file examples, and are shown below. These files contain the annotation information used to determine significance for two distinct functional classes of genes. The files are both tab-delimited
.txt
files. However, comma-separated text (
.csv
) or Excel (
.xls
) are also acceptable formats. Both of these files are included with JMP Genomics.
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For detailed information about the files and data sets used or created by JMP Life Sciences software, see
Files and Data Sets
.
Refer to the
List Enrichment
output documentation for detailed descriptions of the output of this process.