A proteinmicroarray , sometimes referred to as a protein binding microarray , provides a multiplex assay multiplex approach to identify proteinprotein interactions, to identify the substrates of protein kinase s, to identify transcription factor protein activation, or to identify the targets of biologically active small molecules. The array is a piece of glass on which different molecules of protein ... locations in an ordered manner thus forming a microscopic array. The most common proteinmicroarray is the antibody microarray , where antibodies are spotted onto the protein chip and are used as capture molecules to detect proteins from cell lysate solutions. Related microarray technologies also include DNA microarray s, cellular microarray s, antibody microarray s, tissue microarray s and chemical compound microarray s. Applications Protein microarrays also biochip , proteinchip are measurement ... MicroArray and Gene Expression MAGE Cell free protein array Software source code Many software Packages .... This format is often also referred to as a microarray a more general term for chip based biological measurement devices . Types of chips There are several types of protein chips, the most common being glass slide chips and nano well arrays. Production of protein arrays The production process depends on the type of protein chip. ProteinProtein array The proteins can be externally synthesised, purified ... to the array. The proteins can be synthesised through Protein biosynthesis biosynthesis , cell free protein array cell free DNA expression or peptide synthesis chemical synthesis . In situ synthesis ... called SPOT synthesis. DNA Protein array Double stranded DNA the exact binding sequence of the protein is attached spotted on the array. Artifacts to avoid 1 To avoid variability in results ... s surface the conjugated protein should be in the right conformation i.e., folded, NOT denatured , anchored ... preparations. Nevertheless, antibodies still represent the most well characterized and effective protein ... more details
Reverse phase proteinmicroarray RPMA is a protein array designed as a micro or nano scaled dot blot platform Dot blot dot blot that allows measurement of protein expression levels in a large number of biological ... protein across many samples. One microarray, depending on the design, can accommodate hundreds .... Other proteinmicroarray s include forward protein microarrays PMAs and antibody microarray s AMAs ... analytes from the sample applied on the microarray ref name B ref name C . The target protein ... as a bait in here and reverse phase proteinmicroarray at the molecular level. Experimental design ... phase protein microarrays for cell signaling analysis journal Nature Protocols publisher Nature publishing ... body fluids such as serum, CSF, urine, vitreous, saliva, etc., are immobilized on individual spots on a microarray ..., E.F. Petricoin III, J.D. Wulfkuhle year 2005 title Use of Reverse Phase Protein Microarrays and Reference ... year 2008 title Reverse phase protein lysate microarrays for cell signaling analysis journal Nature ..., K. Bussow, H. Lehrach year 2006 title Recent advances of protein microarrays journal Current Opinion ... journal coauthors B. Spurrier, S. Ramalingam, S. Nishizuka year 2008 title Reverse phase protein ... screening database for protein kinetic modeling journal Proteomics publisher WILEY VCH Verlag GmbH ... with unknown copyright status removed Image Forward vs reverse phase protein microarrays.png thumb 400px Forward vs. Reverse phase Protein Microarrays. deletable image caption 1 Monday, 4 May 2009 RPMA has various uses such as quantitative analysis of protein expression in cancer cells, body fluids ... expression of a protein marker level in a single experiment. It is also used for monitoring protein dynamics in response to various stimuli or doses of drugs at multiple time points. ref name A Some other applications that RPMA is used for include exploring and mapping protein signaling ... Reverse phase protein microarrays which capture disease progression show activation of pro survival ... more details
sisterlinks q no commons no species no s no n no A microarray is a multiplex assay multiplex lab on a chip . It is a 2D array on a Substrate materials science solid substrate usually a glass slide or silicon thin film cell that assays large amounts of biological material using high throughput screening methods. Types of microarrays include DNA microarray s, such as cDNA microarrays, oligonucleotide microarrays and SNP microarrays MMChip s, for surveillance of microRNA populations Proteinmicroarray s Tissue microarray s Cellular microarray s also called transfection microarrays Chemical compound microarray s Antibody microarray s Carbohydrate array s glycoarrays Category Microarrays de Microarray nl microarray ja ur ... more details
