The Intracellular Pathogen Cooperative Group @ St George's
ArrayLinkBase and NGS Tools
Last updated : 31 Oct 2009
|St George's Portal||London Technology Network||Funding Sources|
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
Some example Keywords you might find listed:
Bioinformatics, Companies (services, consumables and instrumentation), Courses, Data (public Domain)/Data Analysis, Databases, Data Standards, General Information, Languages (MAML GEML andothers), Link Collections and Resource Pages, Labs European/North American/Rest of the World, News Groups/News and Veiws,Software, Statistcal Analysis, Organisations using or developing Microarrays, Shared/Core facilities, Pathways (regulatory networks), Protocols, QC, References and Reveiws
see also Statistical Analysis
CGH (Comparative Genome Hybridisation)
For Other articles or sites on Cluster Analysis see also: Bioinformatics, Statistical Analysis or Data Analysis
|Agilent Technologies supply both custom array services and off-the-self arrays including Human and Mouse "whole genome" oligo arrays and other Mouse, Rat and other organisms such as Arabidopsis||Affymetrix, Inc., DNA chip technology (oligoarrays), reagents and instrumentation. Santa Clara, California|
|BlueGnome have recently extended there interests from Software for feature extraction and analysis into human Bac arrays for CGH. The companies main product remains BlueFuse and is an image processing and basic analysis suite which is well suited for CGH analysis, feature extraction see also Software or go to their home site.||CombiMatrix develops life science research products based on array technologies in the areas of genomics for clinical applications.|
|DNAmicroarry.com US company based in Maryland provides Custom services Affymetrix, Ilumina and Agilent also pre-fabricated or Oligo, cDNA and miRNA arrays||DIGILAB Gene Expression||Gene Logic is a commercial Microarray service provider of Agilent, Affymetrix and Illumina. along side BioTrove and ABITaqMan based in Maryland US|
|Illumina Inc Bead Arrays, Next Gen Sequencing and HiScan and iScan, provides both instumentation and arrays for its own platform|
|Eurofins mwg/Operon offers a wide and comprehensive range of high-quality oligos, probes, and primers, as well as custom synthesis including a full range of longmers and modified oligos, print sets||Phase-1Molecular Toxicology Inc Human and Rat Glass slide arrays, New Mexico||Research Genetics Human, Yeast gene filters and Affymetrics services|
|Sigma Genosys PanoramaTm Arrays||SuperArray Bioscience supply arrays "GEarray", RNA interference, and QPCR products and services|
|Agilent Technologies 2100 bioanalyzer RNA sample QC system based on Caliper’s LabChip® Microfluidics Technology, Agilent Microarray Slide Scanner Microarray Data analysis software GeneSpring GX||Ambion (Now part of Applied Biosystems) provide an extensive range of labelling kits for all platform technologies||
GE Health Care. Consumables including Cy dye labelled nucleotides and CyScribe kits, a complete hardware range
|ArrayIt Telechem International Inc, Microarray
hardware, reagents and chemicals
Also provide a free to use microarray e-libray
|Axon Instruments is now owned marketed by Molecular Devices. The 4000 range of scannining Instrumentation includes the 4000B to the 4400A along side Data extraction software such as GenePix Pro and Acuity||BioDiscovery, Inc. Data analysis and extraction software||BioRobotics is now owned and marketed by Genomic solutions MicroGridII Array Printing|
|BlueGnome extended there interests from Software for feature extraction and analysis into arrayCGH, CNV analysis of the human genome. The companies main software product remains BlueFuse, an image processing and analysis suite which is well suited for CGH analysis, feature extraction see also Software.||DIGILAB now own and produce the OmniGrid and Microgrid Arrayers||Clontech Labelling kits and hyb chambers|
|Corning Costar CMT-GAPSTm slides Consumables||Engineering Sevices Inc Arrayer||Erie Scientific suppliers of LifterSlips, raised cover slips for hybridisation and Microarray slides||ESInc SDDC Arrayer Toronto|
|Genetix QBot/QArray Instrumentation and consumables UK from 2002 Genpak and Genescreen products became integrated into the Genetix range.||Genisphere sells a range of 3DNA™ labeling kits for microarrays.|
|Grace Bio Labs Nylon and Nitrocellulose coated glass slides for microarrays||GSI Lumonics Scannining Instrumentation: ScanArray series||Imaging Research Inc ArrayVision software||Kreatech Diagnostics Universal Linkage System (ULS) is a technique for binding any marker group or label to DNA and RNA.|
|Molecular Solutions market many of the Telechem producys across the european market, product range covers NA diagnostics, multiplex real-time PCR, microarray technology & microarrays, equipment and reagents||Molecular Probes Now owned by Invitrogen. DNA intercalating dyes and fluors, amino allyl dUTP labelling kits Alexfluor 546, 647 now also 555 and 647 cy3 and cy5 equivalents, Syto stains. Base : Dye calculator for estimating Base:Dye ratio Molecular Probes Alexafluor dyes|
|Nanogen California||NEN Life Sciences is now part of Perkin Elmer MicromaxTm labeling Tyramide Signal Amplification NEN cyanine 3 and cyanine 5 dyes||Pangea Systems, California|
