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# AMEN: Annotation, Mapping, Expression and Network suite of tools #
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This code is distributed under GNU Public License version 2.
Author: Frederic Chalmel
Creation date: February 2006
Last update: 11/26/2013
Version: 1.5.3
Operating system(s): Platform independent
Programming language: Tcl/Tk (>8.6b), R (>2.15.2)
Required R packages: Biobase, affyio, affy, matchprobes, makecdfenv
gcrma, lumi, annotate, mgcv, limma, cluster, survival
multtest, mclust, hopach, RankProducts, samr, gtools,
clValid, kohonen, dynamicTreeCut, GeneCycle, GeneNet,
MASS, longitudinal, corpcor, fdrtool, igraph
Project home page: http://sourceforge.net/projects/amen
Please cite as:
The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology.
Chalmel F, Primig M.
BMC Bioinformatics. 2008 Feb 6;9:86.PMID: 18254954 [PubMed - indexed for MEDLINE]
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1. Introduction:
Background: High-throughput genome biological experiments yield large and multifaceted
datasets that require flexible and user-friendly analysis tools to facilitate their interpretation
by life scientists. Many solutions currently exist, but they are often limited to specific steps
in the complex process of data management and analysis and some require extensive informatics
skills to be installed and run efficiently.
Results: We developed the Annotation, Mapping, Expression and Network (AMEN) software as
a stand-alone, unified suite of tools that enables biological and medical researchers with basic
bioinformatics training to manage and explore genome annotation, chromosomal mapping, protein-protein
interaction, expression profiling and proteomics data. The current version provides
modules for (i) uploading and pre-processing data from microarray expression profiling
experiments, (ii) detecting groups of significantly co-expressed genes, and (iii) searching for
enrichment of functional annotations within those groups. Moreover, the user interface is designed
to simultaneously visualize several types of data such as protein-protein interaction networks in
conjunction with expression profiles and cellular co-localization patterns. We have successfully
applied the program to interpret expression profiling data from budding yeast, rodents and human.
Conclusion: AMEN is an innovative solution for molecular systems biological data analysis freely
available under the GNU license. The program is available via a website at the Sourceforge portal
which includes a user guide with concrete examples, links to external databases and helpful
comments to implement additional functionalities. We emphasize that AMEN will continue to be
developed and maintained by our laboratory because it has proven to be extremely useful for our
genome biological research program.
2. Download and Installation:
AMEN is distributed under GNU Public License version 2. The source code is freely available
from http://sourceforge.net/projects/amen. If you find bugs or have constructive suggestions to
the program, please feel free to send e-mail to the author.
AMEN is mainly written in standard Tcl/Tk language and some R scripts are automatically
created and executed. So It could run under any type of operating systems for which tcl/tk and R are available (including windows, linux and mac).
Prior to the AMEN download, installation and execution, the user has to download and properly installs:
- a tcl/tk distribution such as ActiveTcl (>=8.6 at http://www.activestate.com/activetcl/tcl8_6/)
- R, a freely available language and environment for statistical computing (>=2.9.1 available at http://cran.r-project.org/bin)
If and only if these two programs are properly install user can now download, unzip and execute AMEN:
- create a folder (make sure you have ownership of this folder) such as c:\AMEN on windows.
Try to avoid creation of this folder into system folders such as c:\Program Files for privilege reasons.
- download and unzip the AMEN_X.X.X.zip archive file (where X.X.X corresponds to the release number)
into this folder.
- Run the AMEN_X.X.X.tcl script (c.f. next section).
3. Usage
3.1 How to run AMEN:
- For Windows: Double-click on the AMEN_X.X.X.tcl (where X.X.X corresponds to the release number)
file and associate the tcl extension to the wish.exe program. You may have to manually associate
the tcl extension with the wish executable file (by default C:\Tcl\bin\wish.exe)
- For Linux and Mac OS X: enter the following command at the shell prompt in the directory in which
the AMEN_X.X.X.tcl file is located
$wish AMEN_X.X.X.tcl
- An alternative approach consists of running the wish graphical interface by executing the wish binary
file (by default C:\Tcl\bin\wish.exe on windows), select the menu option "File>Source.." and manually
browse the AMEN_X.X.X.tcl file.