for proteinmicroarray based ligand binding assays was initially developed by Ekins et al. in the late ... http www.mcponline.org content 9 6 1271.abstract ref . See also ELISA proteinmicroarray DNA microarray tissue microarray chemical compound microarray References Reflist External links http www.biosims.fr en home BioSIMS Microarrays DEFAULTSORT Antibody Microarray Category Microarrays ...refimprove date June 2008 Image Antibody microarray.jpg thumb right 300 px Samples of antibody microarray creations and detections. An antibody microarray is a specific form of proteinmicroarray s, a collection of capture antibodies are spotted and fixed on a solid surface such as glass, plastic or silicon chip, for the purpose of detecting antigens. Antibody microarray is often used for detecting protein expression s from cell lysate s in general research and special biomarker s from blood plasma ... Villadangos M, Moreno Paz M, Cruz Gil P, G mez Elvira J, Parro V title A 200 antibody microarray ... of relative protein abundances journal Methods Mol. Biol. volume 441 issue pages 129 ... large protein sets only arose as a result of the achievements in genomics by DNA microarrays and the Human Genome Project . The first antibody array used for proteinprotein interaction and protein ... of their superior protein binding capacity. They were mostly probed with antibodies using ELISA ... them in applications with limiting sample quantities such as protein expression profiling of tumor ..., S, Luft, P, Duschl, A, Syagailo, YV title Antibody microarray based profiling of complex specimens ... antibodies is used and the protein samples are labelled directly by fluorescent dyes or haptens ... samples and many other sample types. One main focus in antibody microarray based profiling studies ... related research the development and application of an antibody microarray comprising 810 different ... profiling of complex samples with a microarray of 810 cancer related antibodies. journal Molecular ... more details
to a microarray such as a tiling array allowing the determination of protein binding ... regions bound by a protein of interest can be isolated and used to probe a microarray to determine ...A DNA microarray also commonly known as gene chip, DNA chip, or biochip is a collection of microscopic ... abundance of nucleic acid sequences in the target. The basic microarray Since an array can contain tens of thousands of probes, a microarray experiment can accomplish many genetic test s in parallel ... known as an Affy chip when an Affymetrix chip is used. Other microarray platforms ... probes on solid surfaces. DNA arrays are different from other types of microarray only ... s SNPs , or to genotype or resequence mutant genomes see DNA microarray Uses and types uses and types ... DNA microarray Fabrication fabrication section . Additional factors for microarray experiments are the experimental design and the methods of analyzing the data see DNA microarray Microarrays and bioinformatics Bioinformatics section . History Microarray technology evolved from Southern blotting , where ... DNA microarray journal Science volume 270 pages 467 470 pmid 7569999 doi 10.1126 science.270.5235.467 issue 5235 ref and a complete Eukaryote eukaryotic genome Saccharomyces cerevisiae on a microarray ... DNA microarray experiment KEEP SECTION SIMPLE The core principle behind microarrays is hybridization ... of the feature is known by its position. File Microarray exp horizontal.svg thumb 900px none The step required in a microarray experiment. Uses and types Image Affymetrix microarray.jpg thumb right ... locations on a single DNA microarray. The alternative bead array is a collection of microscopic ... expression. For example, microarray based gene expression profiling can be used to identify genes ... for disease detection, mostly combining PCR and microarray technology. ChIP on chip Chromatin immunoprecipitation on Chip DNA sequences bound to a particular protein can be isolated by immunoprecipitation ... more details
Image Tissue MicroArray Block.jpg 215px thumb right A Tissue MicroArray Block Image rob7 melanoma.jpg 215px thumb right 0.6 mm core Tissue MicroArray Block Image Tissue MicroArray Slide.jpg 215px thumb right A Tissue MicroArray Section Tissue biology Tissue microarrays also TMA s consist of paraffin blocks in which up to 1000 ref http tissuearray.org yale tisarray.html Yale University Core Tissue MicroArray Facility ref separate Biological tissue tissue cores are assembled in array fashion to allow multiplex assay multiplex Histology histological analysis . History The major limitations in molecular Clinical research clinical analysis of tissues include the cumbersome nature of procedures, limited availability of medical