|PHASE-1 Molecular Toxicology, Inc. New Mexico||Packard Instrument Company BioChipArrayer (Piezotip technology)||Partek® Genomics SuiteTM (Partek GS) is a comprehensive suite of advanced statistics and interactive data visualization specifically designed to reliably extract biological signals from noisy data. Partek GS is unique in supporting all microarray and next generation sequencing technologies|
|Pharma foundation The Pharmaceutical Research and Manufacturers of America and the PhRMA Foundation||PROTEIGENE , supplies Telechem style hybridisation cassettes||Qiagen no longer produce arrays or array ready oligo sets. Liquid Hanling robotics RNA and probe purification extration/stabilation solutions|
|Radius Biosciences, Massachusetts||ResGen™ Genomics Resources tools and services from Invitrogen||Research Genetics, Recently merged with Invitrogen, Genefilters HDGs Alabama|
|RosettaBiosoftware develops bioinformatics software: includes Resolver, Rsolver SDK and Luminator||Schleicher & Schuell FastTm and CastTm modified glass slides|
|SurModics 3D-Link Activated slides for attaching amine modified DNA||Virtek Visoion Instrumentation seems to be sold and badged under the Bio-Rad Versarray Label||V & P Scientific Inc. California|
Data (Public Domain)
Eukaryotic Data Sets
Yeast Data Sets
Prokaryotic Data Sets
Databases (Expression Data)
For a comprehensive survey of microarray databases see Gardiner-Garden and Littlejohn (2001) Breifings in Bioinformatics vol 2 no 2 143-153.
Secondary Databases utilizing expression data
- Experimental Database of functioal networks in organisms Protein Function and Biochemical Pathways (PFBP) Project
Datamining: For Other artcles or sites on Datamining see also: Bioinformatics, Statistical Analysis, Data Analysis or Database
See also News and veiws (listed under N) and/or other Links page (listed under L)
Link Collections and Resource Pages
please also see below : Organisations using or developing Microarray Shared/Core facilities
European based Labs
|The MRC Cooperative at St Georges is a multi-disciplinary collaborative group studying various intracellular pathogens. Our research interests cover areas such as host-pathogen interactions, bacterial gene expression, molecular and cellular biology, cellular immunology, microbiology and vaccine research|
|The microarray facility at the Iinstitute of Food Research is part of a robust genomic approach to the study of food and health related issues and is part of Jay Hinton's group at the IFR|
|Created as a result of increasing technological developments within the field of genomics and in particular microarrays. Set up at the LSHTM around Brendan Wren's group.|
|Richard Wooster at The Institute of Cancer Research UK|
|The Toxicogenomics resources in the MRC Toxicology Unit were first set up in 1999 and primarily service the need of in house research programmes.|
|The CSC/ICSM Microarray Centre forms an integral part of the new Genomics, Proteomics and Informatics Research Laboratories (GPIRL) on the Hammersmith Campus|
|Tim Gant MRC Toxicology Unit DNA Microarray Pages at the University of Leicester UK.|
|Jürg Bähler's group at the Sanger Centre is working on various post-genomics projects using the fission yeast Schizosaccharomyces pombe as a model organism|
|The Genomics Laboratory at the University Medical Center Utrecht ( UMC Utrecht) has been set up to implement technology and resources generated through whole genome sequencing projects.|
|Jörg Hoheisel's group at DKFZ (Deutsches Krebsforschungszentrum). The Division of Functional Genome Analysis is involved in the development of technologies for the analysis of large genomic areas to entire genomes with respect to the encoded functions and their regulation|
|The Molecular Cytogenetics Group Department for Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin work on the characterization of chromosomal aberrations in patients with congenital diseases and in solid tumours. One focus is the search for chromosomal changes responsible for the disruption of brain development and function. using arrayCGH along with other Cytogentic techniques.|
US/Canadian based Labs
|The MGuide : The Brown Lab's complete guide to microarraying for the molecular biologist, Stanford University|
|Vivian Chung's Lab. Direct IBD Mapping is a DNA microarray-based mapping technique that allows isolation and mapping of DNA fragments shared IBD between individuals.|
|Geoffrey Childs lab at Albert Einstein College of Medicine|
|Michael Eisen's lab at the Lawrence Berkeley National Lab (LBNL) and the University of California at Berkeley (UCB).|
|The Washington University microarray core facility offers a variety of services to meet the needs of researchers who wish to utilize spotted microarrays. Our lab has been in existence since June of 2001.|
|Ron Davies Stanford DNA sequencing and technology development center, Stanford University|
|Stanley Falkow's Lab at Stanford. The primary focus of our research is to understand how bacterial agents cause infection and disease|
|Technology, Software and Methods for Biology, Genetics, and Medicine |
The Garner Lab at University of Texas South Western linked to Microarrays at UTSW
|Leroy Hood at Molecular Oncology and Development in the Department of Molecular Biotechnology at the University of Washington|
|Welcome to the website of the DeRisi Lab, Biochemistry &|
Biophysics Department, U.C. San Francisco.
