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| == Latest Build == ''Brain Plugin'': Version 1.0.5 alpha (2007 May 23) - attachment:brainPlugin.jar |
== Downloads == The BRAIN library and plugin are available below for download as Java archive (JAR) files and Java source tree tarballs. |
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| ''Brain Library'': Version 1.0.6 (2007 July 26) - attachment:brainlib-1.1.jar | === Latest Release === |
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| ''Brain Dependencies'': Additional JARs required by BRAIN - attachment:brainDeps.tar.gz | ''BRAIN Plugin'': Version 1.0.5 alpha (May 23, 2007) <<BR>> Build: [[attachment:brainPlugin.jar]] <<BR>> Source: [[attachment:BRAIN-Plugin-1.0.5-src.tgz]] |
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| ==== Release Notes ==== | ''BRAIN Library'': Version 1.4 (September 29, 2008) <<BR>> Build: [[attachment:brainlib-1.4.jar]] <<BR>> Source: To be posted by October 3, 2008 |
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| '''BRAIN Library 1.1''' (2007 July 26) | ''Dependencies'': Additional JARs required by BRAIN - [[attachment:brainDeps.tar.gz]] === Earlier Releases === ''BRAIN Library'': Version 1.3 (May 12, 2008) <<BR>> Build: [[attachment:brainlib-1.3.jar]] <<BR>> Source: [[attachment:BRAIN-Library-1.3-src.tgz]] ---- == Installing the Plugin == === System Requirements === * Java Runtime Environment (JRE) 1.5 or later * [[http://www.cytoscape.org|Cytoscape]] 2.4.1 or later === Installation === * Place ''brainPlugin.jar'' and ''brainlib_1.1.jar'' in the Cytoscape ''plugins'' directory (located in the Cytoscape program directory, e.g. /usr/local/bin/Cytoscape or C:\Program Files\Cytoscape_v2.4.1) * Extract and place all files from brainDeps.tar.gz into the Cytoscape ''plugins'' directory * Launch Cytoscape * Look in the ''Plugins'' menu for the ''BRAIN'' item. If you don't see it there, revisit the above steps to make sure all files are in the right place. ---- == Running the Plugin == * Launch Cytoscape * Set analysis parameters from ''Plugins > BRAIN > Set Parameters'' * Start the BRAIN analysis from ''Plugins > BRAIN > Run BRAIN'' ---- === Notes on Using BRAIN === BRAIN takes one or more query proteins and their respective peptide ligands, builds a PWM-based profile for each protein, searches a protein sequence database for similar profiles, and returns a ranked set of proteins that are predicted to interact with the query proteins. A query protein and its experimentally determined peptide ligands are represented as a [[/PeptideFile|peptide file]], in which the peptide binders are listed as an ungapped multiple sequence alignment. The plugin can open a single peptide file, or multiple peptide files that are grouped into a [[/PeptideFile#ProjectFiles|project file]]. From a peptide file, BRAIN generates a position weight matrix (PWM), or protein profile. The profile constitutes the distributions of amino acids (rows) at each of the positions (columns) of the peptide pattern. In a given column of the PWM, each amino acid is assigned a weight based on its frequency of occurrence at the given position. These weights are normalized to 1.0 to emulate probabilities of occurrence. BRAIN searches a protein sequence database (in FASTA, Swiss``Prot, Gen``Pept, or EMBL format) for the pattern represented by the protein profile. An interaction score (p-value) is calculated for each hit, and all hits exceeding the user-provided score threshold are reported as predicted interactors of the query protein. The output is provided as a Cytoscape network, enabling further graph-based analysis and exploration of node (protein) and edge (interaction) attributes including interaction score, gene name, motif sequence, and associated OMIM or Morbid``Map record (if available). ---- == Release Notes == '''BRAIN Library 1.4''' (September 29, 2008) * Supports the Cytoscape Task API to display a progress bar during logo tree generation '''BRAIN Library 1.3''' (May 12, 2008) * Single linkage hierarchical clustering used to cluster profiles for generating logo tree * Sequence logo alignment algorithm added for generating logo trees * New code for amino acid grouping and coloring schemes to be defined, e.g. for generating sequence logos and logo trees '''BRAIN Library 1.2''' (February 2008) * Internal release for alpha-testing '''BRAIN Library 1.1''' (July 26, 2007) |
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| '''1.0.6''' (2007 June 12) * brain.jar: Ability to retrieve additional database references from ProteinProfile object (previously was only able to retrieve the first ID in the Accession field of the peptide file). |
'''1.0.6''' (June 12, 2007) * brain.jar: Ability to retrieve additional database references from Protein``Profile object (previously was only able to retrieve the first ID in the Accession field of the peptide file). |
