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Protein K (gene expression)
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Encyclopedia results for Protein K (gene expression)

Protein K (gene expression)





Encyclopedia results for Protein K (gene expression)

  1. Protein K (gene expression)

    About the nucleic acid binding protein in eukaryotes the bacterial porin Protein K porin Protein K is a human protein found in the cell nucleus that binds to pre messenger RNA mRNA as a component of heterogeneous ribonucleoprotein particle s. The simian homology biology homolog is known as protein H16 . Both proteins bind to single stranded DNA as well as to RNA and can stimulate the activity of RNA polymerase II , the protein responsible for most transcription genetics gene transcription . The relative affinities of the proteins for DNA and RNA vary with solution conditions and are inversely correlated, so that conditions promoting strong DNA binding result in weak RNA binding. ref name Gaillard Gaillard C, Cabannes E, Strauss F. 1994 . Identity of the RNA binding protein K of hnRNP particles with protein H16, a sequence specific single strand DNA binding protein. Nucleic Acids Res 22 20 4183 4186. ref RNA binding protein domains in other proteins that are similar to the RNA binding domain of protein K are called K homology or KH domains. Protein K has been the subject of study related to colorectal cancer , in which an RNA editing event inducing the gene expression expression of an isoform containing a point mutation was found to be specific to cancerous cells. ref name Klimek Klimek Tomczak K, Mikula M, Dzwonek A, Paziewska A, Karczmarski J, Hennig E, Bujnicki JM, Bragoszewski P, Denisenko O, Bomsztyk K, Ostrowski J. 2006 . Editing of hnRNP K protein mRNA in colorectal adenocarcinoma and surrounding mucosa. Br J Cancer 94 4 586 92. ref Human proteins containing KH domain AKAP1 ANKHD1 ANKRD17 ASCC1 BICC1 DDX43 DDX53 DPPA5 FMR1 FUBP1 FUBP3 FXR1 FXR2 HDLBP HNRPK IGF2BP1 IGF2BP2 IGF2BP3 KHDRBS1 KHDRBS2 KHDRBS3 KHSRP KRR1 MEX3A MEX3B MEX3C MEX3D NOVA1 NOVA2 PCBP1 PCBP2 PCBP3 PCBP4 PNO1 PNPT1 QKI SF1 gene SF1 TDRKH References references Category Proteins protein stub ...   more details



  1. Protein K

    Protein K may refer to Protein K porin , a porin expressed in pathogenic strains of E. coli Protein K gene expression , a DNA and RNA binding protein expressed in the nucleus of eukaryotes disambig ...   more details



  1. Protein K (porin)

    About the bacterial porin the nucleic acid binding protein in eukaryotes Protein K gene expression Protein K is a porin expressed in some pathogenic strains of E. coli bacteria . It has a molecular weight of about 40 kilodalton kDa and is localized to the Bacterial outer membrane outer membrane , through which it allows both inorganic and Organic chemistry organic ion s to pass. The strains in which protein K has been identified are encapsulated , or surrounded by a poly sialic acid capsule that renders them more resistant to phagocytosis by cells in the immune system . References Whitfield C, Hancock RE, Costerson JW. 1983 . Outer membrane protein K of Escherichia coli purification and pore forming properties in lipid bilayer membranes. J Bacteriol 156 2 873 879 Sutcliffe J, Blumenthal R, Walter A, Foulds J. 1983 . Escherichia coli outer membrane protein K is a porin. J Bacteriol 156 2 867 872 Bliss JM, Solver RP. 1996 . Coating the surface a model for expression of capsular polysialic acid in Escherichia coli K1. Mol Microbiol 21 221. Category Outer membrane proteins protein stub ...   more details