|Kim Lab Home Page, (C. elegans Microarray), Department of Developmental Biology, Stanford University|
|Staudt Lab at the NIH home page|
|Stanford Center for Tuberculosis research|
|DNA microarray technology to identify genes controlling spermatogenesis from the Ward Lab, University of Arizona|
|The Wallace lab are developing DNA microarrays to study changes in mitochondrial gene expression at the EMROY University School of Medicine, Atlanta|
|John Weinstein's Laboratory at The National Cancer Institute are to better understand the complex molecular pharmacology of cancer cells and to find new agents for treatment of cancer|
|White Lab: The home of Drosophila DNA Microarrays, Homepage at the Stanford University School of Medicine|
|The Young lab at the Whitehead Institute for Biomedical Research working with high-density oligonucleotide arrays to gain insights into the transcriptional regulatory circuitry of eukaryotic cells during infection by HIV and M.tuberculosis|
Rest of the World
|SRC hosted by University of Queensland Austrailia|
Microarray Gene Expression Data Society-MGED
The Microarray Gene Expression Data (MGED) Society is an international organisation of biologists, computer scientists, and data analysts that aims to facilitate the sharing of microarray data generated by functional genomics and proteomics experiments.
The current focus is on establishing standards for microarray data annotation and exchange, facilitating the creation of microarray databases and related software implementing these standards, and promoting the sharing of high quality, well annotated data within the life sciences community. A long-term goal for the future is to extend the mission to other functional genomics and proteomics high throughput technologies.
General listings of Meetings/Conferences/Symposia
News and Veiws In the Field
||Lab-on-a-Chip.com provides focused information on all Lab-on-a-Chip technologies. It includes published papers, news, events, new products , suppliers, research links, jobs and discussion forums.|
BioArrayNews a weekly news letter available via the web
News Groups & Electronic Forums or BLOGS
Past entries include:
An ontology is an explicit specification of some topic....provide a vocabulary for representing and communicating knowledge about some topic and a set of relationships that hold among the terms in that vocabulary
- MGED Ontology working group
- Department of Computer Science, Wayne State University hosts a collection of GO tools which are free tools to academics and includes Onto-Express (OE) as a novel tool able to automatically translate gene lists of differentially regulated genes into functional profiles.
- Gene Ontology for Significant Collection of Annotations: GO-Scan is a tool that selects and presents relevant Gene Ontology (GO) annotations for a gene "hit" list from an Affymetrix microarray experiment
- GENETOOLS is a collection of web-based tools on top of a database that brings together information from a broad range of resources, and provides this in a manner particularly useful for genome-wide analyses. Today, the two main tools connected to this database are the NMC Annotation Database V2.0 and eGOn V2.0
Organisations using or developing Microarray Shared/Core facilities
|The Bacterial Microarray Group at St George's Hospital Medical School (BµG@S) has been funded by The Wellcome Trust to generate whole genome microarrays for twelve bacterial pathogens. The arrays will be made available for collaborative research with groups around the UK and the rest of Europe. .....|
|The Functional Genomics Laboratory is a central facility within the Microbial Sciences Group, University of Surrey & houses the Streptomyces coelicolor Microarray Resource headed by Colin Smith is part of a coordinated UK program of Streptomyces coelicolor functional genomics funded by the BBSRC.|
|The FlyChip project is a publicly funded resource and its principal aim is to provide a non-profit microarray resource for the UK Drosophila research community. Department of Genetics, Cambridge|
|GARNet microarray pages, the Genomic Arabidopsis Resource Network, was created to establish UK-based facilities for genomics research on Arabidopsis thaliana.|
|ARK-Genomics is a collaborative centre for functional genomics in farm animals (i.e. chickens, pigs, cattle and sheep) funded by the BBSRC.|
|Nylon based arrays made in house at the TAGC :Macroarrays are Nylon (or other) membranes that carry PCR products (or bacterial colonies) with typical diameter of 0.5 to 1 mm and a pitch (center to center spacing) of approximately 2 mm|
|The Netherlands Cancer Institute (NKI / AvL) started a DNA microarray facility in January 1999 The CMF is one of the largest microarray facilities in The Netherlands. Providing oligo arrays printed with the Operon v3 library (35K Human, 32K Mouse) along with 18K Human, 15K Mouse cDNA arrays, BAC and barcode arrays.|