3.2 The first execution, what will happen?
- First AMEN will ask you to indicate a path to the R binary file. By default this file is
"c:\Program Files\R\R-X.X.X\bin\x64\Rterm.exe" or "c:\Program Files\R\R-X.X.X\bin\i386\Rterm.exe"
or "c:\Program Files\R\R-X.X.X\bin\Rterm.exe" on windows depending on the R version and your
configuration. On Linux and MacOSX, the path to this file is /usr/bin/R"
AMEN will also ask you to browse a path to a "gene_ontology.obo" file that you can directly download
using the "DOWNLOAD DATABASES" button.
- AMEN will automatically creates a "TMP" and a "RLIBRARIES" folders into its installation folder.
- Finally, AMEN will automatically download and install the required R packages (it can take several minutes).
NOTE: If AMEN fails to install automatically the R packages please refer to the R manual for a manual
installation procedure. Packages may be distributed in source form or compiled binary
form. Binary packages are platform specific and in general no special tools are needed to install
them (see the documentation of your platform for more details). Here is the list of teh required R packages:
Biobase, affyio, affy, matchprobes, gcrma, lumi, annotate, mgcv, limma, cluster, survival, multtest, mclust,
hopach, RankProducts, samr, gtools, clValid, kohonen, dynamicTreeCut
3.3 How to use AMEN
Please download and read the detailed documentation and manuals available at http://sourceforge.net/projects/amen/files/
Several pdf presentations showing some AMEN functionalities are also available.
4. Future developments
4.1 Short-term developments
- Fix the problem of installation on MAC OSX
4.2 Mid-term developments
- Add a module to import BioPax files
- Add the SOM clustering
- Add a PCA module
- Add the GSEA method
- Add methods to automatically select the cutoff (standard deviation, fold-change)
4.3 Long-term developments
- Improve and add modules to analyze the Affymetrix All-Exon microarrays
4.4 Very-long-term (uncertain) developments
- Add a R console interface
5. Release history
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1.5.3
Bugs fixed
- AMEN did not work on MacOSX. I fixed another bug and now it is supposed to work !!!
1.5.2
Bugs fixed:
- Bugs in the "Unlog2/log2-transformation" module ==> this module was unavailable.
- Bugs in the "Network drawing" and "Community structure detection" modules due to a critical change in R >3.0.0 ==> the "as.real" function is now removed. I replaced all "as.real" by "as.double".
- Bugs in the "Network drawing" and "Community structure detection" modules due to the removal of the medline database in the SRS system (EBI) ==> We now directly query the NCBI website.
1.5.1
Bugs fixed
- I finally find the reason why AMEN failed to work on MacOSX! For each process, MacOSX add automatically a process identifier at the end
of the command line... the consequence was that AMEN tried to interpret this process identifier as a Tcl/tk command!!!
1.5.0
Changes:
- The most important changes since 2006: Annotation and Network data files are now automatically generated!
There's no more need to download different databases and convert them! Just use the "Menu>Options>Download databases" module.
- "Main entries" are now called "Reference entries".
- Annotation and interaction data files could now include "multi-reference entries" (separated by semi-colon ';') as "reference entries" (1rst column)
- "Upload data" was removed and associated modules were placed into either "Expression" or "Options" menu
Modules:
- Two modules allowing one to make the union/intersection of several groups (>=2).
Bugs fixed:
- Bugs in the "Network drawing" and "Community structure detection" modules due to changes in the "igraph" package.
1.3.4
Two bugs fixed:
- Impossible to add gene2go information to an annotation file from IPI.
- Impossible to run some normalization modules and especially the "Surface Intensity Distribution".
One change:
- Change in the hypergeometric distribution calculation used to estimate the over-representation of annotation terms.
over-representation : p <- phyper(x - 1, m, n, k, lower.tail = FALSE)
under-representation : p <- phyper(x , m, n, k, lower.tail = TRUE)
Note:
- The path to the "Rterm.exe" file as changed, please have a look at section 3.2 of the current document.