  1. Protein expression (biotechnology)

    Protein expression is a subcomponent of gene expression . It consists of the stages after DNA has been ... chains, which are ultimately folded into proteins . Citation needed date April 2011 Protein expression ... of one or more proteins in a particular cell or tissue. Protein expression systems are very widely ... medical applications for expression systems, notably the production of human insulin to treat diabetes . Protein expression systems are used to produce certain proteins in biotechnology and industry, and more recently to produce sets combinatorial series of protein that are screened for drug discovery purpose. Expression systems Commonly used protein expression systems include those derived from bacteria , ref name pmid10508629 cite journal author Baneyx F title Recombinant protein expression ..., Cereghino JL, Shi J, Higgins DR title Recombinant protein expression in Pichia pastoris journal Mol ... Baculovirus as versatile vectors for protein expression in insect and mammalian cells journal Nat. Biotechnol ... serum free medium in suspension a rapid mammalian protein expression system journal Protein Expr. Purif ... and stable protein expression in mammalian cells journal Anal. Biochem. volume 380 issue 1 pages ... epigenetic features of plants, insects and mammalians systems, other protein expression ... hosts for artificial gene expression. E. coli is one of the most widely used expression hosts, and DNA ... cost of cell free systems cell based systems are more widely used. See also Gene expression References Reflist 2 Further reading cite book title Protein Expression A Practical Approach author Higgins ... 304 cite book title Protein Expression Technologies Current Status and Future Trends author Baneyx F ... proteins and enzymes many of which are from expression systems particularly DNA polymerase for PCR ... title Protein production in Saccharomyces cerevisiae for systems biology studies journal Methods Enzymol ... url ref ref name pmid18541133 cite journal author Lackner A, Genta K, Koppensteiner H, Herbacek ...   more details



  1. Gene expression

    translation , and post translational modification of a protein. Regulation of gene expression ... of any organism. Any step of gene expression may be modulated, from the DNA RNA transcription step to post translational modification of a protein. The stability of the final gene product, whether it is RNA or protein, also contributes to the expression level of the gene an unstable product ... s in order to kill a cell by overriding its normal gene expression control. Protein synthesis ... gene expression can Identify viral infection of a cell viral protein expression Determine an individual ...about vocabulary Glossary of gene expression terms a non technical introduction to the topic Introduction .... Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product . These products are often protein s, but in non protein coding genes such as rRNA ... is a functional RNA . The process of gene expression is used by all known life eukaryotes including ... the macromolecule macromolecular machinery for life. Several steps in the gene expression process ..., and amount of gene expression can have a profound effect on the functions actions of the gene in a cell or in a multicellular organism. In genetics , gene expression is the most fundamental level ... by gene expression, and the properties of the expression give rise to the organism s phenotype. Mechanism ... into different proteins, splicing extends the complexity of eukaryotic gene expression. Extensive RNA ... gene expression control author Schwanh usser B, Busse D, Dittmar G, Schuchhardt J, Wolf J, Chen ... 17786931 pmc 2613191 doi 10.1002 jcb.21513 ref Regulation of gene expression File Tortie flame.jpg ... . main Regulation of gene expression Regulation of gene expression refers to the control of the amount and timing of appearance of the functional product of a gene. Control of expression is vital ... simple examples of where gene expression is important are Control of insulin expression so it gives ...   more details



  1. XTP3-transactivated gene A protein

    Orphan date February 2009 PBB geneid 79077 dCTP pyrophosphatase 1 is an enzyme that in humans is encoded by the DCTPP1 gene . ref name pmid15740738 cite journal author Moroz OV, Murzin AG, Makarova KS, Koonin EV, Wilson KS, Galperin MY title Dimeric dUTPases, HisE, and MazG belong to a new superfamily of all alpha NTP pyrophosphohydrolases with potential house cleaning functions journal J Mol Biol volume 347 issue 2 pages 243 55 year 2005 month Mar pmid 15740738 pmc doi 10.1016 j.jmb.2005.01.030 ref ref name entrez cite web title Entrez Gene XTP3TPA XTP3 transactivated protein A url http www.ncbi.nlm.nih.gov sites entrez?Db gene&Cmd ShowDetailView&TermToSearch 79077 accessdate ref The PBB Summary template is automatically maintained by Protein Box Bot. See Template PBB Controls to Stop updates. PBB Summary section title summary text References reflist Further reading refbegin 2 PBB Further reading citations cite journal author Strausberg RL, Feingold EA, Grouse LH, et al. title Generation and initial analysis of more than 15,000 full length human and mouse cDNA sequences. journal Proc. Natl. Acad. Sci. U.S.A. volume 99 issue 26 pages 16899 903 year 2003 pmid 12477932 doi 10.1073 pnas.242603899 pmc 139241 cite journal author Stelzl U, Worm U, Lalowski M, et al. title A human protein protein interaction network a resource for annotating the proteome. journal Cell volume 122 issue 6 pages 957 68 year 2005 pmid 16169070 doi 10.1016 j.cell.2005.08.029 cite journal author Rual JF, Venkatesan K, Hao T, et al. title Towards a proteome scale map of the human protein protein interaction network. journal Nature volume 437 issue 7062 pages 1173 8 year 2005 pmid 16189514 doi 10.1038 nature04209 refend PDB Gallery geneid 79077 gene 16 stub The PBB Controls template provides controls for Protein Box Bot, please see Template PBB Controls for details. PBB Controls update page yes require manual inspection no update protein box yes update summary yes update citations yes ...   more details