||Norwegian Microarray Consortium, A consortium, consisting of groups from three centers DNR, NTNU, UiB collaboarting on the establishment of microarray resources for production of human gene resources, and provides arrays. Now runs the National Microarray Platform under the FUGE program|
|Department of Human and clinical Genetics - Leiden University Medical Center Leiden Genome Technology Centre (LGTC) Director: Dr. Johan T. den Dunnen. Providing a non-profit service|
|The National Institute of Environmental Health Sciences has established a cDNA microarray center which provides access to this technology for the intramural and extramural community|
||Ecole Normale Superieure, Paris Contains a nice links page to sites containing information about DNA microarrays and a whole host of other goodies . Includes a microarray newsgroup|
|The Microarray Centre at The Ontario Cancer Institute, University Health Network is a leader in Canadian microarray technology. We are dedicated to providing high quality microarrays, technical support and service to Canadian researchers|
|The Corning/Whitehead Institute Center for MicroArray Technology is a state-of-the-art, full service microarray facility. Located at the Whitehead Institute|
|Microarray Core Facility previously hosted by Vanderbilt University currently a new web under construction|
|Microarrays.org is a public source for microarray protocols and software. This site is built and maintained by the DeRisi Lab, Dept. of Biochemistry & Biophysics, Univ. of California at San Francisco.|
|The DNA microarray core facility for the Genomics and Proteomics Core Labs of the University of Pittsburgh|
|The Biomedical Genomics Microarray (BIOGEM) Core Facility at UCSD|
Microarray Project, National Human Genome Research Institute
|Vanderbilt Microarray Shared Resource VMSR, mouse and human arrays|
|The Pathogen Functional Genomics Resource Center (PFGRC) designs, constructs, and distributes 70-mer glass slide DNA microarrays for pathogens and biodefense related organisms. In 2008 39 microarrays were currently supported by the PFGRC.|
- Molecular Interaction Map of the Mammalian Cell Cycle Control and DNA Repair Systems. Kurt W. Kohn Molec. Biol. Cell 1999 Aug;10(8):2703-34
- The BioCyc Knowledge Library is a collection of Pathway/Genome Databases. Each database describes the genome and metabolic pathways of a single organism, with the exception of the MetaCyc.
- EcoCyc is a bioinformatics database that describes the genome and the biochemical machinery of E. coli.
- MetaCyc metabolic pathway database contains pathways from over 150 different organisms
- Amongst the Pathway Tools available at BioCyc is Expression Viewer (Omics Viewer) this paints expression data onto the Metabolic Overview diagram for an organism
- Kyoto Encyclopedia of Genes and Genomes, KEGG integrates the information about genes and proteins generated by genome sequencing, functional genomics and proteomics with metabolic pathways
- The Reactome knowledgebase relies on collaborations with research biologists to construct expert consensus views of key biological processes
- Skypainter is a tool to determine which events (reactions and/or pathways) are statistically overrepresented in a set of genes as specified by submitted list of identifiers. In other words, given a list of genes, Skypainter can identify common events for these genes
- Database for Annotation, Visualization and Integrated Discovery (DAVID)is a web-based tool that provides integrated solutions for the annotation and analysis of genome-scale datasets derived from high-throughput technologies such as microarray and proteomic platforms. Analysis results and graphical displays remain dynamically linked to primary data and external data repositories, thereby furnishing in-depth as well as broad-based data coverage. The functionality provided by DAVID accelerates the analysis of genome-scale datasets by facilitating the transition from data collection to biological meaning.
Platform Cross Comparability
- TeleChemInternational DNA-Microarray Protocols
- Resources at Vanderbilt University MCF
- Current Protocols at NHGRI
- Brown Lab's at Standford Protocols page
- Protocols used in three papers coming out of MIT
- Geoffrey Child's Lab at ASCOM Protocols page
- Childs / Kucherlapati Lab Protocol cDNA-Microarray Hybridization
- Protocols used in Vivian Chung's lab, has protocols for both Genomic Mismatch Scanning and Microarrays
- NIH-CIT reference page including some protocols
- Jeremy Buhler's Protocol web page for Comparative Gene Expression Studies
- Leroy Hood's Lab protocols page at MOD a mix of protocols for DNA/microcolonys on membranes as well as protocols for microarrays
- cDNA membrane array (methods page), University of Delaware's Center for Agricultural Biotechnology
- Richmond et al. NAR (2000) Genome-wide expression profiling in E.coli pdf, a comparative methods paper from Fred Blattner's Lab University of Wisconsin.