diagnosis diagnostic reagents and limited patient sample size. The technique of tissue microarray was developed to address these issues. Multi tissue blocks were first introduced by H. Battifora in 1986 with his so called multitumor sausage tissue block and modified in 1990 with its improvement, the checkerboard tissue block . In 1998, J. Kononen and collaborators developed the current technique, which uses a novel sampling approach to produce tissues of regular size and shape that can be more densely and precisely arrayed. Procedure In the tissue microarray technique, a hollow needle is used to remove tissue cores as small as 0.6 mm in diameter from regions of interest ... by any method of standard histological analysis. Each microarray block can be cut into 100 500 sections, which can be subjected to independent tests. Tests commonly employed in tissue microarray ... useful in analysis of cancer samples. See also Cytomics MicroArray and Gene Expression MAGE .... External links http tissuearray.org Yale University Core Tissue MicroArray Facility http tmalab.jhmi.edu Johns Hopkins University Tissue MicroArray Facility https cbio.mskcc.org tma Memorial Sloan Kettering Cancer Center Tissue MicroArray Software http bioitalliance.org blogs ocimum archive 2007 10 ... more details
The term microarray database is usually used to describe a wikt repository repository containing DNA microarraymicroarray gene expression data. The key features of a microarray database are to store the measurement data, manage a searchable index, and make the data available to other applications for analysis and interpretation either directly, or via user downloads . Microarray databases can fall into two distinct classes A peer reviewed, public repository that adheres to academic or industry standards and is designed to be used by many analysis applications and groups. A good example of this is the Gene Expression Omnibus GEO from National Center for Biotechnology Information NCBI or http www.ebi.ac.uk arrayexpress ArrayExpress from European Bioinformatics Institute EBI . A specialized repository ... a standard, centralized repository for microarray data. See http www.med.yale.edu microarray ... microarray databases are In order to keep this list short, please add new databases only if they are discussed ... Project, linked below. class wikitable sortable Database Scope Microarray experiment sets Sample profiles ... molecular abundance study 25859 641770 October 28, 2011 http smd.stanford.edu Stanford Microarray database private and published microarray and molecule abundance database 82542 ? October 23, 2011 ... Genevestigator database Manually curated microarray data for expression meta analysis 1500 ... https genome.unc.edu UNC Microarray database provides the service for microarray data storage, retrieval ... modENCODE Microarray database Nimblegen customer 2.1 million array 6 180 July 17, 2009 http proteogenomics.musc.edu ... microarray data generated by MUSC investigators as well as researchers in the global research community ... by microarray analysis within Ume Plant Science Centre UPSC . 100 ? November 15, 2007 http www.fda.gov ... of Microarray Databases, see dmoz Science Biology Biochemistry and Molecular Biology Gene Expression Databases Gene Expression Databases See also Biological database DNA microarray DNA microarray ... more details
A cellular microarray , is a laboratory tool that allows for the multiplex assay multiplex interrogation of living cell biology cells on the surface of a solid support. The support, sometimes called a chip , is spotted with varying materials, such as antibodies , proteins , or lipids , which can interact with the cells, leading to their capture on specific spots. Combinations of different materials can be spotted in a given area, allowing not only cellular capture, when a specific interaction exists, but also the triggering of a cellular response, change in phenotype , or detection of a response from the cell, such as a specific secretion secreted factor. An example of cellular microarrays are PMHC Cellular Microarrays . Cellular microarrays were developed by Daniel Chen, Yoav Soen, Dan Kraft, Patrick Brown and Mark Davis at Stanford University Medical Center . References Chen DS, Davis MM 2006 Molecular and functional analysis using live cell microarrays. Curr Opin Chem Biol 10 28 34 Chen DS, Soen Y, Stuge TB, Lee PP, Weber JS, Brown PO, Davis MM 2005 Marked Differences in Human Melanoma Antigen Specific T Cell Responsiveness after Vaccination Using a Functional Microarray. PLoS Med 2 10 e265 http medicine.plosjournals.org perlserv ?request get document&doi 10.1371 2Fjournal.pmed.0020265 Soen Y., Chen D. S., Kraft D. L., Davis M. M. and Brown P.O. 2003 Detection and characterization of cellular immune responses using peptide MHC microarrays. PLoS Biol. 1 E65 http biology.plosjournals.org perlserv ?request get document&doi 10.1371 journal.pbio.0000065 Chen DS, Davis MM 2005 Cellular immunotherapy Antigen recognition is just the beginning. Springer Semin Immunopathol 27 119 127 Chen DS, Soen Y, Davis MM, Brown PO 2004 Functional and molecular profiling of heterogeneous tumor samples using a novel cellular microarray. J Clin Oncol 22 9507 http meeting.jco.org cgi content ... microarray identifies functional deficiences in tumor specific T cell responses. J Clin Oncol 22 2510 ... more details
