http://bioinformatics.ca/links_directory/category/expression/transcript-expression-analysisThis section contains links to microarray methods, standards for microarray data, and analysis tools for expression data from other high-throughput technologies. Also contains tools for transcript expression in general.http://bioinformatics.ca/links_directory/category/expression/transcript-expression-analysis/feed en http://bioinfo.thep.lu.se/acid.htmlThe Array Clone Information Database (ACID) is a searchable resource for information about human, mouse, and rat cDNA clones. Each clone contains information about the assigned UniGene cluster(s), location in the full-length transcript, assigned gene ontology terms and position in the genome assembly.9215Thu, 16 May 2013 04:50:36 -0400 http://www.arabidopsis.leeds.ac.uk/act/coexpanalyser.phpArabidopsis Co-expression Tool (ACT) is a resource for investigating the co-expression of genes in the NASC/GARNet microarray-based gene expression dataset from Arabidopsis.9216Fri, 17 May 2013 20:20:21 -0400 http://www.affymetrix.com/analysis/index.affxAllows correlation of GeneChip array results with array design and annotation information; provides access to array content information, including probe sequences and gene annotations; free registration is required.11383Thu, 16 May 2013 10:40:38 -0400 http://www.alexaplatform.org/alexa_seq/A method to analyze massively parallel RNA sequence data to catalog transcripts and assess differential and alternative expression of known and predicted mRNA isoforms. Provides alternative expression annotation databases, source code, a data viewer and other resources to facilitate analysis.12823Thu, 16 May 2013 19:40:16 -0400 http://bioalgo.iit.cnr.it/amicaThe All Microarray Clustering @ once (AMIC@) web application provides users with a range of microarray gene expression data clustering algorithms. Algorithms can be run concurrently on the same data sets. Data can be visualized by heat maps and downloaded as a standard clustered data file for further analysis.9229Sat, 18 May 2013 20:30:18 -0400 http://www.ebi.ac.uk/arrayexpress/Public repository for microarray based gene expression data; contains several curated gene expression datasets.9238Thu, 16 May 2013 12:20:26 -0400 http://koch.pathogenomics.ca/cgi-bin/pub/arraypipe.plArrayPipe allows users to customize a processing pipeline for the analysis of microarray data. Includes methods for quality assessment of slides, data visualization, normalization, and detection of differentially expressed genes. Output consists of reports formatted as standard web pages and tab-delimited lists of calculated values.9239Thu, 16 May 2013 03:20:44 -0400 http://string32.embl-heidelberg.de:8080/prophecies_html/prophecies.htmlArrayProspector is a set of predicted functional associations between genes that have been inferred from microarray expression data from the Standford Microarray Database. Users can search for genes linked to query or for links between two genes.9899Sat, 18 May 2013 12:00:19 -0400 http://www.fda.gov/ScienceResearch/BioinformaticsTools/Arraytrack/ArrayTrack™ provides an integrated solution for managing, analyzing, and interpreting microarray gene expression data. Specifically, ArrayTrack™ is MIAME (Minimum Information About A Microarray Experiment)-supportive for storing both microarray data and experiment parameters associated with a pharmacogenomics or toxicogenomics study.12648Wed, 15 May 2013 07:50:18 -0400 http://www.snubi.org/software/ArrayXPath/ArrayXPath is a web-based service for matching microarray gene-expression profiles with known biological pathways. Input is a clustered gene-expression profile in a tab-delimited text format. Output includes pathway diagrams.9240Sat, 18 May 2013 13:30:09 -0400 http://eureka.cbrc.jp/asian/ASIAN (Automatic System for Inferring a Network) is a server for inferring regulatory networks from gene expression profiles that combines cluster analysis, regression analysis, and graphical Gaussian modeling.10000Sat, 18 May 2013 22:30:23 -0400 http://asterias.bioinfo.cnio.es/Asterias is a set of tools for the analyses of high throughput genomic data that includes applications for microarray data normalization, filtering, detection of differential gene expression, class and survival prediction model building, and analysis of array CGH data. Most applications use parallel computing resulting in significant increases in speed.9251Sat, 18 May 2013 11:10:47 -0400 http://www.ijm.fr/en/ijm/resources/bioinformatics/AutoClass is an unsupervised Bayesian classification system. AutoClass@IJM provides a web interface for this clustering algorithm.10571Thu, 16 May 2013 18:30:14 -0400 http://www.babelomics.orgBabelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Other tools include Biocarta pathways, Transfac and a tool de novo functional annotation of sequences.9257Wed, 15 May 2013 19:40:15 -0400 http://giscompute.gis.a-star.edu.sg/~vega/BEARR1.0/Batch Extraction and Analysis of cis-Regulatory Regions (BEARR) takes a list of gene identifiers (such as RefSeq and Unigene IDs), consensus patterns, and (optionally) a position weight matrix as input and returns a list of matches for the patterns in both the sense and anti-sense strands of the relevant genomic sequence. The user specifies what distance up and downstream from both the transcription start site and the 3\' terminus to look for the patterns.9264Thu, 16 May 2013 14:40:30 -0400 http://www.bioconductor.org/Bioconductor is an open source and open development software project that aims to provide access to a wide range of powerful statistical and graphical methods for the analysis of genomic data.9272Sat, 18 May 2013 14:10:15 -0400 http://brak.sdsc.edu/pub/BiologicalNetworks/BiologicalNetworks allows retrieval, construction, and visualization of biological networks and allows for the analysis of high-throughput expression data by mapping onto network graphs. BiologicalNetworks queries the PathSys system, a combined database of biological pathways, gene regulatory networks, and protein interaction maps.10284Sat, 18 May 2013 18:40:16 -0400 http://www.sysbio.se/BioMetThe BioMet Toolbox consists of web-based resources for stoichiometric analysis of metabolic networks and for integration of transcriptome and interactome data into these networks to simulate growth rates, substrate uptake rates and metabolic production rates. Files for model organisms are included.9283Sat, 18 May 2013 05:20:15 -0400 http://bionmf.dacya.ucm.es/A web-based tool based on nonnegative matrix factorization (NMF) that can be used to provide new information from multi-dimensional biological data sets.10430Mon, 06 May 2013 04:00:27 -0400 http://bioportal.bioontology.orgBioPortal is a web accessible open repository of biomedical ontologies. Users may browse, search and visualize ontologies, as well as participate in the evaluation and evolution of ontology reviews by adding notes, corrections, reviews, etc. Data from other sources such as GEO, ClinicalTrials.gov and ArrayExpress may also be integrated with the ontologies.9288Fri, 17 May 2013 21:10:31 -0400 http://robotics.stanford.edu/~xsliu/BioProspector/Server which scans upstream of genes in the same gene expression cluster for regulatory sequence motifs using a Gibbs sampling strategy. The Markov background model is used for non-motif bases, improving specificity of predicted motif locations.9289Sun, 12 May 2013 20:20:10 -0400 http://brop.org/The Bioinformatics Resource for Oral Pathogens (BROP) contains tools for genomics of oral pathogens including Genome Viewer, GOAL (genome wide ORF alignment), an oral pathogen microarray database, an entrez counter, oral pathogen specific BLAST, and a codon usage database.11310Sun, 19 May 2013 00:50:12 -0400 http://bioinformatics.bc.edu/clotelab/BTW/Boltzmann Time Warping (BTW) computes time warping distances and Boltzmann\' pair probabilities for a given input gene expression time series. This tool helps to identify genes that may share similar expression patterns over time.9315Thu, 16 May 2013 17:20:16 -0400 http://cmgm.stanford.edu/pbrown/mguide/index.htmlThe MGuide (version 2.0). The Brown Labs complete guide to microarraying for the molecular biologist.11193Wed, 29 Aug 2012 11:19:45 -0400 http://kinase.uhnres.utoronto.ca/CanArrays.htmlContact information, availabilities and expertise of Canadian microarray centres; includes labs that supply cDNA or oligonucleotide spotted arrays and other services, and labs that can analyse RNA with Affymetrix chips.11245Thu, 31 May 2012 06:41:39 -0400 http://bioinfo.curie.fr/CAPweb/CGH array Analysis Platform (CAPweb) is a tool for storing, analyzing and visualizing CGH-array data.9320Tue, 14 May 2013 05:10:20 -0400 https://carmaweb.genome.tugraz.at/carma/Comprehensive R based Microarray Analysis web service (CARMAweb) is a resource for the analyses of microarray data including data preprocessing, detection for differentially expressed genes, cluster analysis, and GO analysis. Calculations are performed in R using functions provided by BioConductor.9321Sun, 19 May 2013 00:30:26 -0400 http://zlab.bu.edu/CARRIE-webServer which analyzes microarray and promoter sequence data associated with a response to a specific stimulus. After analysis a potential transcriptional regulatory network is created. CARRIE also determines which transcription factors were likely involved in regulation and which genes they regulated.9302Fri, 17 May 2013 21:20:27 -0400 http://ceas.cbi.pku.edu.cnCis-regulatory Element Annotation System (CEAS) is a resource for ChIP-chip analyses that retrieves repeat-masked genomic sequences, calculates GC content, plots evolutionary conservation, maps nearby genes, and identifies enriched transcription factor binding (TFBS) motifs.9336Thu, 16 May 2013 10:20:22 -0400 http://genomics.bioen.illinois.edu/chipinfo/ChipInfo extracts gene annotation and gene ontology information from databases like NetAffx and Gene Ontology (GO) for microarray analysis. Output is provided in tabular