1.3.3
Two changes:
- Network drawing module has changed
- Complete "Annotation file with gene2go" module has changed. Now, the previous annotation is replaced by the gene2go annotations.
Two bugs fixed:
- The "partial correlation network" output file was incomplete.
- Problem with some generated Expression data files containing a empty character at the first position of the header (first line).
1.3.2
One module:
- A Community Structure Detection (CSD) module (based on the igraph R library) was
added into AMEN in order to detect motifs on network.
One change:
- Less (memory) restrictions when loading huge "statistics" data file.
One minor bug fixed:
- Problems during the conversion of the NCBI proteome file.
1.3.1
One minor bug fixed:
- Impossible to run a "Quantile-quantile normalization" properly.
1.3.0
One major bug fixed:
- Due to a recent change, AMEN was enable to start correctly.
1.2.9
One major change:
- The GraphViz program is now replace by the "igraph" R library. So now, no need to
install GraphViz prior to execute AMEN.
One minor change:
- The "interaction" panel into the AMEN GUI was renamed by "network".
4 modules:
- A module allowing one to automatically import protein-protein and protein-gene
association data available at the TFe (Transcription Factor encyclopedia) was added.
- A module dedicated to partial correlation network analysis (using the "GeneNet"
R library) was added.
- A module dedicated to detection of periodically expressed genes (using the "GeneCycle"
R library) was added.
- A module dedicated to "InterQuartile Range Filtration" was added.
One minor bug fixed:
- Incompatibility with Windows 7 during the first AMEN execution when the program
tried to find automatically the R binary file.
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1.2.8
Two modules:
- A module is available to import the NCBI 'interactions' data file
- A module is available to import the NIA MPPI data file
Changes:
- AMEN is now able to import interaction data from DIP, HPRD, CORUM, MatrixDB
- "protein-ribonculeic acid" interactions were renamed "protein-rna" interactions
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1.2.7
One minor bug fixed:
- bug into the AMEN Graphical User Interface.
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1.2.6
Three changes:
- Brand new AMEN Graphicla User Interface
- No more restrictions on the length names
- Synonyms and ORFNames are now extracted when converting EBI proteome file (.dat)
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1.2.5
Two changes:
- A module is now available to pre-process the Affymetrix Exon Array as
well as Affymetrix Gene Array CEL files. Users should download the CDF file available
for each microarray in the "library files" section (into the support menu)
- A module is now available to import the Affymetrix Exon Array as
well as Affymetrix Gene Annotation files (CSV files). Users should download the CSV file available
for each microarray in the "annotation data" section (into the support menu)
Four bugs fixed:
- Redundancies in the "Group" column when exporting data as HTML table. It happened if there were redundancies in
the group files.
- Impossible to convert the BioGRID interaction PSIMI-2.5 files due to changes in their format.
- Impossible to extract the participant identification methods from the MINT and BioGRID interaction
PSIMI-2.5 files.
- An unnecessary message was displayed if the IMG package was not installed. PNG format is now
automatically supported by Tcl/Tk 8.6
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1.2.4
1 bug fixed:
- AMEN was enable to install the required R packages if the path to AMEN contained space characters.
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1.2.3
1 change:
- The missing files (deleted or moved or renamed) in the project will not be loaded into the AMEN interface.
2 minor bugs fixed:
- Impossible to display KEGG pathways anymore.
- Impossible to select a pathway indicated into the displayed KEGG pathway. This bug is due to a change into the KEGG web site.
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1.2.2
The AMEN installer for windows is no more available. See the installation procedure above for more details on how to download, install and execute AMEN.
3 modules:
- A Quality-control module after normalization is now available for intensity signal data directly added to the 'Expression' panel. This module includes boxplot, scatterplot and correlation matrix pictures saved into pdf files.
- A log2-/unlog2-transformation module was added.
- A new visualization module allows user to display the expression signals using a radar view.
1 change:
- The "reorganized expression file" module now allows user to remove samples.