digestion , proteinmicroarray s, ref name Joos2009 which allow the detection of the relative levels ...About a class of molecules protein as a nutrient Protein nutrient other uses pp semi indef File Myoglobin.png thumb right A representation of the 3D structure of the protein myoglobin showing colored alpha helix alpha helices . This protein was the first to have its structure solved by X ray crystallography ... into a globular protein globular or fibrous protein fibrous form, facilitating a biological function ... sequence sequence of amino acids in a protein is defined by the DNA sequence sequence of a gene , which ... . Shortly after or even during synthesis, the residues in a protein are often chemically ... stable protein complex es. One of the most distinguishing features of polypeptides is their ability ... to be single structure. Other proteins undergo large rearrangements from one protein conformation ... signaling event . Thus, the structure of a protein serves as a medium through which to regulate either the function of a protein or activity of an enzyme. Not all proteins require a folding process ... protein into free amino acids that are then used in metabolism. Proteins were first described ... Berzelius in 1838. Early nutritional scientists such as the German Carl von Voit believed that protein ... urease was in fact a protein. ref name Sumner1926 The first protein to be protein sequencing .... The first protein structure s to be solved were hemoglobin and myoglobin , by Max Perutz and John ... be protein purification purified from other cellular components using a variety of techniques such as ultracentrifugation .... Methods commonly used to study protein structure and function include immunohistochemistry , site ... protein folding the statistical analysis techniques employed to calculate a protein s probable tertiary ... chains in a protein that ultimately determines its three dimensional structure and its chemical reactivity ... linked in the protein chain, an individual amino acid is called a residue, and the linked series ... more details
Pfam box Symbol SpA Name Protein A image Protein A 1DEE 1L6X.png width caption Structure of a domain of protein A as a three helix bundle binding to the heavy variable chain of a VH3 human Fab ref name ... JB, Silverman GJ. title Crystal structure of a Staphylococcus aureus protein A domain complexed with the Fab ... month May pmid 10805799 doi pmc 25840 ref left. Minimized protein A bound to Fc fragment of Rituximab ... April pmid 10754313 doi ref Pfam InterPro SMART PROSITE SCOP 1DEE TCDB OPM family OPM protein PDB PDB2 1dee , PDB2 1l6x Protein A is a 40 60 Atomic mass unit kDa MSCRAMM surface protein originally found ... opsonization and phagocytosis . Protein A antibody binding Protein A binds with high affinity to human IgG1 and IgG2 as well as mouse IgG2a and IgG2b. Protein A binds with moderate affinity to human ... or IgD , nor will it react to mouse IgM, IgA or IgE. The capacity of protein A to bind antibodies .... The protein A used for production of antibodies in bio pharmaceuticals is most commonly bound to a stationary phase chromatography resin. Other antibody binding proteins In addition to Protein A, other immunoglobulin binding bacterial proteins such as Protein G , Protein A G and Protein L ... Staphylococcus aureus utilizes Protein A, along with a host of other proteins and surface factors to aid its survival and, thus, virulence. Protein A helps inhibit phagocytic engulfment and acts as an immunological disguise. Mutants of S. aureus lacking protein A are more efficiently phagocytosed ... toxin. J. Exp. Med. 2003 197 1125 1139. ref Research Recombinant Staphylococcal Protein ... form of Protein A is called MabSelect ref http www.gelifesciences.com aptrix upp00919.nsf Content 17D93C2E6A580E57C1257628001CE677 file 18114994AE.pdf ref . Protein A is often coupled to other molecules ... beads. Protein A is often immobilized onto a solid support and used as reliable method for purifying total IgG from crude protein mixtures such as blood serum serum or ascites fluid, or coupled with one ... more details