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| '''1.0.5''' (2007 May 23) | '''1.0.5''' (May 23, 2007) |
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| '''1.0.4''' (2007 May 15) | '''1.0.4''' (May 15, 2007) |
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| '''1.0.3''' (2007 April 23) | '''1.0.3''' (April 23, 2007) |
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| '''1.0.2''' (2007 April 11) | '''1.0.2''' (April 11, 2007) |
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| '''1.0.1''' (2007 February 21) | '''1.0.1''' (February 21, 2007) |
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| == Running the Plugin == * Place the plugin (brain.jar) in your Cytoscape 'plugins' folder * Launch Cytsocape * Set parameters (''Plugins-->BRAIN-->Set Parameters'') * Run (''Plugins-->BRAIN-->Run BRAIN'') ---- == Source == '''SVN path:''' svn1.ccbr.utoronto.ca/svn/baderlab/csplugins/brain |
== Future Developments == |
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| Tagged Releases are available under ''svn1.ccbr.utoronto.ca/svn/baderlab/csplugsin/tags/''. | (in order of priority) 1. Regular expression filtering of profile search results. 1. Expose auto-score threshold functionality in Profile Search panel (allow the user to specify automatic score threshold setting instead of having to specify a score threshold themselves). 1. Expose "regex" search features - new Pattern Search panel similar to Profile Search 1. New feature: consider aa groups in PWM searching 1. Design an improved scoring scheme (e.g. take into account surface accessibility) and drop down box to select different scores. |
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| == Resources == '''Human RefSeq Database''' (GenPept Format, 2007 Feb 21): attachment:human.protein.gpff.gz '''Peptide file (new 1.1 format):''' attachment:peptide_file_v1.1.txt A peptide file contains a set of experimentally observed ligands for a given domain-containing query protein. Information in the peptide file includes query protein annotation (database identifiers), domain sequence, ligand sequence, and ligand expression data. '''Peptide file conversion script:''' attachment:ConvertBrainPeptideFile.pl Converts peptide files from format version 1.0 to version 1.1. It takes an input file or directory path, and an output directory path. e.g. ConvertBrainPeptideFile.pl ~/data/oldfiles/ ~/data/newfiles/ This will convert all peptide files in ~/data/oldfiles to the new format; converted files are written to the directory ~/data/newfiles/. To convert a single file, provide the path (including filename) to the peptide file in the first argument. If the output directory doesn't exist, it is created. Make sure read permissions are correctly set for the input file/directory, and write permissions are correctly set for the output directory. Paths can be relative or absolute. For usage, run the script with no arguments. ---- == Requirements == Java Runtime Environment (JRE) 1.5 or later is required to run LOLA. All other dependencies are included in the download. == Installing and Running == * Extract the TAR file. This will create a directory named "lola". * On Linux, open the command shell and run "lola.sh" from the "lola" directory. * On Windows, double click "lola.bat". * On Mac, double click lola-1.0-beta.jar * You can open a single peptide file, or a project file linked to multiple peptide files. Here's a view of LOLA after opening a PDZ domain project file: attachment:lolaScreenShot.png == Input Format == LOLA accepts one or more ''peptide file'' as shown in the example below. A peptide file describes a protein containing a specific domain, and provides known peptide ligands of this domain obtained by an experimental technique. The peptide file consists of a '''Header Section''' that describes the protein and domain sequence, and a '''Peptide Section''' that lists and describes the peptide ligands. Example: {{{ Gene Name DLG1 Accession Refseq:NP_004078 Organism Homo Sapiens (Human) NCBITaxonomyID 9606 Domain Number 3 Domain Type PDZ Interpro ID IPR001478 Technique Phage Display High Valency Domain sequence KVVLHRGSTGLGFNIVGGEDGEGIFISFILAGGPADLSGELRKGDRIISVNSVDLRAASHEQAAAALKNAGQAVTIVA Domain Range 466-525 Comment PeptideName Peptide CloneFrequency QuantData ExternalIdentifier 1 XLHFWRESSV 66 2 XXRLWKQTSL 3 3 ILKIWRETSL 3 4 KRTIWRETSL 2 A KNLRSNSMLG 2 6 HLKFWRSTRV 2 7 AHSKWRSTSV 2 8 XXXHRRETTV 1 9 VISRWRQTSL 1 10 TTWLGRQTRV 1 11 SRSSYRETSV 1 12 XXXSRRETSV 1 13 RLFRYRETSL 1 B PIRKRWTMTL 1 15 XXXNHRETSV 1 16 KIVRWKNTSV 1 17 KHRTWYETSV 1 18 XXXXFKQTSV 1 19 ARPKWRTTRV 1 20 ALPRRRETSV 1 }}} ==== Header Section ==== Describes the protein, domain, and experiment. Required fields are indicated with a '''*'''. '''NOTE:''' This