http://bioinformatics.ca/links_directory/tag/oligonucleotide-array-sequence-analysishttp://bioinformatics.ca/links_directory/tag/oligonucleotide-array-sequence-analysis/feed en 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://chibi.ubc.ca/ermineJErmineJ is software for the analysis of functionally interesting patterns in large gene lists drawn from gene expression profiling data or other high-throughput genomics studies. It can be used by biologists with no bioinformatics background to conduct sophisticated analyses of gene sets with multiple methods. It allows users to assess whether microarray data or other gene lists are enriched for a particular pathway or gene class.13893Mon, 20 May 2013 14:30:31 -0400 http://gemma.chibi.ubc.caGemma is an open source database, analysis software system and web site for expression data re-use and meta-analysis. It currently contains analyzed data from over 3300 expression profiling studies, yielding billions of data points that can be searched and explored. Gemma offers web-based access to differential expression results and coexpression data in a meta-analysis framework. 13891Mon, 20 May 2013 20:50:11 -0400 http://eaa.mpi-bn.mpg.deThe Exon Array Analyzer (EAA) allow to process CEL files from Affymetrix, Inc. GeneChip® Exon 1.0 ST Arrays. Various processign steps and visualizations are implemented to identify alternative splicing events. Three simple steps have to be performed to submit a set of CEL files. After the processing is completed the results can be viewed in the browser. 13631Sun, 19 May 2013 13:50:22 -0400 http://sigreannot-mart.toulouse.inra.fr/biomart/martview/430b028768948e41c781761b26ba2cc6Re-annotating oligo sets used for expression microarrays is essential to supply biologists with up-to-date annotations. SigReannot-mart is a query environment populated with regularly updated annotations for different oligo sets. t permits easy extraction in different formats using filters. It is used to compare probe sets on different criteria, to choose the set for a given experiment to mix probe sets in order to create a new one.13431Sun, 19 May 2013 19:10:24 -0400 http://www.cs.utoronto.ca/~juris/data/GB10/Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging. A method where the biomarkers are networks of genes selected based on age-dependent activity and a graph-theoretic property called modularity. These modular biomarkers are applied to assign novel aging-related functions to poorly characterized longevity genes.13406Tue, 21 May 2013 11:10:09 -0400 http://wodaklab.org/genepro/A Cytoscape plug-in for advanced visualization and analysis of interaction networks.13389Mon, 20 May 2013 21:50:16 -0400 http://biit.cs.ut.ee/mem/MEM (Multi-Experiment Matrix) provides gene expression similarity searches, visualisation and analyses across many datasets from ArrayExpress and GEO. MEM uses rank aggregation to merge information from different datasets into a single global ordering with simultaneous statistical significance estimation. Each dataset can be also accessed through ExpressView gene clustering and visualisation, and DiffExp for differential expressed genes search. 12832Sun, 19 May 2013 13:11:04 -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.12823Sun, 19 May 2013 19:00:19 -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, 22 May 2013 07:10:25 -0400 http://woldlab.caltech.edu/rnaseq/A package of python scripts designed to analyze ultra-high-througphut sequencing data from the Illumina/Solexa platform for RNA-seq and ChIP-seq in metazoan genomes. The RNA-seq portion of ERANGE is described in our Nature Methods paper "Mapping and quantifying mammalian transcriptomes by RNA-Seq" (Mortazavi, 2008). ERANGE is built on top of Cistematic. 12630Fri, 17 May 2013 20:00:28 -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. 12628Tue, 21 May 2013 00:30:20 -0400 http://bioinfo.townsend.yale.edu/The filamentous fungal gene expression database (FFGED) is a user-friendly management of gene expression data, which are assorted into experimental metadata, experimental design, raw data, normalized details, and analysis results. FFGED functions as a collective and collaborative platform, by connecting each experiment with similar related experiments made public by other users, and correlating diverse gene expression levels under multiple experimental designs within different experiments.12246Wed, 22 May 2013 16:30:35 -0400 http://www.btool.org/ADGO2ADGO is a web tool that provides composite interpretations for microarray data comparing two sample groups. It also provides composite interpretations and enrichment analysis for lists of genes from diverse sources of biological information.12158Tue, 21 May 2013 10:50:23 -0400 http://wanglab.hku.hk/ChIP-ArrayChIP-Array is a web server that integrates ChIP-seq and microarray gene expression data to discover direct and indirect target genes regulated by a transcription factor of interest.12147Fri, 17 May 2013 17:10:28 -0400 http://ted.bti.cornell.eduTomato Functional Genomics Database (TFGD) provides a comprehensive resource to store, query, mine, analyze, visualize and integrate large-scale tomato functional genomics data sets. Computational pipelines have been developed to process microarray, metabolite and sRNA data sets archived in the database, and TFGD provides downloads of all the analyzed results. TFGD is also designed to enable users to