PBB geneid 5627 Protein S is a vitamin K dependent plasma glycoprotein synthesized in the endothelium. In the circulation, Protein S exists in two forms a free form and a complex form bound to complement system complement protein C4b. In humans, protein S is encoded by the PROS1 gene . ref name pmid2944113 ... J, Wydro R title Isolation and sequence of the cDNA for human protein S, a regulator of blood coagulation ... in Seattle , Washington first discovered protein S and arbitrarily named it after the city ... , and protein S journal Biochemistry volume 16 issue 4 pages 698 706 year 1977 month February pmid ... Characterization of protein S, a gamma carboxyglutamic acid containing protein from bovine and human ... 10.1021 bi00572a026 ref Function The best characterized function of Protein S is its role in the anti coagulation pathway, where it functions as a cofactor to Protein C in the inactivation of factor ... cite journal author Castoldi E, Hackeng TM title Regulation of coagulation by protein S journal Curr ... MOH.0b013e328309ec97 url ref Protein S can bind to negatively charged phospholipids via the carboxylated Gla domain GLA domain . This property allows Protein S to function in the removal of cells which ... . Protein S can bind to the negatively charged phospholipids and function as a bridging molecule between the apoptotic cell and the phagocyte. The bridging property of Protein S enhances the phagocytosis ... such as inflammation occurring. Pathology Mutations in the PROS1 gene can lead to Protein S deficiency ... of, and molecular defects underlying, inherited protein S deficiency in the general population ... P, Fuentes Prior P, Hurtado B, Sala N title Molecular basis of protein S deficiency journal Thromb ... Protein S has been shown to Proteinprotein interaction interact with Factor V . ref name pmid10593904 ... Y, Rosing J, Tans G, Griffin J H year 1999 month Dec. title C terminal residues 621 635 of protein ... of protein S to factor Va associated with inhibition of prothrombinase that is independent of activated ... more details
A chemical compound microarray is a collection of organic chemical compounds spotted on a solid surface, such as glass and plastic. This microarray format is very similar to DNA microarray , proteinmicroarray and antibody microarray . In chemical genetics research, they are routinely used for searching proteins that bind with specific chemical compounds, and in general drug discovery research, they provide a multiplex assay multiplex way to search potential drugs for therapeutic targets. There are three different forms of chemical compound microarrays based on the fabrication method. The first form is to covalently immobilize the organic compounds on the solid surface with diverse linking techniques this platform is usually called small molecule Small Molecule Microarray, which is invented and advanced by Dr. Stuart Schreiber and colleagues http cgr.harvard.edu macbeath research small mol.html . The second form is to spot and dry organic compounds on the solid surface without immobilization, this platform has a commercial name as Micro Arrayed Compound Screening ARCS , which is developed by scientists in Abbott Laboratories http jbx.sagepub.com cgi content abstract 9 1 12 . The last form is to spot organic compounds in a homogenous solution without immobilization and drying effect, this platform is developed by Dr. Scott Diamond http www.seas.upenn.edu diamond and later commercialized as DiscoveryDot technology by Reaction Biology Corporation http www.reactionbiology.com . Polymer Microarrays Polymer microarrays have been developed to allow screening for new polymeric materials to direct different tissue lineages. Research has also been directed towards studying the surface ... Kinase Profiling.jpg thumb DiscoveryDot Microarray for Kinase Profiling References Uttamchandani ..., H. et al. 2005 Nanoliter Homogenous Ultra High Throughput Screening Microarray for Lead Discoveries ... content refs 11 1 48 . Ma, H. and Horiuchi, K.Y. 2006 Chemical Microarray a new tool for drug screening ... more details
Image Microarray.svg thumb 300px steps involved in a microarray experiment some steps omitted For DNA microarrays in general DNA microarray This is an example of a DNA microarray experiment , detailing a particular case to better explain DNA microarray experiments, while enumerating possible alternatives. The two samples to be compared pairwise comparison are grown acquired. In this example treated sample Case control case and untreated sample Case control control . The nucleic acid of interest is purified this can be all RNA for expression profiling , DNA for comparative hybridization , or DNA RNA bound to a particular protein which is immunoprecipitated ChIP on chip for Epigenetics epigenetic or regulation studies. In this example total RNA is isolated total as it is nuclear and cytoplasm ic by Guanidinium