- UTSW basic microarray protocols page
- TIGR Protocols page includes Biotechniques (2000) A concise guide to microarray analysis. Available as text or pdf from the TIGR web site
- LGTC (Netherlands) Protocol last update is limited to protocols for amplification, processing and printing arrays
- Protocols currently in use at the Ontario Cancer Institue microarray center
- Chris Seidel's general protocols page. Includes a link page for incorporation of amino-allyl modified nucleotide for esterification of the Cyanine dyes and hybridisation of labelled random nano-mer.
- Commercial Protocols
- AtlasTm glass slide array user manual pdf, membrane array user manual pdf, generic product page with links to various manuals and FAQs
- Detailed protocols for indirect labeling can be found Microarrays.Org. Alternatively, fluorescent labeling kits can be purchased from Stratagene , Clontech or Molecular Probes.
Primer/Probe design software
- WWW programs for primer design :
- Primer3 at MIT: http://www-genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi
- Xprimer: http://alces.med.umn.edu/xprimerinfo.html
- Primers for the WWW: http://www.williamstone.com/primers/index.html
- Array Designer (Premier Biosoft)- windows application designs primer pairs for PCR or oligonucleotide probes in batch mode. Amplicons or probes are tested for specificity by accessing the NCBI blast server and designed to standardised hybrisation PCR conditions.HMS Beagal review
- GAP (Genome- wide Automated Primer finder servers) - Originally written to design primer pairs to upstream regions of the E.coli genome but will also now also finds genome-wide primers given the ORF coordinates. GAP allows primers to be designed to the regions chosen with some degree of freedom. GAP (Genome-wide Automated Primer finder) has two interfaces PIORF (Primer InterORFinder) and PORF (Primer ORFinder)
- ArrayOligoSelector from the DeRisi Lab systematically designs gene specific long oligonucleotide probes for entire genomes. For each open reading frame, the program optimizes the oligo selection based upon several parameters, including uniqueness in the genome, sequence complexity, lack of self-binding, GC content and proximity to the 3'end of the gene.
- OligoArray2.1 - An Oligo nucleotide probe design based on three major criteria: melting temperature, specificity and absence of stable secondary structure at the hybridization temperature. OligoArray: genome-scale oligonucleotide design for microarrays Rouillard et al. (2002). Bioinformatics 18 (3) 486-487
- ProbeSelect: They have described algorithms to optimize the selection of specific probes for each gene in an entire genome.
- Featurama / ProbePicker: The Featurama software is intended as a tool to aid biological researchers employing custom designed oligonucleotide microarrays with oligonucleotide design for their experiments.
- OligoPicker: This program is to help selecting one 70-mer oligo for each of the DNA sequences you provided for microarray experiments.
- ROSO: optimizing oligonucleotide probes for microarrays Bioinformatics 2004.ROSO is software to design optimal oligonucleotideprobe sets for microarrays. "Selected probes show no significant cross-hybridization, no stable secondary structures and their Tm are chosen to minimize the Tm variability of the probe set".
- YODA: selecting signature oligonucleotides Bioinformatics 2005 21(8):1365-1370. YODA is an application for assisting biological researchersin selecting signature sequences. It incorporates a custom sequencesimilarity search to find potential cross-hybridizing non-targetsequences. For this task, most oligo design tools rely on BLAST,which is ill suited for it due to an unacceptable risk of false negatives. YODA supports multiple probe design goals including single-genome, multiple-genome, pathogen-host and species/strain-identification.
- Oligodb -a batch web-based system for interactive design of oligonucleotides for transcription profiling (hybridization) of human genes based on the ENSEMBL database. Mrowka et al. Oligodb-interactive design of oligo DNA for transcription profiling of human genes. Bioinformatics. 2002 Dec;18(12):1686-7. (pdf). Criteria for selecting oligos are:
- low similarity to all other known human transcripts or genes
- positive minimum folding energy to avoid formation of secondary structures
- the length of the oligo
- the exclusion of low complexity regions.
Furthermore, the user may select oligos according to information on:
- the position in the 5'-3' direction of the transcript and the melting temperature Tm.
- PRIMEGENS (PRIMEr Design Using GEN Specific Fragments) is program to select gene-specific fragments and then design primer pairs for PCR amplifications. Xu D, Li G, Wu L, Zhou J, Xu Y. Bioinformatics 2002 Nov;18(11):1432-7
- ProbeWiz Server - The CBS ProbeWiz WWW server predicts optimal PCR primer pairs for generation of amplicon based probes for cDNA arrays. see Avoiding cross hybridization by choosing nonredundant targets on cDNA arraysH. B. Nielsen and S. Knudsen. Bioinformatics ( 2002) 18: 321-322
- Primer3 - download page at MIT probably the most commonly used software for designing primers for PCR.
