My Microarray Software Comparison - Network/pathway Reconstruction and Analysis Software

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Definition of pathway reconstruction and analysis software
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Network/pathway reconstruction and analysis software (in alphabetical order)

Promoter analysis software

Network/pathway reconstruction and analysis software

Definition of Network/pathway reconstruction and analysis software

Network/pathway reconstruction from microarray data is commonly based on steady-state data like targeted mutation and time-series data. These experiments share the common goal of identifying cause-consequence relationships of which genes are controlled by other genes. The analysis often involves the promoter analysis of the genes inside the same cluster to identify common regulatory elements. A number of different targeted mutations can also be combined to infer the possible underlying network by various algorithms. Besides, the result of expression profiling can be mapped onto known biological pathways in order to have further insights on the underlying biological changes on a pathway sense.

Network/pathway reconstruction and analysis software (in alphabetical order)

Promoter analysis

AlignACE (Aligns Nucleic Acid Conserved Elements) - AlignACE is a program which finds sequence elements conserved in a set of DNA sequences. Reference 1 [PubMed]; Reference 2 [PubMed]
BindGene - search for transcription factor binding sites - especially those of the transcription factor HNF1A. Reference [PubMed][Full text]
BioProspector - Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes. Reference [PubMed]
Cis-analyst - Cis-analyst is a tool for finding clustered transcription factor binding sites in the Drosophila genome. Reference [PubMed][pdf][web supplement]
FastM & ModelInspector - FastM is a program for the generation of models for regulatory regions in DNA sequences. These models can be built using various individual elements (like transcription factor binding sites, repeats, hairpins) and their sequential order. ModelInspector directly use FastM-generated models to scan any DNA sequence or GenBank sections for matches to the model. Reference [PubMed]
Greedy EM algorithm - Discovering probabilistic motifs in a set of biological sequences by learning a mixture of motifs model through likelihood maximization. The algorithm adds sequentially motifs to a mixture model by performing a combined scheme of global and local search for appropriately initializing component parameters. A kd-tree partitioning scheme is also used to speed-up the global search procedure. Reference [PubMed]
INCLUSive - INCLUSive is suite of web based tools and is aimed at the automatic multistep analysis of microarray data (clustering and motif finding). Reference [PubMed]
MatInd and MatInspector - MatInd derives a matrix description of a consensus from a number of short sequences on which the definition of a IUPAC code would be based. MatInspector is a second software tool that utilizes this library of matrix descriptions to locate matches in sequences of unlimited length. Reference [PubMed]
MDscan - a motif finding algorithm with applications to chromatin immunoprecipitation microarray experiments. Reference [PubMed]
MELINA - Melina assists users to compare the results of four public softwares for DNA motif extraction in order to both confirm the reliability of each finding and avoid missing important motifs. Reference [PubMed]

MEME (Multiple Expectation-maximization for Motif Elicitation) & MAST (Motif Alignment & Search Tool)

PubMed

<>Microarray Promoter Extractor - Freeware tool for extracting promoters from files with affymetrix identifiers.
MSCAN - an algorithm that detects clusters of transcription factor binding sites in genomic sequences. Reference [PubMed]
MULTIPROFILER - MULTIPROFILER utilizes multiprofiles which generalize the notion of a profile to detect subtle patterns that might escape detection by the standard profiles.
OTFBS (Over-represented Transcription Factor Binding Site Prediction Tool) - a method base on TRANSFAC Matrix, it can detect over-represented motifs of known transcription factors from a set of related sequences. Reference [PubMed]
Pattern Search - Find short consensus motifs, 3' or 5' UTR sequences, and other small sequences using regular expression matching.
PatternBranching/ProfileBranching - a new approach which searches motif space by branching from sample strings, and implement this idea in both pattern-based and profile-based settings.
PatSearch - The PatSearch program is a pattern matching tool, that can find a well defined pattern against a given sequence(s) or database (primary or specialized) divisions. Reference [PubMed]
ProGA - Eukaryotic Promoters Recognition by Genetic Algorithm. Reference [PubMed]
PROMO - PROMO is aimed at the identification of short sequences with high similarity to known transcription factor binding sites. The TRANSFAC database is used as the source of known binding sites and transcription factors. Weight matrices representing factor-binding sites are constructed dynamically from factor-specific binding site sequences. After matrix construction matches to a sequence of interest can be inspected. Expectation values and a list of genes containing binding sites for the different transcription factors in the predictions are provided. Reference [PubMed]
Promoter Scan - Predicts Promoter regions based on scoring homologies with putative eukaryotic Pol II promoter sequences. Reference [PubMed]
Sequence Logos - a graphical way of representing and visualizing binding site. Reference [PubMed][ps]
Signal Scan - Find and list homologies of published signal sequences with the input DNA sequence. Reference [PubMed]
TFBIND - Software for searching transcription factor binding sites (including TATA boxes, GC boxes, CCAAT boxes, transcription start sites (TSS)). This tool uses weight matrix in transcription factor database TRANSFAC R.3.4 developed by Dr. Wingender et al, and the cut-offs originally estimated by our research. Reference [PubMed]
Toucan - Toucan is a workbench for regulatory sequence analysis on metazoan genomes, especially for detecting significant transcription factor binding sites. It is a platform independent, standalone Java application and was built using the BioJava package. Reference [PubMed]