format and the program is available for download for use on your own machine.9345Tue, 14 May 2013 07:20:28 -0400 http://cibex.nig.ac.jp/The Center for Information Biology gene EXpression database (CIBEX) is a public repository for gene expression experimental data. The database system is compliant with the MIAME standard.9346Fri, 17 May 2013 21:20:35 -0400 http://gexp2.kaist.ac.kr/clicCLIC performs clustering analysis of large microarray datasets. Genes are first clustered in individual dimensions and then using the ordinal labels of clusters for each dimension, full dimension wide clustering is performed.9351Fri, 17 May 2013 13:50:18 -0400 http://www.gene-regulation.com/pub/programs/cma/CMA.htmlComposite Module Analyst (CMA) defines promoter models based on the composition of transcription factor binding sites (TFBS) in regulatory sequences for sets of coregulated genes.9356Mon, 13 May 2013 05:40:14 -0400 http://compareprospector.stanford.edu/Server which attempts to identify any motifs related to genes predicted to share regulatory elements. It alters Gibbs sampling through biasing searches towards conserved sequences across multiple species.9367Mon, 13 May 2013 19:00:12 -0400 http://morenolab.whitehead.emory.edu/cgi-bin/confac/login.plThe Conserved Transcription Factor Binding Site Finder (CONFAC) takes a list of human gene names and identifiers as input, and compares them with their mouse orthologues to identify conserved transcription factor binding sites. Further information from the user allows CONFAC to identify binding sites that are enriched in the promoter regions of gene clusters from microarray analyses when compared to control gene sets.9916Sat, 18 May 2013 10:20:20 -0400 http://www.copub.orgCoPub is a text mining tool for the detection of biomedical terms that co-occur in abstracts with the list of input genes (human, rat, and mouse genes). CoPub also graphically displays differentially expressed genes and over-represented keywords in a network for better visualization of relationships. CoPub 5.0 uses a new thesauri. It allows for searching of keywords, provides highlighting and sorting mechanisms and statistics. It also searches for indirect relations between genes, pathways, drugs and diseases.9377Sat, 18 May 2013 22:40:17 -0400 http://140.120.213.10:8080/crsd/main/home.jspComposite Regulatory Signature Database (CRSD) is a microarray analysis pipeline aimed at the discovery of motifs involved in gene regulation including microRNA signatures and transcription factor binding sites (TFBS).9388Fri, 17 May 2013 14:00:21 -0400 http://cybert.ics.uci.edu/.Cyber-T provides differential analysis tools for high-throughput data such as data from microarrays, next generation sequencing platforms and mass spectrometry. Various statistical analyses are computed using R-code.13747Tue, 14 May 2013 04:10:07 -0400 http://dario.bioinf.uni-leipzig.de/DARIO is a web service for the study of short read data from small RNA-seq experiments. It provides a wide range of analysis features including qulity control, read normalization, ncRNA quantification and prediction of putative ncRNA candidates.12140Thu, 31 May 2012 06:44:44 -0400 http://www.bioinf.med.uni-goettingen.de/services/deep/DEEP (Differential Expression Effector Prediction) is a tool that can identify effectors of specific expression profiles by combining gene expression data with biological expert knowledge about biomolecular interaction networks (provided by resources like TRANSPATH, for example).9403Thu, 16 May 2013 17:20:14 -0400 http://www.vessels.bwh.harvard.edu/This website contains microarray analysis software (Argus and Z-pool), an Endothelial Cell Expression Database, and other resources related to Vascular Endothelium research. See the PubMed abstracts for more information.11301Sat, 18 May 2013 08:50:22 -0400 http://dire.dcode.orgA web server for predicting distant (outside of proximal promoter regions) regulatory elements (DiRE) in higher eukaryotic genomces using gene co-expression data, comparative genomics as well as transcription factor binding site information. DiRE allows users to start analysis with raw microarray expression data.9415Fri, 17 May 2013 13:30:43 -0400 http://www.transcriptome.ens.fr/doelan/Doelan is an tool designed to monitor the quality of DNA microarray production.9424Wed, 15 May 2013 21:30:18 -0400 http://dsap.cgu.edu.twDeep-Sequencing Small RNA Analysis Pipeline (DSAP) is an automated web service designed to provide analysis of deep sequencing small RNA datasets from the Solexa sequencing platform. Non-coding RNA and miRNA matching are output based on homology mapping to Rfam and miRBase databases.10639Thu, 16 May 2013 02:50:24 -0400 http://www.esat.kuleuven.be/endeavourENDEAVOUR is a computational approach to prioritize candidate genes for further study. Users input training genes already known to be involved in the process under study and the candidate genes to prioritize. The web server supports multiple species and integrates multiple genomic