  1. Haemolysin expression modulating protein family

    pmc 139531 doi url ref YmoA modulates the Gene expression expression of various virulence factors ...Infobox protein family Symbol HHA Name HHA image PDB 1jw2 EBI.jpg width caption solution structure of hemolysin expression modulating protein hha from escherichia coli. ontario centre for structural proteomics target ec0308 1 72 northeast structural genomics target et88 Pfam PF05321 Pfam clan InterPro IPR007985 SMART PROSITE MEROPS SCOP 1ir6 TCDB OPM family OPM protein CAZy CDD In molecular biology, the haemolysin expression modulating protein family is a protein family family of proteins . This family consists of haemolysin gene expression expression modulating protein Hha from Escherichia coli and its Enterobacteria enterobacterial homologues, such as YmoA from Yersinia enterocolitica , and RmoA encoded on the R100 plasmid . These protein proteins act as modulators of bacteria bacterial gene expression . Members of this family act in conjunction with members of the H NS family, participating in the thermoregulation of different virulence factor s and in plasmid transfer. ref name pmid11890540 cite journal author Madrid C, Nieto JM, Juarez A title Role of the Hha YmoA family of proteins in the thermoregulation of the expression of virulence factors journal Int. J. Med. Microbiol. volume 291 issue 6 7 pages 425 32 year 2002 month February pmid 11890540 doi url ref Hha, along with the chromatin associated protein H NS, is involved in the regulation of expression genetics expression ... protein protein interaction between members of the enterobacterial Hha YmoA and H NS families ... gene of plasmid R100 1 journal FEMS Microbiol. Lett. volume 169 issue 1 pages 59 66 year 1998 month December pmid 9851035 doi url ref The HHA protein family family of proteins display striking similarity to the oligomerisation protein domain domain of the H NS proteins. References reflist InterPro content IPR007985 Category Protein families ...   more details



  1. Glossary of gene expression terms

    during expression. A form of gene action, epistasis can either be additive or multiplicative in its effects on specific phenotypic traits. Gene expression the transcription of DNA into messenger RNA by RNA polymerase . The messenger RNA is then translated into protein by the ribosome . In gene expression ... decreasing the rate of gene expression. Repressor a DNA binding protein that regulates the expression ...See also gene expression , List of glossaries List of Glossaries , List of glossaries Natural sciences ... of the gene expression level of a gene or genes prior to a perturbation in an experiment, as in a negative ... . Conditional gene expression is controlled inducible expression of transgene either in vitro or in vivo . Constitutive gene or constitutive expression a gene that is transcribed continually ... coregulator s are proteins that work with transcription factor s to regulate gene expression ... of gene expression clustering via mutual information distance measure journal BMC Bioinformatics ... the rate of gene expression. Down regulated describes a gene which has been observed to have lower ... or R reporter G Gene expression omnibus or GEO a National Center for Biotechnology Information database for gene expression Gene knockout is a genetic technique in which an organism is engineered ... theory graph that represents the regulatory complexity of gene expression. The vertices nodes are represented ... that with respect to a gene expression assay, hybridization is a step in the experimental paradigm ... I Inducible gene is a gene whose expression is either responsive to environmental change or dependent ... and Gene Expression , a group that aims to provide a standard for the representation of DNA microarray gene expression data that would facilitate the exchange of microarray information between ... of gene expression data It stands for Minimum information about a microarray experiment . ref ... to make a single measurement in a gene expression experiment. See R reporter , probe set . Probe set ...   more details