section is in a 2 column format. Field names must be separated from their values with a single TAB character. Multiple TABs or spaces are not accepted. '''Gene Name:*''' An identifier that represents the gene or protein sequence. Not required to be unique. '''Accession:*''' A space-separated list of database accession identifiers for the protein or corresponding gene. '''Organism:''' Description of taxon of the protein. '''NCBITaxonomyID*:''' Taxon identifier from NCBI's Taxonomy repository. '''Domain Number*:''' A number that represents the position of the domain sequence within the protein. For proteins containing multiple instances of the domain, this number helps distinguish the position of these instances. Set to "0" if instance information is not known. '''Domain Type:*''' The formal name of the domain, e.g. WW, PDZ, SH3. '''Interpro ID:''' The Interpro database identifier for the domain. '''Technique:''' The experimental method used to identify potential ligands of the protein. '''Domain Sequence:*''' The amino-acid sequence of the domain region. '''Domain Range:''' The amino-acid position range for the domain region within the protein. '''Comment:''' Notes, additional information, personal comments pertaining to this file. ==== Peptide Section ==== Describes the experimentally determined peptide ligands. The peptide sequences must be in '''multiple alignment format'''. The sequences should contain '''no gaps''', and should be padded with the '''X''' symbol on both sides, where required, such that all sequences have identical length. '''NOTE:''' This section is in a 5-column format. Column headers and values must be separated with a single TAB character. Multiple TABs or spaces are not accepted. Required fields are indicated with a '''*'''. '''!PeptideName:*''' A ''unique'' numerical symbol assigned to each peptide ligand. To omit a peptide, set to a non-numeric value (e.g. "A"). '''Values in this column must be unique.''' '''Peptide:*''' The peptide ligand sequence. '''!CloneFrequency:''' Applies only to phage display data: the observed frequency of the peptide in the cloning step. '''!QuantData:''' A number that relatively or absolutely quantifies the protein-ligand interaction. E.g. The optical density (OD) from a protein chip experiment. '''!ExternalIdentifier:''' A database identifier for the peptide. === Using Project Files === To open several peptide files at once, simply link them all in a single '''project file'''. A project file is a text file containing the absolute paths of multiple peptide files. Opening the project file in LOLA will open each of the underlying peptide files in a single step, allowing logos to be constructed for multiple profiles. Example: {{{ #ProjectFile /Users/moyez/research/ppi/profiles/PDZ/Human/SidhuPhage/APBA3-1.pep.txt /Users/moyez/research/ppi/profiles/PDZ/Human/SidhuPhage/CASK-1.pep.txt /Users/moyez/research/ppi/profiles/PDZ/Human/SidhuPhage/DLG1-1.pep.txt /Users/moyez/research/ppi/profiles/PDZ/Human/SidhuPhage/DLG1-2.pep.txt /Users/moyez/research/ppi/profiles/PDZ/Human/SidhuPhage/DLG1-3.pep.txt /Users/moyez/research/ppi/profiles/PDZ/Human/SidhuPhage/DLG2-3.pep.txt /Users/moyez/research/ppi/profiles/PDZ/Human/SidhuPhage/DLG3-2.pep.txt /Users/moyez/research/ppi/profiles/PDZ/Human/SidhuPhage/DLG4-3.pep.txt /Users/moyez/research/ppi/profiles/PDZ/Human/SidhuPhage/DVL2-1.pep.txt /Users/moyez/research/ppi/profiles/PDZ/Human/SidhuPhage/ERBB2IP-1-hi.pep.txt }}} '''NOTE:''' The first line of the project file '''must''' contain the text "#ProjectFile". == Future Developments == * Generate a "logo tree" by hiearchically clustering logos [Initial PDZ (no alignment) use case completed in version 1.1] * Allow colours to be selected for individual amino-acids * Add support for nucleic acids * Additional visualization options (e.g. font, axis labels) |
BRAIN Project
The Biologically Relevant Analysis of Interaction Networks (BRAIN) is a set of algorithms for predicting and analyzing protein domain-peptide ligand interactions based on experimentally known binding evidence (e.g. from protein chip or phage display experiments).
BRAIN can be accessed as a Cytoscape plugin which reads peptide binding profiles and generates interactions displayed as a Cytoscape network.
Contents
BRAIN consists of a library or API, and of a Cytoscape plugin.
BRAIN Library
The BRAIN library holds the algorithms and methods for interaction prediction. This library is required to build the BRAIN plugin.
BRAIN Plugin
The BRAIN plugin is a way of running various BRAIN algorithms from the Cytoscape user interface. The plugin runs a prediction analysis and presents the results visually as an interactive Cytoscape network.
Downloads
The BRAIN library and plugin are available below for download as Java archive (JAR) files and Java source tree tarballs.