2 minor bugs fixed:
- even if an expression file was imported directly into the "Expression" panel as unlog2-transformed signal data, this data was still considered as log2-transformed.
- impossible to display gene profiles if they had a flat expression pattern (no or low variations across samples).
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1.2.1
One major change:
- During the installation process, the "TMP" folder is not required anymore. AMEN automatically creates this folder into its installation directory. Moreover AMEN automatically installs the required R packages into the "AMEN/RLIBRARIES" folder. This change should facilitate the installation for users which do not have administrator privileges. On the other hand, the user must be the owner of the installation folder ("AMEN" by default).
Apparently, there's still a problem to install automatically R packages on MAC OS. This beug should be fixed on the next version.
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1.2.0
IMPORTANT: User must install the 8.6beta version of Tcl/Tk (ActiveTcl) which already include the tkImg package. So user will not need to install this package.
3 beugs corrected:
- sometimes the "Profiles" module did not work depending on the signal distribution.
- better colors in KEGG pathways
- "Biological_process", "molecular_function", "cellular_component" were found always enriched in the over/under-representation module.
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1.1.9
- IMPORTANT: User should now install the tkImg1.3 package available in sourceforge. This package will allow you to display KEGG metabolic pathways because they change their image format (GIF->PNG) and PNG format is not initially compatible in Tcl.
- One change in the hypergeometric p-value calculation.
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1.1.8
7 modules:
- Module to estimate if a biological entity (protein for exemple) interacts or regulates more genes/proteins in a cluster of genes as compared to whole genes (Enrichment on regulatory or interaction networks). Written by Aurélie Lardenois.
- Module to visualize these enrichments as a network. Written by Aurélie Lardenois.
- Two modules for semi-supervised k-means and PAM methods.
- Module to add gene set files (.gmt files from GSEA) into the annotation file.
- Module to normalize with positive or negative control genes.
- Module to reorganize the samples into an expression file
Two changes:
- When importing group files they are now sorted in the alphabetical order and then imported into AMEN
- The R packages installation module was modified.
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1.1.7
Three bugs occured when expression data contained missing values in the following modules:
- Average/median expression calculation
- Standard deviation filtration
- Standardized normalization
The "affy" package does not provide the "normalize.quantiles" function anymore. AMEN now uses the "normalizeBetweenArrays" function from the "Limma" package into the quantile-quantile normalization module.
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1.1.6
Three bugs were fixed i the new AMEN version:
- the "DynamicTreeCut" R package was not automatically downloaded and installed into the R environment.
- there was an bug in the R script when using the "DynamicTreeCut" R package.
- Problems occured when space characters were present into the mapping or annotation filenames!
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1.1.5
- one MAJOR bug was fixed and 4 changes were added
One major bug fixed:
- A problem when indexing expression data file (ExpressionPanel procedure) gave several problems in procedure using these expression data files and especially statistical modules (Standard deviation, Find similar patterns, Limma modules). These errors occured when not all the samples were selected.
4 changes:
- Over/under-representation module allows one to estimate enrichment by comparing groups together and not only by comparing groups to whole genome.
- Affymetrix All-exon modules use now the "transcript cluster ids" to estimate the Gene-level intensity signals.
- KEGG importation module ask the user to select the interesting species for his current project.
- KEGG visualization module allows users to choose between several species for the same pathway.
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1.1.4
Changes:
- NOTE: Apparently, Statistical modules do not work with Windows vista. I will try to fix this problem as soon as possible.
3 bugs fixed:
- Typos in the 'Merged expression files' module
- Typos in the 'Gene-level intensities' module
- Impossible to compute summary statistics for expression data containing empty values.
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1.1.3
19 changes:
- Affymetrix all-exon array preprocessing module.
- Affymetrix all-exon annotation file importation module.
- Affymetrix all-exon Gene-level summary file calculation module.
- Affymetrix all-exon probe Gene-level normalized intensities calculation module.
- Affymetrix all-exon splicing-index calculation module (a probe Gene-level normalized intensities file is required!).
- Two-color array preprocessing scanned with GenePix module (including Sigma Antibodies arrays and Operon arrays).