  1. Spatiotemporal gene expression

    crystalline promoter drives expression of the green fluorescent protein reporter gene exclusively in the eye ...Image Gene expression patterns.png thumb 250px Gene expression patterns are regulated both spatially and temporally in embryos of Drosophila melanogaster . Spatiotemporal gene expression is the gene expression activation of gene s within specific biological tissue tissues of an organism at specific times during developmental biology development . Gene activation patterns vary widely in complexity. Some ... that cell, if gene expression was uniform spatially and temporally, there could be at most one kind of cell. Consider the gene wingless, a member of the wnt family of genes. In the early embryonic development ... pattern of wingless gene expression is determined by a genetic regulatory network network of regulatory .... What causes spatial and temporal differences in the expression of a single gene? Because current expression patterns depend strictly on previous expression patterns, there is a regressive problem of explaining what caused the first differences in gene expression. The process by which uniform gene expression becomes spatially and temporally differential is known as symmetry breaking . For example ... is expressed. The expression distribution of the reporter gene can be determined by visualizing it. For example, the reporter gene green fluorescent protein can be visualized by stimulating ... visualizes the protein generated by the gene, if the protein product diffuses between cells, or has ... trap screening reveals the diversity of spatiotemporal gene expression patterns possible in an organism ... frnt page.html Browse spatiotemporal gene expression patterns organized by human chromosome number https www.genevestigator.com Spatiotemporal gene expression in Genevestigator http expression.gnf.org ... hybridization Category Molecular genetics Category Gene expression ar ... and model, with expression fluctuating wildly from minute to minute or from cell to cell. Spatiotemporal ...   more details



  1. Gene expression profiling

    Image Heatmap.png right thumb 200px Heat map s of gene expression values show how experimental conditions ... of molecular biology , gene expression profiling is the measurement of the activity the gene expression ... techniques, like serial analysis of gene expression SAGE, SuperSAGE are also used for gene expression ... 15123278 doi 10.1016 j.chembiol.2004.02.003 ref Gene expression profiling may become an important ..., so a given gene serves as the basis for many possible versions of a particular protein. In any case ... much messenger RNA is made from each gene, gene expression profiling provides the most global picture ... Chen JJ title Key aspects of analyzing microarray gene expression data journal Pharmacogenomics volume ... problem. The relatively short length of gene lists published from expression profiling experiments ... or base pairing of complementary nucleic acid sequences, and both are used in gene expression profiling ... of qPCR, it takes about the same time to measure the gene expression of a few dozen genes via qPCR ... M, Shedden K, Hankenson KD, Woolf JP title GAGE generally applicable gene set enrichment for pathway ... protein each gene product makes and what function this protein performs. Gene annotation provides ... a changing understanding of protein function. Use of standardized gene nomenclature helps address ... MG title Analysis of gene expression profiles in HeLa cells in response to overexpression or siRNA ... gene creates a protein to make an enzyme that activates a protein to turn on a second gene ... whose combined expression pattern is uniquely characteristic to a given condition constitutes the gene ... to see whether any previously defined gene sets exhibited unusual behavior in the current expression ... profiling experiments. See also Gene expression profiling in cancer References Reflist 2 DEFAULTSORT Gene Expression Profiling Category Molecular genetics Category Microarrays de Genexpressionsanalyse es Perfil de expresi n g nica it Gene expression profiling no Genuttrykksprofilering zh ...   more details