Network/pathway reconstruction and analysis software

BioMiner - BioMiner is a software system for analyzing and visualizing complex biochemical networks and processes. The pathfinder algorithm integrates known metabolic information for a group of organisms collected from diverse data sources into a metabolic graph. Reference [PubMed]
Cytoscape - Cytoscape is a bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. Reference [PubMed]
DBmcmc - DBmcmc is a free software package written in MATLAB for inferring dynamic Bayesian networks with MCMC. The programs invoke functions of the Bayes Net Toolbox written by Kevin Murphy; so you need to download his software package first. Reference [PubMed]
Dynamic Signaling Maps - A web-based software allows you to create, edit, annotate, and store biological signaling pathways, do consistency checks when integrating pathway data from multiple sources, produce biomolecular network maps in multiple vector graphics formats, and integrate pathways with protein-protein interaction data from external databases such as BIND. The "Gene Networks from Time-Series Expression Profiles" module can generate small gene networks from time-series microarray data. Product of Hippron Physiomics.
GenMAPP (Gene MicroArray Pathway Profiler) - a free computer application designed to visualize gene expression data on maps representing biological pathways and groupings of genes. Reference [PubMed]
Genetic Network Analyzer (GNA) -GNA (Genetic Network Analyzer) is a computer tool for the modeling and simulation of genetic regulatory networks. The aim of GNA is to assist biologists and bioinformaticians in constructing a model of a regulatory network using knowledge about regulatory interactions in combination with gene expression data. Reference [PubMed]
GenePath - a program that may assist in the construction of genetic pathways from genetic data. Reference [PubMed]
Graphviz - open source graph drawing software
GSCope - GSCope is an Internet Explorer plug-in module designed for viewing and analyzing gene expression data in the context of biological pathways. Data files for GSCope is XML-based. GSCope has a function that filters thousands of gene expression data to extract statistically similar expression profiles. It also utilize a visualization method for understanding multi-linked comprex biomolecular network graphs by combining advantages of fisheye conversion function and clipping of connected structures. Reference [PubMed]
INCLUSive - INCLUSive is suite of web based tools and is aimed at the automatic multistep analysis of microarray data (clustering and motif finding). Reference [PubMed]
InterViewer3 - A new layout algorithm with complexity management operations in visualizing a large-scale protein interaction network. Reference [PubMed]
Kinetikit - Kinetikit is an interface and utility for developing simulations of chemical kinetics. Reference [PubMed]
KnowledgeEditor - KnowledgeEditor is the software to provide biologists to import a probe information from microarray data to a biomolecular network, and to modify a known metabolic pathway based on novel microarray experiments.
Osprey - The Osprey Network Visualization System is an application for graphically representing physical and genetic biological interactions. It provides many features that are helpful in analysis of interaction data. Reference [PubMed][pdf]
PathFinder - reconstruction and dynamic visualization of biochemical pathways online. Reference [PubMed]
Pathtracker - Pathtracker enables the researcher to study a Gene, mRNA transcript and the resultant protein in a sequential manner starting at any stage of a metabolic pathway.
Pathway Assist - Pathway Studio uses a specialized proprietary graph visualization engine to represent biological pathways, gene regulation networks and protein-protein interaction maps for intuitive exploration and prediction. The software can handle a variety of tasks, including graphic drawing and layout optimization, data filtering and pathway expansion, and classification and prioritization of proteins. Product of Ariadne Genomics.
Pathway Editor - a platform independent interactive Java drawing tool for the construction of biological pathway diagrams in a visual way and the annotation of the components and interactions between them. Reference [PubMed]
Pathway Finder - Pathway Finder helps you map highlighted probes on a microarray chip to KEGG human pathway(s) by probe id. After mapping the pathway, statistical significance will be calculated for each pathway hit according to the probe sets on the chip selected and then be corrected by a simple multiple testing algorithm.
Pathway Processor - Pathway Processor is a statistical package which organizes profiles of gene expression according to the metabolic pathways that are affected and features a unique graphical output. Reference [PubMed]
PubGene- Analyze gene expression data with literature network information. Reference [PubMed]
Subnetwork hierarchies - a method to decompose biochemical networks into subnetworks based on the global geometry of the network. This method enables us to analyze the full hierarchical organization of biochemical networks and is applied to 43 organisms from the WIT database. Reference [PubMed]
Vector PathBlazer - a bioinformatics tool providing the ability to build, visualize and analyze biological pathways, using metabolic and protein-protein interaction data from multiple sources including KEGG, DIP, and BIND.

last updated: 12 Jan 2004
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