easily retrieve biologically important information through a set of efficient query interfaces and analysis tools, including improved array probe annotations as well as tools to identify co-expressed genes, significantly affected biological processes and biochemical pathways from gene expression data sets and miRNA targets, and to integrate transcript and metabolite profiles, and sRNA and mRNA sequences.11897Wed, 15 May 2013 20:50:40 -0400 http://cistrome.dfci.harvard.edu/CaSNP/CaSNP database for storing and interrogating quantitative copy number alterations (CNA) data from SNP arrays on 34 different cancer types in 104 studies. With a user input of region or gene of interest, CaSNP will return the CNA information summarizing the frequencies of gain/loss and averaged copy number for each study, and provide links to download the data or visualize it in UCSC Genome Browser. CaSNP also displays the heatmap showing copy numbers estimated at each SNP marker around the query region across all studies for a more comprehensive visualization. 11888Sun, 19 May 2013 16:50:16 -0400 http://ricexpro.dna.affrc.go.jp/RiceXPro is a gene expression database to provide the transcriptional changes throughout the growth of the rice plant in the field. RiceXPro contains two data sets corresponding to spatiotemporal gene expression profiles of various organs and tissues, and continuous gene expression profiles of leaf from transplanting to harvesting. A user-friendly web interface enables the extraction of specific gene expression profiles by keyword and chromosome search, and basic data analysis, thereby providing useful information as to the organ/tissue and developmental stage specificity of expression of a particular gene. Analysis tools such as t-test, calculation of fold change and degree of correlation facilitate the comparison of expression profiles between two random samples and the prediction of function of uncharacterized genes.11860Tue, 21 May 2013 05:20:09 -0400 http://www.ebi.ac.uk/arrayexpressThe ArrayExpress Archive is a public repository of functional genomics data supporting publications. It includes data generated by sequencing or array-based technologies. Data are submitted by users and imported directly from the NCBI Gene Expression Omnibus. The ArrayExpress Archive is closely integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Advanced queries provided via ontology enabled interfaces include queries based on technology and sample attributes such as disease, cell types and anatomy.11818Wed, 22 May 2013 02:10:44 -0400 http://www.agbase.msstate.edu/AgBase provides resources to facilitate modeling of functional genomics data and structural and functional annotation of agriculturally important animal, plant, microbe and parasite genomes. One of seven new tools available at AgBase, GOModeler, supports hypothesis testing from functional genomics data. Moreover, we provide comprehensive training resources (including worked examples and tutorials) via links to Educational Resources at the AgBase website.11803Tue, 21 May 2013 04:10:22 -0400 http://rafalab.jhsph.edu/barcodeGene Expression Barcode is a database that provides reliable absolute measures of expression for most annotated genes for human and mouse tissue types, including diseased tissue. This is made possible by an algorithm that leverages information from the GEO and ArrayExpress public repositories to build statistical models that permit converting data from a single microarray into expressed/unexpressed calls for each gene. For selected platforms, users may upload data and obtain results.11757Tue, 21 May 2013 02:50:29 -0400 http://affymetrix2.bioinf.fbb.msu.ruPLANdbAffy contains the results of the alignment of probe sequences from five Affymetrix expression microarrays to the human genome. Probes matching the transcript-coding regions in the correct orientation have been determined. For each such probe alignment region, the mRNA and EST sequences that contain the probe sequence have also been determined. In the textual part of the database interface, data on the sequences that cover the probe alignment region and SNPs that are located inside it is summarized. The graphical part of our database interface is implemented as custom tracks to the UCSC genome browser that allows one to utilize all the data that are offered by UCSC browser.11731Wed, 22 May 2013 09:20:30 -0400 http://compbio.dfci.harvard.edu/genesigdbGeneSigDB is a manually curated database of gene expression signatures. GeneSigDB focuses on cancer, development, and stem cell gene signatures and was constructed from thousands of publications from which we manually transcribe gene signatures. Gene signatures are mapped to the genome to extract standardized lists of EnsEMBL gene identifiers. GeneSigDB provides the original gene signature, the standardized gene list and a fully traceable gene mapping history for each gene from the original transcribed data table through to the standardized list of genes. GeneSigDB release 3.0 (Decemeber 2010) contained over 2,000 gene signatures.11730Tue, 21 May 2013 10:10:19 -0400 http://www.cyclebase.org/Cyclebase is an online resource of cell-cycle-related experiments. This database provides an easy-to-use web interface that facilitates visualization and download of genome-wide cell-cycle data and analysis results. Data from different experiments are normalized to a common timescale