  1. Regulation of gene expression

    protein coding genes. Any step of the gene expression gene s expression may be modulated, from DNA RNA transcription genetics transcription to the post translational modification of a protein. Gene regulation ... of a protein. The following is a list of stages where gene expression is regulated, the most ... in decreased gene and corresponding protein expression. Up regulation occurs, for example, when ...Gene modulation redirects here. For information on therapeutic regulation of gene expression, see therapeutic gene modulation . For vocabulary, see Glossary of gene expression terms File Gene expression control.png thumb Diagram showing at which stages in the DNA mRNA protein pathway expression can be controlled Regulation of gene expression or gene regulation includes the processes that cell biology ... of different cell types that possess different gene expression profiles though they all possess the same genome sequence. Regulated stages of gene expression Any step of gene expression may ... may up or down regulate the expression of gene. Certain of these modifications that regulate gene expression are inheritable and are referred to as epigenetic regulation . Chemical DNA ... . Such modifications are considered to be responsible for more or less permanent changes in gene expression ... for DNA to be packed more densely, lowering gene expression. citation needed date January 2011 Regulation ... s progress along the strand, thus impeding the expression of the gene. General transcription factor ... and a particular promoter biology promoter , encouraging the expression of the gene. Activators do ... their expression. Examples of gene regulation Enzyme induction and inhibition Enzyme induction is a process ... is an interesting example of how gene expression can be regulated. Viruses, despite having only a few genes, possess mechanisms to regulate their gene expression, typically into an early and late ... that allows for gene expression. The molecule is said to induce expression . The manner by which ...   more details



  1. Gene E. K. Pratter

    Gene Ellen Kreyche Pratter born 1949 in Chicago, Illinois is a Federal judge judge on the United States District Court for the Eastern District of Pennsylvania and former nominee to the United States Court of Appeals for the Third Circuit . Background Judge Pratter received her bachelor s degree from Stanford University in 1971, and her Juris Doctor from University of Pennsylvania Law School in 1975. She was appointed to the court by President George W. Bush on November 3, 2003, to a seat on the United States District Court for the Eastern District of Pennsylvania vacated by William H. Yohn . She was confirmed by the United States Senate Senate on June 15, 2004, and received her commission on June 16, 2004. Prior to her appointment to the bench, she served as general counsel to the law firm of Duane Morris Duane Morris LLP . ref http www.duanemorris.com site past and present.html Duane Morris firm history ref Third Circuit nomination under Bush On November 15, 2007, she was nominated by President George W. Bush to a seat on the United States Court of Appeals for the Third Circuit vacated by Judge Franklin Stuart Van Antwerpen , who assumed senior status in 2006. ref http www.uscourts.gov cfapps webnovada CF FB 301 index.cfm?fuseaction Reports.ViewVacancies Current federal judicial nominees pending ref In February 2008, the liberal group Leadership Conference on Civil Rights sent a letter to the Democrat controlled Senate Judiciary Committee , then chaired by Senator Patrick Leahy , D VT. The group claimed that Pratter had as a district court judge, exhibited a willingness to prematurely dismiss the claims of civil rights plaintiffs and to inhibit advocacy by their counsel, thus denying these plaintiffs access to a full and fair legal process. ref http saveourcourts.civilrights.org ..., Gene E.K. ALTERNATIVE NAMES SHORT DESCRIPTION American judge DATE OF BIRTH 1949 PLACE OF BIRTH DATE OF DEATH PLACE OF DEATH DEFAULTSORT Pratter, Gene E.K. Category 1949 births Category Living people ...   more details



  1. MicroArray and Gene Expression

    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



  1. Mouse gene expression database

    Orphan date May 2011 infobox biodatabase title The mouse Gene Expression Database logo File Database.png description The mouse Gene Expression Database scope organism Mus musculus center The Jackson Laboratory laboratory author pmid Finger & al. 2011 ref name pmid21062809 released 2010 standard format url http www.informatics.jax.org expression.shtml download webservice sql sparql webapp standalone license versioning frequency curation bookmark version The Gene Expression Database is a community resource of mouse developmental expression information. ref name pmid21062809 cite journal quotes yes last Finger first Jacqueline H authorlink coauthors Smith Constance M, Hayamizu Terry F, McCright Ingeborg J, Eppig Janan T, Kadin James A, Richardson Joel E, Ringwald Martin year 2011 month Jan title The mouse Gene Expression Database GXD 2011 update journal Nucleic Acids Res. volume 39 issue Database issue pages D835 41 publisher location England issn pmid 21062809 doi 10.1093 nar gkq1132 bibcode oclc id url pmc 3013713 language eng format accessdate laysummary laysource laydate quote ref See also Mus musculus Gene expression Mouse genome database References references External links http www.informatics.jax.org expression.shtml http www.informatics.jax.org expression.shtml Category Biological databases Category Mice Category Gene expression Biodatabase stub ...   more details