thiocyanate phenol chloroform extraction e.g. Trizol which isolates most RNA whereas ... miRNA microarray ligate an oligonucleotide to the purified small RNA isolated with a fractionator ... if present. The sense that is labelled depends on the microarray, which means that if the label ... and Methylamine formamine . This mix is denatured and added to a pin hole in a microarray, which can be a gene chip holes in the back or a glass microarray which is bound by a cover, called a mixer, containing two pinholes and sealed with the slide at the perimeter. The holes are sealed and the microarray hybridized, either in a hyb oven, where the microarray is mixed by rotation, or in a mixer, where the microarray is mixed by alternating pressure at the pinholes. After an overnight hybridization, all nonspecific binding is washed off SDS and SSC . The microarray is dried and scanned ... short oligonucleotides . See also DNA microarray Microfluidics or lab on chip Quantification of nucleic ... labs microarray DNA microarray virtual experiment Molecular Biology References Gibson and Muse ... found on microarray labs http www.microarrays.ca support proto.html http www.daf.jhmi.edu microarray ... more details
Summary Cartoon schematic of a typical microarray experiment Licensing PD self date September 2007 Copy to Wikimedia Commons priority true ... more details
Image Microarray2.gif thumb 350px Example of an approximately 40,000 probe spotted oligo microarray with enlarged inset to show detail. Microarray analysis techniques are used in interpreting the data generated from experiments on DNA, RNA, and proteinmicroarray s, which allow researchers to investigate the expression state of a large number of genes in many cases, an organism s entire genome in a single experiment. Such experiments generate a very large volume of genetic data that can be difficult to analyze, especially in the absence of good gene annotation. Introduction Microarray data analysis involves several distinct steps, as outlined below. Changing any one of the steps has the potential ... science centers toxicoinformatics maqc title MicroArray Quality Control MAQC Project accessdate 2007 ... ref Creating raw data Most microarray manufacturers, such as Affymetrix and Agilent ref cite web url ... software with microarray equipment such as plate readers. Background correction Depending on the type ... Linear Models for Microarray Data accessdate 2008 01 01 format work ref . A common method for evaluating ... in median polish summarization of Microarray data journal BMC Bioinformatics volume 11 pages 553 year ..., Wang K, Lefebvre C, Califano A title Comparative analysis of microarray normalization procedures effects ... 2007 pmid 17646307 doi 10.1093 bioinformatics btm201 ref Factor Analysis for Robust Microarray Summarization ... L, Reid LH, Jones WD, et al. title The MicroArray Quality Control MAQC project shows inter and intraplatform ... EK, Wang C, et al. title Rat toxicogenomic study reveals analytical consistency across microarray ... from one or several microarray experiments. A wide variety of microarray analysis tools are available ... and other microarray tools ref cite web url http www stat.stanford.edu tibs SAM title Significance ... for statistical analysis to determine the extent of over or under expression of a gene in a microarray ... farms.html FARMS Factor Analysis for Robust Microarray Summarization, an R package &mdash software ... more details
The MicroArray and Gene Expression MAGE group is a project of the FGED Society to develop a standard for the representation of gene expression data from DNA microarray microarrays to facilitate the exchange of information between different data systems. ref cite web url http www.mged.org mage title MAGE Project homepage work FGED Society website accessdate 2008 11 23 ref MAGE has in the past worked with the OMG Object Management Group , which provided a framework for developing, ratifying, and publishing the MAGE based standards documents. The MAGE standards include a data exchange model MAGE OM Microarray Gene Expression Object Model and data exchange formats MAGE ML Microarray Gene Expression Markup Language MAGE TAB Microarray Gene Expression Tabular format for microarray expression experiments. See also LSID Life Science Identifier DNA microarray FGED Society SDRF Strand Life Sciences Genespring References references bioinformatics stub Category Standards organizations Category Microarrays ... more details