- Operon annotation file importation module
- Pre-processing modules: boxplot before and after normalization, and scatter plot pdf files.
- Annotation file: allow multiple lines for each main entries.
- Module to complete annotation files with mapping data. The 'Mapping' panel is no more in the AMEN panel.
- Module to complete annotation files with 'gene2accession' file.
- Module to complete annotation files with KEGG metabolic pathway data.
- Module to visualize KEGG metabolic pathways. (INTERNET connection required !)
- Memory optimization in AnnotationPanel, ExpressionPanel
- Memory optimization when creating and saving files.
- Module allowing developpers to reload the AMEN tcl script when running.
- Summary statistics file is created for each expression file.
- Automatic color scale bar for the expression heatmap and profile modules pusing the Summary statistics file of each expression file to generate a intensity signal color scale.
- Module dedicated to download databases directly into AMEN (using the ftp and log Tcllib packages).
4 bugs:
- LIMMA module: problem if the replicat data are not close together in the expression file.
- Problem with the SRS URL to download pubmed abstracts in the (Protein-protein) Interaction viewer.
- Illumina change their annotation file format (CSV to tab-delimited text format).
- Problem in the Illumina array pre-processing script.
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1.1.2
Four changes:
- A clustering module using the SOTA self-organizing map classification method was implemented.
- A clustering module using the dynamicTreeCut (Hybrid Adaptative Tree Cut For Hierarchical Clustering Dendograms) was implemented.
- A clustering validation module using the APN, AD, ADM, FOM, dunn, connectivity and silhouette width methods was implemented.
- Affymetrix changed its CSV annotation file format, I updated the AMEN importation module to take into account these changes.
Three bugs:
- Now you can import ".cel" or ".CEL" affymetrix files.
- When adding elements into one of the AMEN panels (Group, Annotation, Expression, ...) if the file name contained space characters it was not correctly added.
- If a group contained only one ID, an error occured when lauching a hierarchical classification.
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1.1.1
In the current version of AMEN, two changes were added and one minor bug was fixed
Two changes:
- The "two-class paired" SAM filtration module was added.
- The statistical filtration menu was changed. Statistical modules are now organized according to their type of filtration (time-course, two class unpaired, two class unpaired time course, ...)
One minor bug:
- Impossible to display under-representation terms.
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1.1.0
Three major bugs:
- the "CLARA" clustering module did not work anymore. It was just a typo mistake on a procedure name.
- the Heatmap and the Mapping modules did not work. I used "global" with a cell of a array instead of with the corresponding array.
One minor bug:
- In the new Tcl/Tk version (8.5.0) there is a bug using the "pow" option of the expr procedure. puts [expr pow(10,-1)] returns 0.10000000000001 instead of 0.1. I correct this error.
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1.0.9
One major bug:
- In the LIMMA statistical filtration, the contrast matrix was not well-designed.
One minor bug:
- When exporting data as HTML table file, the HTML document had a title corresponding to one of our existing project.
Two changes:
- In the LIMMA statistical filtration, the samples can only be selected in one condition.
- There is a bug in the new version of GraphViz. To solve this problem, AMEN does not use the fontname option to define the .dot file.
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1.0.8
One minor bug was fixed in the current AMEN release:
- Enrichment calculation was impossible if there were space characters in the selected mapping or annotation file names.
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1.0.7
Interaction changes:
- Optimization of the interaction graphical representation.
- User can now import other type of interactomic data (not only protein-protein interactions) such as protein-gene, protein-rna, gene-rna, gene-gene or rna-rna. These interactions will be displayed with different colors in the graphical representation. So the interaction file format was change in order to take into account these types of interactions.
- A new interaction format was defined including: type of interaction (ex protein-protein), the interaction detection methods used (ex two hybrid), the participant identification methods (ex mass spectrometry), and the number of participants in the related complex.
- User can now filter according to the interaction detection methods and/or the participant identification methods.
- The MacOS X graphviz default path was added into AMEN in order to try to automatically find it.