and are complimented with key cell-cycle information and derived analysis results. Included is information on cyclin-dependent kinase (CDK) substrates, predicted degradation signals and loss-of-function phenotypes from genome-wide screens. The web interface provides a single, gene-centric graph summarizing the available cell-cycle experiments. Links to orthologous and paralogous genes are included to further facilitate comparison of cell-cycle regulation across species.11727Tue, 21 May 2013 22:10:18 -0400 http://www.h-invitational.jp/The H-Invitational Database (H-InvDB) is a comprehensive annotation resource of human genes and transcripts. The latest release of H-InvDB (release 6.2) provides the annotation for 219,765 human transcripts in 43,159 human gene clusters based on human full-length cDNAs and mRNAs. H-InvDB now provides several new annotation features, such as mapping of microarray probes, new gene models, relation to known ncRNAs and information from the Glycogene database. H-InvDB also provides useful data mining resources-'Navigation search', 'H-InvDB Enrichment Analysis Tool (HEAT)' and web service APIs.11717Wed, 22 May 2013 17:50:14 -0400 http://silkworm.genomics.org.cn/The SilkDB is an open-access database for genome biology of the silkworm (Bombyx mori). SilkDB contains the genomic data, including genome assembly, gene annotation, chromosomal mapping, orthologous relationship and experiment data, such as microarray expression data, Expressed Sequence Tags (ESTs) and corresponding references. Several new tools, including SilkMap, Silkworm Chromosome Browser (SCB) and BmArray, are developed to access silkworm genomic data conveniently.11689Wed, 22 May 2013 06:20:24 -0400 http://www.MicrobesOnline.orgMicrobesOnline portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms. MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources.11679Wed, 22 May 2013 03:40:37 -0400 http://www.interferome.org/INTERFEROME is an open access database of types I, II and III Interferon regulated genes collected from analysing expression data sets of cells treated with IFNs. This database integrates expression information with annotation, ontology, orthologue sequences from 37 species, tissue expression patterns and gene regulatory information.11449Wed, 22 May 2013 07:50:35 -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.11383Wed, 22 May 2013 02:20:37 -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.11384Tue, 21 May 2013 15:10:24 -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.11301Tue, 21 May 2013 09:20:15 -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.11310Mon, 20 May 2013 04:20:12 -0400 http://www.arabidopsis.org/Comprehensive resource for the scientific community working with Arabidopsis thaliana.11228Wed, 22 May 2013 09:10:46 -0400 http://genomebiology.com/series/drosophilaA series of refereed research articles describing Release 3 of the Drosophila genome are freely available online. The articles describe the finishing and annotation of the genome sequence, computational tools, and functional studies.11237Wed, 22 May 2013 18:40:17 -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://wavi.bioinfo.cnio.eswaviCGH is a web server for the analysis and comparison of genomic copy number alterations in multiple same species samples. For human, mouse and rat genomes, results are mapped back onto the genome.10690Tue, 21 May 2013 11:40:27 -0400 http://bioinfo-mml.sjtu.edu.cn/mGS/mGenomeSubtractor performs mpiBLAST-based comparison of reference bacterial genomes against multiple user-selected genomes. Such in silico subtractive hybridization also allows for definition of species-specific gene pools and can be used to develop genomic arrays.10667Tue, 21 May 2013 21:10:19 -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://www.ijm.fr/en/ijm/resources/bioinformatics/AutoClass is an unsupervised Bayesian classification system. AutoClass@IJM provides a web interface for this clustering algorithm.10571Wed, 22 May 2013 02:50:42 -0400 http://gopubmed.biotec.tu-dresden.de/gogeneGoGene performs high-throughput text mining to complement annotation of genes. GoGene supports search for genes in PubMed, EntrezGene and BLAST.10541Wed, 22 May 2013 03:10:24 -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, 22 May 2013 04:00:26 -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.10495Wed, 22 May 2013 09:00:18 -0400 http://rsat.ulb.ac.be/neat/Network Analysis Tools (NeAT) is a suite of tools for the analysis of biological networks, clusters, classes and pathways. Tools are available as web services for integration into programmatic work flows.10499Mon, 20 May 2013 06:30:16 -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.10442Wed, 22 May 2013 11:30:13 -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://mml.sjtu.edu.cn/MobilomeFINDER/MobilomeFINDER (Mobile Genome FINDER) is a tool for high-throughput genomic island discovery.10377Fri, 17 May 2013 18:10:08 -0400 http://fred.bioinf.uni-sb.de/sepacs.htmlSEPACS (Seroreactivity Pattern Classification System) is a a web-based application for classification of seroreactivity profiles.10370Mon, 20 May 2013 01:30:30 -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://estexplorer.biolinfo.orgESTExplorer is an automated suite of programs to pre-process, assemble and functionally annotate ESTs at both DNA and protein level.10339Mon, 20 May 2013 08:20:19 -0400 