data to generate the final prioritization. ENDEAVOUR has been benchmarked in silico and experimentally validated leading to the discovery of novel disease genes in several genetic diseases.12956Mon, 13 May 2013 18:40:25 -0400 http://www.ebi.ac.uk/expressionprofiler/Expression Profiler is a web based platform for microarray data analysis developed at the EBI. This resource is integrated with the ArrayExpress database, a public repository for microarray data.9907Fri, 17 May 2013 15:00:12 -0400 http://array.mbb.yale.edu/analysis/ExpressYourself is a web-based platform to process microarray data. It includes tools for background correction, normalization, data processing and filtering.10141Sat, 18 May 2013 00:40:23 -0400 http://www.fatigo.org/FatiGOplus is a tool for the functional profiling of genome-scale experiments oriented to the interpretation of microarray experiments. As part of the Babelomics suite, FatiGOplus finds differential distributions of biological terms (GO, KEGG pathways, Interpro motifs, Transfac motifs, CisRed motifs, etc.) between two groups of genes.9307Sun, 19 May 2013 01:50:27 -0400 http://www.mged.orgGroup facilitating the development of an international repository for gene expression data and the experimental and database standards required for such an endeavour.11365Fri, 13 Jul 2012 15:24:52 -0400 http://biit.cs.ut.ee/gprofiler/g:Profiler is a set of tools for functional annotation of gene lists that includes: g:GOSt, which retrieves the most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs; g:Convert, for conversion between gene or protein names/IDs; g:Orth, for retrieving orthologs; and, g:Sorter, which searches for similar expression profiles. Functional analysis of SNPs and other DNA polymorphisms is also supported, as is enrichment analysis.10393Sat, 18 May 2013 23:30:31 -0400 http://genomics10.bu.edu/terrence/gems/GEMS (Gene Expression Mining Server) is a tool for biclustering microarray data. It is available as a web tool and as a standalone command-line program.10061Sun, 12 May 2013 11:40:14 -0400 http://bioinformatics.upmc.edu/GE2/GEDA.htmlThe Gene Expression Data Analyzer (GEDA) is a tool for discovering differential gene expression in a subset of patients. It is tailored to cancer-related microarray studies and offers extensive options for visualization, classification and normalization.9764Thu, 16 May 2013 14:00:10 -0400 http://genecat.mpg.deThe Gene Co-expression Analysis Tool-box (GeneCAT) is a suite of microarray co-expression analysis tools for plant biology. The platform includes both standard co-expression tools such as gene clustering and expression profiling, as well as tools that combine co-expression analysis with BLAST for functional inferencing. Arabidopsis thaliana and Barley are featured plants.10442Sat, 18 May 2013 21:10:31 -0400 http://www.cbs.dtu.dk/services/GenePublisherGenePublisher performs automatic normalization, statistical analysis, and visualization of DNA microarray data.10140Sat, 18 May 2013 10:30:27 -0400 http://genetrail.bioinf.uni-sb.de/index.phpGeneTrail analyzes gene sets for statistically significant accumulations of genes belonging to functional categories. Two common statistical approaches are implemented including: Over-Representation Analysis (ORA) for comparing a reference set of genes to a test set; and, Gene Set Enrichment Analysis (GSEA) for scoring sorted lists of genes.10391Wed, 15 May 2013 12:20:22 -0400 http://www.genmapp.org/GenMAPP (Gene MicroArray Pathway Profiler) is a microarray expression data visualization tool, allowing data to be viewed on maps representing gene groupings and biological pathways.9775Sat, 18 May 2013 02:20:34 -0400 http://www.gepas.orgThe Gene Expression Pattern Analysis Suite (GEPAS) is a collection of tools for the analysis of microarray data. GEPAS includes tools for data pre-processing, clustering, differential gene expression, predictors, array CGH and functional annotation. A new pipeline module allows for automation of sequential analysis steps.9917Sat, 18 May 2013 22:40:13 -0400 http://www.medinfopoli.polimi.it/GFINDer/Genome Functional INtegrated Discoverer (GFINDer) takes a list of gene/clone IDs with classification information as input, and allows the user to characterize the different gene classes in the list using annotations of various types from several different sources.9905Sat, 18 May 2013 04:30:46 -0400 http://omicslab.genetics.ac.cn/GOEAST/Gene Ontology Enrichment Analysis (GOEAST) is a toolkit for the identification of over-represented GO terms in a given gene set. Distinguishing features include: capacity to analyze data from various sources and from multiple species, and the capacity to cross compare GO enriched terms across experiments to identify correlations.10498Sun, 12 May 2013 01:40:15 -0400 http://bioinformatics.bioen.illinois.edu/gosurfer/GoSurfer is a tool for visualizing and comparing gene sets by mapping them onto Gene Ontology (GO) information in the form of a hierarchical tree. It is useful for