- The '-K' option is not available in the Mac OS X graphviz options. So if the operating system is Windows or Mac OS X, AMEN directly used the executable method (ex method 'neato' -> executable 'neato.exe') whereas in Linux systems AMEN uses the -K option.
- Bug: User can now manually select all the interactors even those that are not present in the selected Groups.
- Bug: Selection of interactors which are not in the selected groups according to their subcellular localizations.
- Bug: Gene names of the interactors which are not in the selected groups are now displayed
- Bug: if there is "-" in the interactor ID (such as Yeast ORF names).
- Bug: Some of the interactor entries were not extracted. The PSI-MI2.5 parsor was remade.
Annotation changes:
- when converting EBI proteome annotation file, GeneID category is now converted in EntrezGene.
- Sometimes, there is no 7 numbers in a GO term ID... AMEN forces the GO ID with 7 numbers ex 5575 -> 0005575.
Mapping data:
- in the 1.0.5 release, we changed the ISCN chromosome ideogram in order to have the same scale for each histogram. Problem, the selected groups do not contain the same number of genes so we need to use different scales.
Statistical filtration modules:
- Bug: if LIMMA failed to detect differentially expressed gnes, there is warning message if user restarts the analysis.
- LIMMA and multtest are now downloadable at the bioconductor website and not the CRAN website
- The samr and RankProduct R packages have been implemented into AMEN in order to provide novel statistical filtration options.
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1.0.6
One major bug fixed
- If the temporary directory pathname contained "blank space", it was impossible to run R script.
Two minor bugs fixed:
- In the interaction display, if only the groups were displayed (and not the cellular components), the color spectrum was not right.
- The default close button (cross up to right) did not close the window properly.
One major change:
- The first running of AMEN does not require to reboot AMEN.
Five minor changes:
- A splash screen was added during the AMEN initialization process.
- The control window of the mapping and heatmap visualization modules stays open after displaying the results.
- Column headers (Conditions and Replicats) were added in the LIMMA and Permutation-test statistical modules.
- In the interaction visualization module, a message appears when there is no interaction between gene products.
- The "Edit" function directly displays the number of entities belonging to the selected groups.
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1.0.5
The new AMEN release contains two minor changes:
- In the ISCN chromosome ideogram representation, the same scale is used to display group statistics for a given chromosome.
- In the interaction graphical module, color-codes are not redundant between groups and cellular components.
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1.0.4
Five minor changes have been added in AMEN:
- Alert messages appear if no entries are selected after a statistical filtration step.
- Sometimes, Affymetrix CSV annotation files use "0" as EntrezGene ID if there is no association with EntrezGene (instead of "-").
- New module (HelloWorld) to explain how to integrate additional modules in the main AMEN GUI.
- The last current directory used is conserved in memory in the procedure called 'AddAndModifyCategoryElements4MAIN'.
- Alert messages appear if no group files are created at the end of a clustering process.
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1.0.3
One more bug fixed in the new AMEN release v.1.0.3:
- The "union / intersection / difference" option was not correctly associated with its module.
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1.0.2
5 minors bugs were fixed in the new one AMEN_1.0.2 release.
BUG FIXED:
- Mapping visualization module: UP and DOWN buttons were not associated with the listbox allowing user to select chromosomes.
- Mapping visualization module: Minus and Plus orientated sequences were not correctly color-coded (red for 'minus' strand and blue for 'plus' strand).
- Mapping visualization module: 'X' and 'Y' zooming options were associated both with the 'XY' zooming option.
- Interaction visualization module: It was impossible to select 'groups'.
- Interaction visualization module: In SVG format, 'arc' object were bigger than in the Tk graphical representation.
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1.0.1
I fixed one bug concerning the "expression profiles" and "expression heatmap" options which were not associated with the right modules!
One more unsupervised clustering module was integrated based on the HOPACH R package
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1.0.0
The first publically available release of AMEN is out. We expect this biological high-throughput data analysis environment will greatly assist life scientists to deeply explore their own (or external) overwhelming data and thus to rise to rise meaningful biological hypotheses.
Download Latest Version
AMEN_1.5.5.zip (332.2 kB)