Primer design reference papers and notes
- A "manual" on primer design: http://www.hgmp.mrc.ac.uk/MANUAL/faq/faq-primers.html
- A review of some on-line primer design packages, with links. http://www.alkami.com/reviews/rvwdsgn3.htm
- A GNU/Linux-based system, called DEgenerate Oligonucleotide Design & Analysis System (DEODAS), for designing and electronically analyzing consensus-degenerate oligonucleotides is being developed by integrating published software tools from other authors: Clustalw, CODEHOP, and EMBOSS, for an easy to read overview see the O'Rielly Network page.
- Genome-directed primer for selective labelling of bacterial transcripts for DNA microarray analysis. Talaat AM, Hunter P, Johnston SA Nature Biotech 18 June 2000. A brief description of the process used to obtain the minimal primer set for M.tuberculosis.
- FindGDPs: identification of primers for labeling microbial transcriptomes for DNA microarray analysis. Robert J. Blick, Andrew T. Revel and Eric J. Hansen (2003). A program that uses a greedy algorithm to quickly identify a set of genome-directed primers that specifically anneal to all of the open reading frames in a genome and that do not exhibit full-length complementarity to the members of another user-supplied set of nucleotide sequences.
- Raddatz G, Dehio M, Meyer TF, Dehio C.(2000) Bioinformatics 17: 98-99. PrimeArray: genome-scale primer design for DNA-microarray construction. PDF version
- Tomiuk S, Hofmann K. Microarray probe selection strategies. Brief Bioinform. 2001 Dec;2(4):329-40. [PubMed]
QC: Quality control
- The Ecole Normale SupErieure microarray platform team released Doelan 1.0.1 late in 2005. Doelan is designed as an tool to monitor the array quality for production QC ( see Jourdren & Le Crom Bioinformatics 2005). The software executes a series of quality control tests on hybridizations carried out on batches of arrays. The reports generated by Doelan aim at providing quality certification such as ISO 9001. The Doelan application is written in Java and works with a plug-in system that allows everyone to add custom validation tests.
- MicroArray Quality Control Project (MAQC) The MicroArray Quality Control (MAQC) project involves six FDA Centers, major providers of microarray platforms and RNA reference samples, EPA, NIST, academic laboratories, and other stakeholders. The MAQC project aims to establish QC metrics and thresholds for objectively assessing the performance achievable by various microarray platforms and evaluating the advantages and disadvantages of various data analysis methods. The first publications coming from this project recently appeared available online see: Nature Biotechnology. Data sets are also available for download from the MAQC project home pages (MAQC)
References and Review Articles on Microarrays
Lab Publication Pages or Listings of other labs publications
Important or Early publications
Search Engines (datamining)
Software (for primer design software see primer design)
|Agilent Technologies Feature Extraction Software Rosetta Resolver® suite and Agilent now own Silicon Genetics suite of software including GeneSpring (see below).||Applied Maths, Belgium. GenExplore™ :2-way cluster analysis, principal component analysis, discriminant analysis, self-organizing maps.||ArrayDesigner from Premier Biosoft, Batch primer design and Blast hybridization tool for Windows.|
|ArrayMining - Online Microarray Data Mining Ensemble and Consensus Analysis Methods for Gene Expression Data - web based data analysis to perform various gene selection analysis and discovery approaches to Microarray data mining see BMC Bioinformatics|
|ArrayMiner® is a set of analysis tools using advanced algorithms, commercial package from Optimal Design||ArrayPipe is a Perl program that can be run through the Web or from the command line. It consists of functions and filters that can be arranged into a pipeline to process and analyze microarray data.
It was developed for the Genome Canada Pathogenomics project (www.pathogenomics.ca) and is made freely available to the public as a new tool for microarray research.
|Arrayplot visalisuation and normalisation of microarray data in a user-friendly Windows interface. Allows visualisation of data distribution and viewing of most variant genes.