investigating the results of microarray analyses or genome-wide computations.9795Fri, 17 Aug 2012 16:19:32 -0400 http://idconverter.bioinfo.cnio.es/IDconverter.phpIDconverter is a tool that converts gene, clone or protein IDs to other IDs which can be especially useful for microarray data analyses. This application is part of the suite Asterias.10317Tue, 21 Aug 2012 10:59:33 -0400 http://www.esat.kuleuven.ac.be/inclusiveINCLUSive is a set of tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements.10138Sat, 18 May 2013 18:50:22 -0400 http://bioinfo.cipf.es/isacghtracISACGH (In Silico Array CGH) is a tool for visualizing array CGH data and/or expression arrays onto chromosomal coordinates to allow for correlations between copy number and gene expression to be observed. ISACGH is included in the GEPAS package.10348Sat, 18 May 2013 01:10:53 -0400 http://www.jprogo.de/index.jspJProGO is a tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information.10298Thu, 16 May 2013 13:40:54 -0400 http://biryani.med.yale.edu/karma/cgi-bin/mysql/karma.plKARMA (Keck Array Manager and Annotator) allows you compare and annotate your own microarrays against other available arrays. Comparison of arrays can be achieved within the same species as well as across species (array comparison is based on UniGene Cluster ID and/or Homologene data). Annotation data includes LocusLink, SwissProt, and Gene Ontology.9898Fri, 17 May 2013 01:30:12 -0400 http://www.exiqon.com/oligo-toolsLNAtools is a collection of tools for the design of LNA (locked nucleic acid) substituted oligonucleotides including: melting temperature (Tm) analysis; secondary structure prediction; and probe design for expression arrays, real time PCR, and SNP genotyping.10149Sat, 18 May 2013 18:30:08 -0400 http://www.bioinfo.hr/madnetMicroarray Database Network (MADNet) is a data mining and visualization tool for analysis of diverse high-throughput biological data such as microarrays and phage display experiments. Data is integrated with information from NCBI, KEGG TRANSFAC and DrugBank.10495Mon, 06 May 2013 10:20:35 -0400 http://gencomp.bio.unipd.it/magia2/start/miRNA and Genes Integrated Analysis (MAGIA2) is a web tool for the integrative analysis of in silico target prediction, and reconstruction of post-transcriptional regulatory and mixed regulatory networks from miRNA and gene expression data.10672Sat, 18 May 2013 22:20:28 -0400 http://www.magma-fgcz.unizh.ch/pages/loginuser.jsfMAGMA can be used for the analyses of two-channel microarray experiments and computes genes with significant differential expression using R and Bioconductor. Automatically generated R-scripts are available for download.10350Fri, 17 May 2013 16:30:16 -0400 http://magnet.case.eduMicroarray Gene Expression and Network Evaluation Toolkit (MAGNET) is a web tool with three components: generation of coexpression networks, weighted protein-protein interaction networks and bimodality of coexpression.13818Sat, 18 May 2013 21:00:14 -0400 http://marq.dacya.ucm.esMARQ is a web based application that allows users to compare a query set of genes (query signature) against a gene signature database built from GEO datasets for different organisms and platforms.10680Sat, 18 May 2013 21:50:20 -0400 http://discover.nci.nih.gov/matchminer/MatchMiner is a tool to compare and convert gene identifiers. Users can translate single or lists of identifiers from one form to another, or compare two lists of identifiers for common gene references.9925Sat, 18 May 2013 04:00:40 -0400 http://chibi.ubc.ca/matrix2pngMatrix2png is a simple but powerful program for making visualizations of microarray data and many other data types. It generates PNG formatted images from text files of data. It is fast,easy to use, and reasonably flexible. It can be used to generate publication-quality images, or to act as a image generator for web applications. A web interface is included.13895Fri, 17 May 2013 15:10:33 -0400 http://robotics.stanford.edu/~xsliu/MDscan/Server designed to pinpoint protein-DNA interaction sites at the base pair level. Uses ChIP-array data, word enumeration and position-specific weight matrix updating to search for motifs representing these interaction sites.9870Wed, 15 May 2013 06:40:16 -0400 http://discover.nci.nih.gov/host/1999_medminer_abstract.jspMedMiner can be used to select genes from a microarray set based on GeneCards information. Based on the genes selected one can then search PubMed abstracts using known gene synonyms and other user-specified search parameters. The PubMed search can also be done independently of a microarray gene set. Results are grouped based on a set of relational keywords.9926Sat, 18 May 2013 09:30:14 -0400 http://www.ebi.ac.uk/microarray/MIAMExpress/miamexpress.htmlMIAME (minimum information about a microarray experiment) compliant microarray data submission tool.9645Sat, 18 May 2013 00:00:42 -0400 http://www.lgtc.nl/MaRe/Microarray Retriever (MaRe) is a web tool that enables batch search and retrieval of microarray