Orphan date November 2006 Methylation specific oligonucleotide microarray was developed as a technique to map methylation changes in DNA in cancer . This technique was developed by Professor Tim Hui Ming Huang and was published in journal Genome Research on 2002 Gitan et al., 2002 . The method utilizes bisulfite modified DNA that is used as templates for PCR amplification , which is subsequently hybridized to oligonucleotide microarray. External links Commons Methylation specific oligonucleotide microarray http www.epigeneticstation.com Resources, information and specific protocols for DNA Methylation Analysis Category Cancer research Category Microarrays genetics stub medicine stub ... more details
PMHC cellular microarrays are a type of cellular microarray that has been spotted with pMHC complexes peptide MHC class I or peptide MHC class II . These biochips can be used to interrogate immune cells, particularly antigen specific T cell s, from clinical samples for what they are capable of recognizing. They can also be co spotted with other molecules, such as antibodies that capture cytokines, allowing for high throughput functional analysis of the captured T cells. Molecules spotted on a pMHC cellular microarray can be classified as capture molecules, detector molecules and effector molecules. They were developed by Daniel Chen, Yoav Soen, Dan Kraft, Pat Brown and Mark Davis at Stanford University Medical Center . References Chen DS, Davis MM 2006 Molecular and functional analysis using live cell microarrays. Curr Opin Chem Biol 10 28 34 Chen DS, Soen Y, Stuge TB, Lee PP, Weber JS, Brown PO, Davis MM 2005 Marked Differences in Human Melanoma Antigen Specific T Cell Responsiveness after Vaccination Using a Functional Microarray. PLoS Med 2 10 e265 http medicine.plosjournals.org perlserv ?request get document&doi 10.1371 2Fjournal.pmed.0020265 Soen Y., Chen D. S., Kraft D. L., Davis M. M. and Brown P.O. 2003 Detection and characterization of cellular immune responses using peptide MHC microarrays. PLoS Biol. 1 E65 http biology.plosjournals.org perlserv ?request get document&doi 10.1371 journal.pbio.0000065 Chen DS, Davis MM 2005 Cellular immunotherapy Antigen recognition is just the beginning. Springer Semin Immunopathol 27 119 127 Soen Y, Chen DS, Stuge TB, Weber JS, Lee PP, et al. 2004 A novel cellular microarray identifies functional deficiences in tumor specific T cell responses. J Clin Oncol 22 2510 Category Microarrays ... more details
for more gene expression terminology Glossary of gene expression terms MIAME Minimum Information About a Microarray Experiment is a standard created by the FGED Society for reporting microarray experiments ref cite web url http www.mged.org miame title MIAME home page work FGED Society website accessdate 2008 11 23 ref . It is intended to specify all the information necessary to interpret the results of the experiment unambiguously and to potentially reproduce the experiment. While the standard defines the content required for compliant reports, it does not specify the format in which this data should be presented. There are a number of file formats for representing this data, and both public and subscription based repositories for such experiments. References references See also MIAPE Category Minimum Information Standards Category Microarrays bioinformatics stub pl MIAME ... more details
of experimental techniques, including yeast two hybrid screening two hybrid systems, protein fragment complementation assays PCA , affinity purification mass spectrometry , proteinmicroarray s, fluorescence ...Proteinprotein interaction prediction is a field combining bioinformatics and structural biology in an attempt ... proteinprotein interaction s is important for the investigation of intracellular signaling pathways, modelling of protein complex structures and for gaining insights into various biochemical ... in other organisms. In addition, a number of bound protein complexes have been structurally solved ... pairs of protein families with similar patterns of presence or absence across large numbers of species ... imply physical interaction. Prediction of co evolved protein pairs based on similar phylogenetic ... protein in the hypothesized interacting pair. If the matrices are sufficiently similar as measured ... ref Ogmen builds a library of known proteinprotein interfaces from the Protein Data Bank PDB , where ... a known structure i.e. present in the Protein Data Bank PDB . Bayesian network modelling Bayesian ... potential protein interaction is a true positive result. These methods are useful because ... circumstantial evidence that a particular pair of proteins might interact. 3D template based protein complex modelling This method ref Aloy ref Chen ref Fukuhara ref Kittichotirat makes use of known protein complex structures to predict as well as structurally model interactions between query protein ... to search for protein complex structures that are homologous to the query sequences. These known ... sequences. This method has the advantage of not only inferring protein interactions but also suggests ... is limited to a relatively small number of known protein complex structures. Supervised learning problem ... the known protein interactions supervise the estimation of a function that can predict whether an interaction .... . Relationship to docking methods The field of proteinprotein interaction prediction is closely related ... more details
