Welcome to the L2L Microarray Analysis Tool

A simple tool for discovering the hidden biological significance
in microarray expression data
Downloads
L2L Application and Website Databases (incl. L2L MDB)
Source data for L2L MDB Gene Ontology Tools
Other Tools

See the Supplemental Data page for sample data and results described in the L2L manuscript.

All components of L2L, inclduing the database files, are released as Free Software
under the terms of the GNU General Public License.

L2L Application and Website

The L2L Microarray Analysis Tool is available for download in two forms. The smaller package, "L2L Application", includes only the application itself and all necessary supporting files, including translator libraries and the four sets of lists (see below). Download this package to run L2L from the command-line, or in batch mode, for rapid and customizable analysis of large data sets. The README file contains extensive documentation, including examples of how to use L2L in batch mode.

The larger package, "Complete L2L Website", contains all of the files needed to host L2L on your own web server. It is an archive of the complete contents of this site, including documentation. Instructions for how to install L2L on your web sever are also in the README file (see Section VI). Detailed instructions are provided for Mac OS X.

For previous versions, please see the revisions page.

back to top
Databases (incl. L2L MDB)

The sets of lists used in L2L, including the L2L Microarray Database, consist of plain-text files that each contain a list of the genes associated with a particular experimental condition or trait. Here you can download all of these lists for each of the sets currently used by L2L. These may be of greatest interest to those who wish to extract the gene symbols from these lists for use in another software tool or for bioinformatical analysis.

If you wish to include the database lists for distribution in another Free analysis program, we ask only that you acknowledge L2L in a place obviously visible to users, and cite us in any manuscript describing such a tool. Please contact us if you have any questions.

For previous versions, please see the revisions page.

back to top
Source data for L2L MDB

The L2L Microarray Database is compiled from published data. Beginning in 2007, we are releasing this compiled data in raw, "source" form. The periodic releases of the L2L MDB are created by generating updated lists of gene symbols from this static source data. Each source file is identical to an L2L MDB list file, with two changes. First, replacing the usual list of gene symbols is a list of the original published gene identifiers that was used to create the L2L MDB list - usually probe IDs or GenBank accessions. Second, the "Platform" field has two values, separated by a comma. The new, first value is a code used to specify the species and format of the published gene identifiers. If the list is from a non-human species, the first few letters in the code are a species prefix (mm, mouse; rn, rat; mmu, Rhesus). Human lists do not have a prefix. The remainder of the code is self-descriptive (e.g. genbank, clone, symbol, unigene). Data that was reported from multiple platforms is indicated as "mixed"; the format is then specified for each individual identifier, such as "symbol:ERCC6" or "mmgenbank:AC154412".

L2L translator library files are generated from similar source files, which are in turn derived from microarray manufacturers' annotations. These can also be downloaded below.

As for the processed database lists, these compiled data are released under the GNU GPL. If you wish to include the database lists for distribution in another Free analysis program, we ask only that you acknowledge L2L in a place obviously visible to users, and cite us in any manuscript describing such a tool. Please contact us if you have any questions.

back to top
GO-L2L

Perl application used to create the Gene Ontology sets of lists for L2L. Complete instructions for replicating the lists can be found in the README file.

back to top
Other Tools

Probes2Names: A set of Perl applications that assist in the conversion of microarray probe identifiers to HUGO gene symbols. See the README file for documentation and instructions.

MammalHom: A set of Perl applications that assist in the interconversion of human, mouse, and rat gene symbols. See the README file for documentation and instructions. See also the web-based MammalHom tool.

L2L-Utilities: A collection of Perl applications for mining the L2L microarray database. It includes programs for counting the number of genes and references in the database, finding common genes between a group of lists, finding co-expression relationships, and more. See the README file for documentation and instructions.

All software and files are (c) 2005-2006 John Newman, and are released as Free Software under the GNU General Public License. This license grants the freedom to use, modify, and re-distribute the software, with certain conditions. The software comes with absolutely no warranty. See the complete text of the license for details.