datasets matching user specified criteria from the data in GEO and ArrayExpress microarray repositories. Such batch download facilitates gene expression meta-analysis.10483Sat, 18 May 2013 21:30:15 -0400 http://midaw.cribi.unipd.it/dnachip/MIDAW (MIcroarray Data Analysis Web tool) is a data normalization and analysis tool for microarray data.10056Wed, 15 May 2013 18:30:45 -0400 http://chevreux.org/projects_mira.htmlThe mira genome fragment assembler is a specialised assembler for sequencing projects classified as 'hard' due to high number of similar repeats. For EST transcripts, miraEST is specialised on reconstructing pristine mRNA transcripts while detecting and classifying single nucleotide polymorphisms (SNP) occuring in different variations thereof. 12619Tue, 24 Jul 2012 14:53:06 -0400 http://sysbio.ustc.edu.cn/software/mirActmirACT web server is a tool designed to investigate miRNA activity in gene expression data. It uses the negative regulation relationship between miRNAs and their target genes.12053Sat, 18 May 2013 21:40:20 -0400 http://cancer.informatics.indiana.edu/mmiamicroRNA and mRNA Integrated Analysis (MMIA) is a web server that integrates miRNA and mRNA expression data with predicted miRNA target information. MMIA incorporates miRNA prediction algorithms (TargetScan, PITA, PicTar).10607Tue, 14 May 2013 00:10:17 -0400 http://research.nhgri.nih.gov/microarray/index.htmlProtocols, analysis and resources; BLAST against the 15K set cDNA library clones (from 15,000 human UniGene clusters; clones are available).9465Thu, 31 May 2012 06:34:25 -0400 http://www.o-miner.org)-miner is a webserver that automates the analysis and annotation of complex -omics data. Specifically deals with genomics and transcriptomics data.13733Fri, 17 May 2013 10:50:26 -0400 http://berry.engin.umich.edu/oligoarray2_1/OligoArray is free software that computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction. A database of pre-designed oligonucleotide microarray probes for organisms with a fully sequenced genome can be found at http://berry.engin.umich.edu/oligoarraydb/index.html10510Wed, 15 May 2013 07:30:28 -0400 http://www.cbs.dtu.dk/services/OligoWiz2/OligoWiz 2.0 is a client for microarray probe design that allows for the integration of sequence annotations, probe quality parameters, and the placement of multiple probes per transcript.10017Sat, 18 May 2013 15:00:17 -0400 http://vortex.cs.wayne.edu/Projects.htmlOnto-Tools is a suite of tools for data mining based on information from Gene Ontology (GO). Onto-Tools includes an annotation database and the data mining tools: Onto-Express, Onto-Compare, Onto-Design, Onto-Translate, Onto-Miner, Pathway-Express, Promoter-Express, nsSNPCounter, TAQ, and OE2GO; free registration is required.9912Sat, 18 May 2013 01:10:42 -0400 http://biocomp.bioen.uiuc.edu/oscar/OSCAR (Open System for Clustering Analysis) is a platform for cluster analysis of microarray data.10411Fri, 10 May 2013 02:50:20 -0400 http://pals.bioinfo.cnio.esPathway and Literature Strainer (PaLS) highlights those members on a user inputted list that share descriptors from PubMed, GO, KEGG and Reactome.10467Sat, 18 May 2013 02:20:35 -0400 http://www.pantherdb.org/tools/The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function. The PANTHER research tools allow you to score proteins against the PANTHER HMM library, use PANTHER to do gene expression analyses, and download PANTHER tools and data.10246Sat, 18 May 2013 05:00:33 -0400 http://bioinformatics.wustl.edu/webTools/portalModule/PromoterSearch.doPromoter Analysis Pipeline (PAP) can identify potential transcriptional regulators for sets of co-expressed genes and identify potential regulatory targets of transcription factors.10428Sat, 18 May 2013 10:20:15 -0400 http://bioinfoserver.rsbs.anu.edu.au/utils/PathExpress/PathExpress is a tool developed to interpret gene expression data obtained from microarray experiments by identifying and visualizing the most relevant metabolic pathways associated with a subset of genes (e.g. differentially expressed genes). Enzyme Neighborhood (a sub-network of linked enzymes with a limited path length) allows identification of the most relevant sub-network affected in a gene expression experiment.10358Sun, 19 May 2013 02:00:12 -0400 https://pathwayexplorer.genome.tugraz.at/Pathway Explorer is a tool for visualizing high throughput expression data simultaneously with biological pathway data available from KEGG, BioCarta, and GenMAPP.10010Fri, 17 May 2013 20:50:18 -0400 http://www.peace-tools.orgParallel Environment for Assembly and Clustering of Gene Expression (PEACE) web tool performs high-throughput ab initio clustering of transcript fragment sequences from next-generation sequencing platforms.10691Sat, 18 May 2013 18:00:08 -0400 http://archive.gersteinlab.org/proj/PeakSeq/PeakSeq is a program for identifying and ranking peak regions in ChIP-Seq experiments. It takes as input, mapped reads from a ChIP-Seq experiment, mapped reads from a control experiment and outputs a file with peak regions ranked with increasing Q-values. 