Bioinformatics (2002)18: 888-889
|Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data including many packages based around R||The amongst the Web Pathway Tools available at BioCyc is Expression Viewer this paints expression data onto the Metabolic Overview diagram for an organism|
|BioDiscovery, Inc. Aquisition & Analysis software Imagene: image processing and data extraction software, GeneSight: clustering, principal component analysis, time series, Autogene, California||BlueFuse (BlueGnome) for Microarrays is an image processing basic analysis suite including extensions for CGH analysis, feature extraction is fully automated; removing human subjectivity and raising experimental repeatability. BlueFuse uses advanced statistical modelling techniques.||BRB ArrayTools is an integrated package for the visualization and statistical analysis of DNA microarray gene expression data||Brown Lab Software download page|
|CAGED (Cluster Analysis of Gene Expression Dynamics) is a program for the analysis of temporal profiles of gene expression data||Various tools produced at CBS Denmark.Includes affyR package, ClustArray and ProbeWiz||Chip2Chip: A web tool to map gene sets betweeen microarray platforms or between organisms||Clondiag Chip Technologies Image analysis software : Image processing; automated/pure spot identification ; interactive and scripting|
|CisGenome is an "integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis"|
|Cluster, TreeVeiw, GMEP & ScanAlyze from Mike Eisen's lab||Cluster Calculator Free software at University of Alberta cluster analysis, by John Brzustowski||Cose, France. XDotsReader software|
|CrazyQuant program is used to locate and quantify spot intensities on a DNA microarray. Available free from University of Washington||Cyber-T Long et al. (2001) J. biological Chem 276:19937-19944.||EDGE designed specifically for statistical analysis of time- course data. You can download EDGE from this website and read about it in their PNAS paper (JD Storey et al, Sept 6, 2005 "Signficance analysis of time course microarray experiments")|
|Expression Profiler is free a set of tools for the analysis and clustering of gene expression data being developed at the EBI by Jaak Vilo||FlexArray is a Microsoft Windows software package for statistical analysis of microarray expression data. Currently, the analysis of Affymetrix GeneChip ® and Illumina BeadChip ® expression arrays is supported, but many other types of studies (e.g. proteomics or gene methylation) are supported through the feature of importing custom normalized data.|
|F-SCAN: Fluorescently Probed cDNA Microarray Analysis is for quantification and analysis of fluorescently probed microarrays. It reads various image storage formats. The quantification strategy employs a hybrid of automated and interactive determination spot placement and image segmentation.||FuzzyK is a C++ command line program that will perform fuzzy k-means clustering on gene expression data from the Gasch & Eisen|
|GACK, CGACK and other software tools from Stanley Falkows lab in Stanford, usually avalable as either perl scripts or windows exe versions||GATConsortium Affymetrics and Molecular Dynamics software specification|
|GENAT microarray data analysis tool, developed at Systems Biology Center Technical University of Delft Faculty of Information Technology and Systems by Eugene van Sommeren||GeneMaths - From applied-Maths.com||GenMAPP is a free computer application designed to visualize gene expression data on maps representing biological pathways and groupings of genes.|
|Gene Expression Pattern Analysis Suite (GEPAS): Expression Pattern Preprocessor, PlotCorr, Sotarray, TreeView , SOM, SomTree, Cluster, SotaTree Servers as well as a data up-loader and tools||GenePlus commercial suite of products. Includes database management, visualization tools and cluster analysis, into a single platform from Enodar.com||Software from MIT GenePattern, GeneSet Enrichment Analysis (GSEA), GeneCruiser and Cnnectivity Map|
|GeneData AGSwitzerland, analysis of genomics and proteomics data: GeneData WorkBench, GeneData Expressionist||GenePix Data extraction software supplied with Axon Scanners, Axon Instruments||Genesis: cluster analysis of microarray data and other data analysis packages. See Sturn,Quackenbush and Trajanoski. Bioinformatics Vol. 18 no.1 (2002)|
|GeneSOM R package for Clustering Genes using Self-Organizing Map||GENETOOLS is a collection of web-based tools on top of a database that brings together information from a broad range of resources, and provides this in a manner particularly useful for genome-wide analyses. Today, the two main tools connected to this database are the NMC Annotation Database V2.0 and eGOn V2.0|
|Ginkgo: CGH and Expression Microarray Statistical Analysis and Normalization Platform from the PFGRC. Ginkgo is a spotted microarray data pre-processing platform featuring analysis functionalities for CGH and expression data. This application provides a user-friendly graphical interface that allows viewing, analyzing, generating and reporting microarray data, easily and intuitively. Within the software there are a number of algorithms to address microarray data analysis needs, including normalization, filtering, data imputation, replicates merge, and expression statistical distribution tests.|
|GOToolBox web server. This site provides a series of programs allowing the functional investigation of groups of genes, based on the Gene OntologyTM ressource.||Department of Computer Science, Wayne State University hosts a collection of GO tools which are free tool academics and includes Onto-Express (OE) as a novel tool able to automatically translate gene lists of differentially regulated genes into functional profiles.|
|Gene Ontology for Significant Collection of Annotations: GO-Scan is a tool that selects and presents relevant Gene Ontology (GO) annotations for a gene "hit" list from an Affymetrix microarray experiment||Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states|