http://david.abcc.ncifcrf.gov/home.jspThe Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.10322Tue, 21 May 2013 13:50:25 -0400 http://www.cisreg.ca/oPOSSUM_new/oPOSSUM is a web-based system for the detection of over-represented transcription factor binding sites in the promoters of sets of genes.10310Sun, 19 May 2013 01:20:31 -0400 http://www.jprogo.de/index.jspJProGO is a tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information.10298Wed, 22 May 2013 00:20:32 -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.10284Sun, 19 May 2013 05:10:17 -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.10277Mon, 20 May 2013 04:00:31 -0400 http://greengenes.lbl.gov/cgi-bin/nph-NAST_align.cgiNearest Alignment Space Termination (NAST) is a multiple sequence alignment server for comparative analysis of 16S rRNA gene sequences from bacteria and archaea.10261Tue, 21 May 2013 15:10:15 -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.10245Tue, 21 May 2013 18:40:35 -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.10149Mon, 20 May 2013 13:20:30 -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.10141Mon, 20 May 2013 18:50:23 -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://www.cbs.dtu.dk/services/GenePublisherGenePublisher performs automatic normalization, statistical analysis, and visualization of DNA microarray data.10140Sun, 19 May 2013 16:50:30 -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.10138Wed, 22 May 2013 12:40:55 -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.10061Tue, 21 May 2013 09:40:19 -0400 http://midaw.cribi.unipd.it/dnachip/MIDAW (MIcroarray Data Analysis Web tool) is a data normalization and analysis tool for microarray data.10056Wed, 22 May 2013 06:30:19 -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.10039Wed, 22 May 2013 04:50:18 -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://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.10017Wed, 22 May 2013 06:10:36 -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://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.10000Wed, 22 May 2013 03:10:21 -0400 http://genome.ucsd.edu/microarray/VAMPIRE is a collection of Java tools designed to perform Bayesian statistical analysis of gene expression array data.9985Wed, 22 May 2013 01:20:36 -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.9942Wed, 22 May 2013 11:10:31 -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.9925Mon, 20 May 2013 03:50:24 -0400 http://www.biorag.org/pathway.htmlPathway Miner is a tool for searching lists of genes for associations in known pathway data from KEGG, BioCarta, and GenMAPP. Also provides statistical analyses.9923Mon, 20 May 2013 07:00:13 -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.9917Wed, 22 May 2013 11:20:23 -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.9915Wed, 22 May 2013 15:10:26 -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.9905Sun, 19 May 2013 03:40:19 -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.9898Tue, 21 May 2013 06:50:17 -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.9899Wed, 22 May 2013 17:00:23 -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.9907Mon, 20 May 2013 22:40:24 -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.9870Mon, 20 May 2013 21:30:25 -0400 http://biowulf.bu.edu/zlab/PromoSer/Server which aims to extract proximal promoter sequences from mammalian genomes. Does so by mapping mRNA and EST sequences and tracking overlapping alignments to find the transcription start site.9854Wed, 22 May 2013 10:20:39 -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.9775Tue, 21 May 2013 03:40:25 -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.9764Wed, 22 May 2013 01:30:37 -0400 http://www.pubgene.org/Searchable literature network of human genes with tools for gene expression analysis. Choose from the free public service, or purchase the commercial package.9478Tue, 21 May 2013 18:50:22 -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://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://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.9346Wed, 22 May 2013 15:30:09 -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://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.9336Sun, 19 May 2013 07:20:25 -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.9321Tue, 21 May 2013 06:30:13 -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.9307Mon, 20 May 2013 08:10:16 -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.9302Tue, 21 May 2013 11:40:31 -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.9289Tue, 21 May 2013 14:10:23 -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.9264Tue, 21 May 2013 20:10:15 -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.9251Mon, 20 May 2013 08:10:07 -0400 http://genome.imim.es/astalavista/AStalavista (alternative splicing transcriptional landscape visualization tool) dynamically identifies, extracts, and displays alternative splicing events from whole genome annotations and user provided gene sets.9250Sun, 19 May 2013 21:00:32 -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.9240Wed, 22 May 2013 16:40:44 -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.9229Wed, 22 May 2013 17:40:19 -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.9216Tue, 21 May 2013 05:00:17 -0400 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.9215Tue, 21 May 2013 02:10:27 -0400