12628Sun, 12 May 2013 09:00:30 -0400 http://pilgrm.princeton.eduThe Platform for Interactive Learning by Genomics Results Mining (PILGRIM) is an interactive data driven discovery platform for biology. Expression levels of known relevant genes (specified by the user) are used to discover additional genes with similar expression patterns in large compendia of microarray data. By carefully defining the lists of relevant genes, the user controls the specificity of discoveries.12187Fri, 17 May 2013 05:20:12 -0400 http://ekhidna.biocenter.helsinki.fi/poxo/pobo/POBO is a tool to summarize, verify and screen predetermined cis-element motifs from a set of sequences. POBO reports the results in as understandable format as possible for biologists.9865Fri, 17 May 2013 18:40:34 -0400 http://pomelo2.bioinfo.cnio.esPomelo II is a web-server for the analysis of gene (and protein) expression and tissue array data. Different statistical tests are applied depending on the input data. Links are also provided to additional sources of information such as PubMed references, Gene Ontology terms, GO terms, etc.10532Wed, 15 May 2013 09:00:19 -0400 http://www.bioinfo.biocenter.helsinki.fi/poxoPOXO is a series of tools that can be used to discover, search and verify possible regulatory cis-element(s) from set(s) co-expressed genes.10277Sat, 18 May 2013 08:00:24 -0400 http://www.pathogenomics.ca/probelynxUsing current releases of genomic sequence data, ProbeLynx allows users to assess the specificity of probe sequences used for microarray experiments. The user provides probe sequences in FASTA or tab-delimited format, and ProbeLynx reports specificity information for each probe and functional annotations from Ensembl or TIGR for each probe target hit.9915Sat, 18 May 2013 06:40:35 -0400 http://www.prodonet.tu-bs.deA web-based application for the mapping of prokaryotic genes and the corresponding proteins to common gene regulatory and metabolic networks. Users input a list of genes from which shared operons, co-expressed genes and shared regulators are detected. Common metabolic pathways are then viewed on KEGG maps.10473Sat, 11 May 2013 07:20:32 -0400 http://webclu.bio.wzw.tum.de/profcom/Profiling of complex functionality (ProfCom) is a web based tool for the interpretation of genes that were identified to be functionally linked. Combinations of annotation terms are used to profile complex functions.10472Fri, 17 May 2013 09:50:31 -0400 http://gibk21.bio.kyutech.ac.jp/PrognoScan/index.htmlPrognoScan is a database for meta-analysis of the prognostic value of genes. It has features of 1) a large collection of publicly available cancer microarray datasets with clinical annotation, as well as 2) a tool for assessing the biological relationship between gene expression and prognosis.12349Fri, 17 May 2013 19:50:31 -0400 http://www.beaconlab.it/pscanPscan is a web server scans a set of sequences to find over-represented transcription factor binding site motifs within co-regulated or co-expressed genes.10584Tue, 14 May 2013 12:20:22 -0400 http://r2.amc.nlThe R2 platform is an online genomics analysis tool which can analyze a large collection of public data, but also allows shielded analysis of your own microarray dataset. freely accessible and intended to be used by biologists, even those with little or no bioinformatics training.13267Wed, 01 Aug 2012 16:26:28 -0400 http://race.unil.ch/RACE (Remote Analysis Computation for gene Expression data) is a collection of web tools designed to assist with the analysis of DNA microarray data and results.10039Fri, 17 May 2013 02:20:24 -0400 http://recountdb.cbrc.jp/A secondary database derived from primary data in NCBI's short read archive. Database for corrected read counts and genome mapping on NCBI's transcriptomics archives.13567Thu, 16 May 2013 23:30:26 -0400 http://bussemaker.bio.columbia.edu/reduce/REDUCE uses a motif-based regression method for the identification of TFBS (transcription factor binding sites) from microarray data in yeast, worm and fly. A free registration is required.10143Sat, 18 May 2013 09:50:23 -0400 http://compbio.dfci.harvard.edu/tgi/cgi-bin/magic/r1.plTool for cross-referencing microarray data derived from different species and across different expression analysis platforms. Built using the analysis of ESTs, the TIGR Gene Index (TGI), and Eukaryotic Gene Orthologs (EGO) databases.9942Sat, 18 May 2013 13:00:34 -0400 http://mapman.gabipd.org/web/guest/robinRobiNA is an integrated web tool for analysis of microarray and RNA-Sequence based transcriptomes. 