Refimprove date January 2009 A protein isoform is any of several different forms of the same protein . Different forms of a protein may be produced from related genes , or may arise from the same gene by alternative splicing . A large number of isoforms are caused by single nucleotide polymorphisms or SNPs, small genetic differences between alleles of the same gene. These occur at specific individual nucleotide positions within a gene. The discovery of isoforms partly explains the apparently small number of coding regions genes revealed by the human genome project the ability to create categorically different proteins from the same gene increases the diversity of the proteome . Isoforms are readily described and discovered by microarray studies and cDNA libraries. Glycoforms A glycoform is an isoform of a protein that differs only with respect to the number or type of attached glycan . Glycoproteins often consist of a number of different glycoforms, with alterations in the attached saccharide or oligosaccharide . These modifications may result from differences in biosynthesis during the process of glycosylation , or due to the action of glycosidases or glycosyltransferases . Glycoforms may be detected through detailed chemical analysis of separated glycoforms, but more conveniently detected through differential reaction with lectins , as in lectin affinity chromatography and lectin affinity electrophoresis . Typical examples of glycoproteins consisting of glycoforms are the blood proteins as orosomucoid , antitrypsin , and haptoglobin . An unusual glycoform variation is seen in neural cell adhesion molecule neuronal cell adhesion molecule, NCAM involving polysialic acid polysialic acids, PSA . Examples list is best here for now G actin , despite its conserved nature, has ... mesh&list uids 68020033&dopt Full MeSH entry protein isoforms http ghr.nlm.nih.gov glossary isoforms Definitions Isoform DEFAULTSORT Protein Isoform Category Molecular biology Category Proteins protein ... more details
Protein database may refer to Any protein structure database Any protein sequence database Exact names Protein NIH Protein database of the National Institute of Health Protein Database of Bio Synthesis, Inc. disambig ... more details
Protein supplement may refer to Dietary supplement s Bodybuilding supplement Protein Bodybuilding supplement Protein bar See also Protein Disambig ... more details
forms a proteinprotein interaction with the ribonuclease protein. The contacts between the two proteins are shown as coloured patches. 250px Proteinprotein interactions occur when two or more protein s bind together, often to carry out their function biology biological function . Many ... molecular machines that are built from a large number of protein components organised by their proteinprotein interactions. Protein interactions have been studied from the perspectives of biochemistry ... or genetic epigenetic graph theory networks . Indeed, proteinprotein interactions are at the core ... cell are mediated to the inside of that cell by proteinprotein interactions of the signaling molecules ... and in many diseases e.g. cancer s . Proteins might interact for a long time to form part of a protein complex , a protein may be carrying another protein for example, from cytoplasm to cell nucleus nucleus or vice versa in the case of the nuclear pore importins , or a protein may interact briefly with another protein just to modify it for example, a protein kinase will add a phosphate to a target protein . This modification of proteins can itself change proteinprotein interactions. For example ..., proteinprotein interactions are of central importance for virtually every process in a living cell ... for new therapeutic approaches. Methods to investigate proteinprotein interactions Main Methods to investigate proteinprotein interactions As proteinprotein interactions are so important there are a multitude ... such as yeast two hybrid screening can be used to detect novel proteinprotein interactions. There are also ... methods. ref Mashaghi A et al. Investigation of a protein complex network EUROPEAN PHYSICAL JOURNAL ... of the human interactome where each point represents a protein and each blue line between them is an interaction. 200px Visualization of proteinprotein interaction networks is a popular application of scientific visualization techniques. Although protein interaction diagrams are common ... more details
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