|lcDNA is a software program for calculating statistical confidence levels of DNA microarray data based on Markov Chain Monte Carlo simulation based on: Tseng, G.C.et al.. (2001) Nucleic Acid Res, 29, 2549-2557.||Imaging Research Inc ArrayVisionTm software used for rapid and automated analysis of genome arrays.Canada|
|J-Express is a Java application that allows the user to analyze gene expression (microarray) data in flexible way giving access to multidimensional scaling, clustering, and visualization methods in an integrated manner.From molmine.com||Limma (limmaGUI) is an open-source Bioconductor package for linear models for microarrays (Graphical User Interface) it may be used for two-color microarray analysis. There is also has a version for affymetrix arrays both handle experiments using a loop design.||KATSURA: KEGG PATHWAY COVERAGE AND EXPRESSION ANALYSIS. The Katsura tool is a free open source Java application designed to overlay gene expression data, comparative genomics data, or quantitative shotgun proteomics data onto metabolic pathways. Katsura uses data from the Kyoto Encyclopedia of Genes and Genomes (KEGG, 1-3), Kanehisa Laboratory at Kyoto University, to build a small database containing KEGG pathway and enzyme data relating to one or more user specified organisms.||Microarray Explorer (MAExplorer) is a Java-based data-mining facility for cDNA or oligonucleiotide microarray databases|
|MAIA (Microarray Image Analysis) software package from Institute Curie for automatic processing of the one- and two- (typically, Cy3-green/Cy5-red) color images||Microarray Software developed by Stanford University, Scanalyse, Cluster and TreeVeiw||Molecular Applications Group CA. Stingray™ is integrated software and database products for gene expression, gene function, and gene sequence analysis from microarray data.||MolecularWare, Inc.: ArrayAnalyzerDB|
|ProbeLynx offers microarray users the ability to upload their probe sequences and continuously assess probe specificity and annotation based on latest releases of genomic sequence data and gene prediction. The tool currently focuses on arrays built from human, mouse, bovine or chicken genomes.||Peak quantification using Statistical Comparative ANalysis: P-SCAN is an automated computer algorithm for quantification and analysis of cDNA arrays. It is oriented towards data files acquired from phosporimager devices and correctly reads Molecular Dynamics, Fuji, .gel, and 16-bit .tiff storage formats.|
|"Omics Viewer". implemented by BioCyc can be used through a Web or locally. the Web interface , click on "Omics Viewer". It includes documentation on file formats, etc.|
|NHGRI Microarray Project: ArrayViewer is a Java Applet which allows real-time interaction with the data on ArrayDB||Prediction Analysis of Microarrays (PAM) software for sample classification is available from Rob Tibshirani's lab in Stanford. PAM available as an add-on R library & Excel add-in. See also SAM|
|Partek, Inc. Missouri. Provider of pattern recognition and data visualization software for science and engineering. Its Partek Pro 2000 system has been used by companies to analyze microarray gene expression data.||Phase-1Molecular Toxicology Inc MatixExpress Data-capture and analysis software, Data warehousing, New Mexico||An increasing number of specialist packages for R are being developed, many are listed with links to home pages at the University of Munich|
|Research Genetics, Recently merged with Invitrogen, Pathways Anaysis software Alabama||Rosetta Inpharmatics, Kirkland, Washington. Resolver™ Expression Data Analysis System.||RosettaBiosoftware develops bioinformatics software: includes Resolver (analysis software, database, and server framework), Resolver SDK (software development kit) and Luminator (analysis software)|
|SAM: Significance Analysis of Microarrays written in
Rob Tibshirani 's lab in Stanford see also PAM
Supervised learning software for genomic expression data mining. Available as an EXCEL add in!
GeneSpring Now produced own by Agilent Technologies Gene expression analysis software, clustering, principal component analysis, time series, metabolic pathway mapping was once arguably the commercial market leader.
|Terry Speeds Software page includes links to R and S-plus and a download page for the R package SMA||The SNOMAD gene expression data analysis tools were developed by Carlo Colantuoni and George W. Henry. consists of a collection of algorithms directed at the normalization and standardization of DNA microarray data||SOMViewer - a Perl Application for viewing Self Organizing Maps.|
|Source - a nice online resource for retrieving information about cDNA clones, and the genes to which they map||Spotfire, Inc. Data visualization gene cluster analysis and metabolic pathway mapping. Massachusetts|
|STEM The Short Time-series Expression Miner is a Java program for clustering, comparing, and visualizing short time series gene expression data from microarray experiments||Synomics Ltd., Cambridge, UK (bioinformatics)|
|This is a nice easy to use tool for creating VENN diagrams from up to four sets Oliveros, J.C. (2007) VENNY. An interactive tool for comparing lists with Venn Diagrams.||TIGR Software tools, Microarray subsection TM4 package including MIDAS, MADAM, MEV, Spotfinder & ArrayVeiwer. More information available at TM4 OnLine|
|YASMA is an add-on library for the R statistical package and can be used to analyse simple replicated experiments written by Lorenz Wernisch at Birkbeck UK||XCluster - cross platform software for analysing MicroArray Data.||X-MINE produce several products based around X-miner 1.0 providing the standard (unsupervised) clustering algorithms as well as some of the less common 'supervised' machine learning pattern recognition algorithms|
Statistical Analysis (see also Data Analysis)
This listing is by no means comprehensive and is meant to wet the appetite, you might also try above
Tutorials and Technology Overview