13808Sat, 18 May 2013 12:50:33 -0400 http://galaxy.fml.mpg.derQuant.web is a web service for quantitative analysis of RNA sequencing data based on quadratic programming. rQuant.web is available as a tool in Galaxy.10696Wed, 15 May 2013 17:50:45 -0400 http://tesla.pcbi.upenn.edu/savorSAVoR webserver allows the user to visualize RNA-seq data and other genomic annotations on RNA secondary structures. SAVoR is designed to help researchers visualize sequencing data in the context of RNA secondary structures. Useful if you want to see the distribution of smRNA-seq reads along a microRNA precursor, how a set of SNPs might impact RNA structure, or in a control vs. treatment sequencing experiments you would like to see regions of enrichment along an RNA structure.13741Sat, 18 May 2013 14:50:21 -0400 http://rana.lbl.gov/EisenSoftware.htmEisen Lab software for microarry image processing, analysis and visualization; available for download to windows platforms only; free with registration for non-commercial use.9585Fri, 17 Aug 2012 13:14:35 -0400 http://sea.bioinfo.cipf.esSerial Expression Analysis (SEA) suite of tools provides a complete resource for the analysis of serial transcriptomic data.10709Fri, 17 May 2013 06:00:14 -0400 http://seqanswers.com/A wiki database of tools for high-throughput sequencing analysis. The wiki provides an extensive catalogue of tools, technologies and tutorials for high-throughput sequencing (HTS), including information about HTS service providers.13598Fri, 17 May 2013 16:50:14 -0400 http://dir.nhlbi.nih.gov/papers/lmi/epigenomes/sissrs/SISSRs (Site Identification from Short Sequence Reads), an algorithm for precise identification of binding sites from short reads generated from ChIP-Seq experiments. 12629Fri, 17 May 2013 03:10:17 -0400 http://bioinfo.ebc.ee/snpmasker/SNPmasker masks SNPs in a given sequence using information from the dbSNP database. This tool can also be used to mask repeat sequences. SNPmasker is primarily designed for masking the sequences before primer and probe design.10079Sat, 18 May 2013 13:00:25 -0400 http://source.stanford.eduStanford Online Universal Resource for Clones and ESTs pools publicly available data commonly sought for any clone, GenBank accession, or gene from human, mouse, rat.11384Fri, 17 May 2013 20:20:32 -0400 http://speed.sys-bio.net/Signaling Pathway Enrichment using Experimental Datasets (SPEED) is a web server for enrichment of signaling pathways responsible for gene expression changes.10675Thu, 16 May 2013 09:20:40 -0400 http://genome-www5.stanford.edu/SMD stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, SMD provides interfaces for data retrieval, analysis and visualization.9731Sat, 18 May 2013 06:40:44 -0400 http://www.t-profiler.org/T-profiler is a tool for the analysis of gene expression data from yeast that uses the t-test to score changes in the average activity of pre-defined groups of genes.10025Sat, 18 May 2013 06:50:44 -0400 http://targetfinder.org/Targetfinder.org provides a web based resource that allows users to find genes that have a similar expression to a query gene signature.10685Sun, 19 May 2013 01:40:08 -0400 http://www.ebi.ac.ukThe European Bioinformatics Institute (EMBL-EBI) provides access to a comprehensive, integrated set of biological data. Resources include information on genes, genomes, proteins, expression, literature, and molecular interactions as well as many other useful resources.11619Sat, 18 May 2013 12:50:19 -0400 http://www.tigr.org/software/A list of open-source software packages available for free from The Institute for Genomic Research (TIGR).11293Sat, 18 May 2013 06:20:09 -0400 http://genome.ucsd.edu/microarray/VAMPIRE is a collection of Java tools designed to perform Bayesian statistical analysis of gene expression array data.9985Sat, 18 May 2013 03:50:46 -0400 http://whipple.cs.vt.edu/virgoperl/welcome.cgiVirtual Gene Ontology (VIRGO) provides gene function predictions for yeast and human by constructing a functional linkage network (FLN) from gene expression and molecular interaction data. VIRGO then labels genes in the FLN with their annotations from Gene Ontology, and systematically propagates these labels across the FLN in order to predict the functions of unlabelled genes.10245Sat, 18 May 2013 08:30:32 -0400 http://visant.bu.edu/VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, as a java web application, or downloaded and run locally. New functions in VisANT 3.5 allow determination of over-representation and expression enrichment.10070Sat, 18 May 2013 14:30:22 -0400 http://biit.cs.ut.ee/vishicVisHiC is a web server for clustering and compact visualization of gene expression data combined with automated function enrichment analysis. Output includes a heatmap of the expression matrix highlighting enriched clusters.10606Tue, 14 May 2013 05:00:24 -0400 http://bioinfo.vanderbilt.edu/webgestalt/WebGestalt (WEB-based GEne SeT AnaLysis Toolkit) is a system facilitating the analysis of sets of genes. Gene sets can be compared using set operations (intersection, union, etc.), different annotations can be selected and retrieved for the set, and sets can be visualized and organized by a user-selected method (Gene Ontology, chromosomal distribution, etc.). WebGestalt can also perform a statistical analysis to suggest areas of interest with respect to the set of genes selected.10054Sun, 19 May 2013 00:40:27 -0400