Latest Release
BRAIN Plugin: Version 1.0.5 alpha (May 23, 2007)
Build: brainPlugin.jar
Source: BRAIN-Plugin-1.0.5-src.tgz
BRAIN Library: Version 1.4 (September 29, 2008)
Build: brainlib-1.4.jar
Source: To be posted by October 3, 2008
Dependencies: Additional JARs required by BRAIN - brainDeps.tar.gz
Earlier Releases
BRAIN Library: Version 1.3 (May 12, 2008)
Build: brainlib-1.3.jar
Source: BRAIN-Library-1.3-src.tgz
Installing the Plugin
System Requirements
- Java Runtime Environment (JRE) 1.5 or later
Cytoscape 2.4.1 or later
Installation
Place brainPlugin.jar and brainlib_1.1.jar in the Cytoscape plugins directory (located in the Cytoscape program directory, e.g. /usr/local/bin/Cytoscape or C:\Program Files\Cytoscape_v2.4.1)
Extract and place all files from brainDeps.tar.gz into the Cytoscape plugins directory
- Launch Cytoscape
Look in the Plugins menu for the BRAIN item. If you don't see it there, revisit the above steps to make sure all files are in the right place.
Running the Plugin
- Launch Cytoscape
Set analysis parameters from Plugins > BRAIN > Set Parameters
Start the BRAIN analysis from Plugins > BRAIN > Run BRAIN
Notes on Using BRAIN
BRAIN takes one or more query proteins and their respective peptide ligands, builds a PWM-based profile for each protein, searches a protein sequence database for similar profiles, and returns a ranked set of proteins that are predicted to interact with the query proteins.
A query protein and its experimentally determined peptide ligands are represented as a peptide file, in which the peptide binders are listed as an ungapped multiple sequence alignment. The plugin can open a single peptide file, or multiple peptide files that are grouped into a project file. From a peptide file, BRAIN generates a position weight matrix (PWM), or protein profile. The profile constitutes the distributions of amino acids (rows) at each of the positions (columns) of the peptide pattern. In a given column of the PWM, each amino acid is assigned a weight based on its frequency of occurrence at the given position. These weights are normalized to 1.0 to emulate probabilities of occurrence.
BRAIN searches a protein sequence database (in FASTA, SwissProt, GenPept, or EMBL format) for the pattern represented by the protein profile. An interaction score (p-value) is calculated for each hit, and all hits exceeding the user-provided score threshold are reported as predicted interactors of the query protein. The output is provided as a Cytoscape network, enabling further graph-based analysis and exploration of node (protein) and edge (interaction) attributes including interaction score, gene name, motif sequence, and associated OMIM or MorbidMap record (if available).
Release Notes
BRAIN Library 1.4 (September 29, 2008)
- Supports the Cytoscape Task API to display a progress bar during logo tree generation
BRAIN Library 1.3 (May 12, 2008)
- Single linkage hierarchical clustering used to cluster profiles for generating logo tree
- Sequence logo alignment algorithm added for generating logo trees
- New code for amino acid grouping and coloring schemes to be defined, e.g. for generating sequence logos and logo trees
BRAIN Library 1.2 (February 2008)
- Internal release for alpha-testing
BRAIN Library 1.1 (July 26, 2007)
- Added PDZ symbol style for PDZ type residue colouring in sequence logo generation code (required by LoLA tool)
1.0.6 (June 12, 2007)
brain.jar: Ability to retrieve additional database references from ProteinProfile object (previously was only able to retrieve the first ID in the Accession field of the peptide file).
1.0.5 (May 23, 2007)
- Code reorganization: brainPlugin.jar now holds only those classes related to the Cytoscape plugin. All other code has been moved to a new Brain Library project.
1.0.4 (May 15, 2007)
- Network node can represent a single domain or a protein containing multiple domain instances (via new Advanced Options tab)
- Lower scoring motif hits are now reported
New node attribute Domain Name to hold a semantic domain identifier (Gene Name + Domain Number, for now)
1.0.3 (April 23, 2007)
- Support for new peptide file format version 1.1 (and back-compatible with format version 1.0)
New node attributes Sequence Start, Sequence Stop, Comment for profiles generated from new peptide file format
1.0.2 (April 11, 2007)
- Report SNPs for entire protein sequence and for domain subsequence only.
- Option to specify codon bias file
- Option to load unique peptides only from peptide file(s)
1.0.1 (February 21, 2007)
- Port to Cytoscape API 2.4 and Java SE 5.0
Future Developments
(in order of priority)
- Regular expression filtering of profile search results.
- Expose auto-score threshold functionality in Profile Search panel (allow the user to specify automatic score threshold setting instead of having to specify a score threshold themselves).
- Expose "regex" search features - new Pattern Search panel similar to Profile Search
- New feature: consider aa groups in PWM searching
- Design an improved scoring scheme (e.g. take into account surface accessibility) and drop down box to select different scores.
Contact
If you have any questions or feedback, please email Moyez Dharsee at mdharsee@infochromics.com.