  1. Gene expression programming

    Gene Expression Programming GEP is an evolutionary algorithm that evolves populations of computer program s in order to solve a user defined problem. GEP has similarities, but is distinct from, the evolutionary computational method of genetic programming . In genetic programming the individuals comprising a population are typically symbolic s expression expression trees however, the individuals comprising a population of GEP are encoded as linear chromosome s, which are then translated into s expression expression trees . The important difference is that the recombination operators of genetic programming operate directly on the tree structure e.g. swapping sub trees , whereas the recombination operators of gene expression programming operate directly on the linear encoding i.e. before it is translated into a tree . As such, after recombination, the modified portions of the resulting expression trees often bear little semblance to their direct ancestors. The expression trees are themselves computer programs evolved to solve a particular problem and are selected according to their performance fitness in solving the problem at hand. After repeated iteration, populations of such computer programs will ideally discover new traits and become better adapted to a particular selection environment. The desired endpoint of the algorithm is that a good solution has been evolved by the evolutionary process. C ndida Ferreira , the inventor of the technique, claims that GEP significantly surpasses ... title Gene Expression programming mathematical modeling by an artificial intelligence publisher Springer ... Ferreira first C. title Gene Expression Programming Mathematical Modeling by an Artificial Intelligence publisher Angra do Heroismo location Portugal year 2002 isbn 9729589054 url http www.gene expression programming.com GepBook Introduction.htm References http www.gene expression programming.com ... organization of GEP chromosomes. For further details of GEP see the http www.gene expression ...   more details



  1. Gene expression profiling in cancer

    of genes simultaneously. In the context of cancer, gene expression profiling has been used to more accurately classify tumors. The information derived from gene expression profiling often has an impact ... a common profile of gene expression. Gene expression profiling Gene expression profiling is a technique ... techniques such as serial analysis of gene expression SAGE . Current cancer research makes use ... information about the expression of the particular gene corresponding to the spotted cDNA sequence ... Of note, similar gene expression patterns associated with metastatic behaviour of breast cancer tumor ... canine mammary carcinomas can be identified by a gene expression profile that partly overlaps with human ... doi 10.1016 j.tvjl.2010.10.018 ref Presented below are ways that gene expression profiling has been ... as mRNAs at any given time. The unique pattern of gene expression for a given cell or tissue ... gene expression information allowing for the generation of a molecular signature, each unique ... journal doi 10.1038 73432 author Ross D.T. et al. year 2000 title Systematic variation in gene expression ... lines based on the similarity by which the pattern of gene expression varied. In this study by Ross ... of tumor type based on gene expression. Tumor subclass A more powerful result of gene expression profiling ... A.A. et al. year 2000 title Distinct types of diffuse large B cell lymphoma identified by gene expression ... by Perou, C.M. characterized gene expression patterns across 8,102 genes for 65 biopsies obtained ... pages 747 752 pmid 10963602 ref The goal of the study was to identify patterns of gene expression .... et al. year 2001 title Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical ... the ER positive tumors into two distinct groups and found that tumor classification based on gene expression ... based on patterns of luminal specific gene expression with different outcomes. The authors further ... gene expression profiles associated with prognosis. It is agreed upon that patients with tumors exhibiting ...   more details



  1. Cap analysis gene expression

    Cap analysis gene expression CAGE is a technique used in molecular biology to produce a snapshot of the 5 end of the messenger RNA population in a biological sample. The small fragments usually 20 21 nucleotide s long from the very beginnings of mRNAs 5 ends of 5 cap capped transcripts are extracted, reverse transcription reverse transcribed to DNA, PCR amplified and DNA sequencing sequenced . CAGE was first published by Hayashizaki and co workers in 2003. ref name Shiraki 2003 cite journal journal Proc Natl Acad Sci U S A. date 2003 12 23 volume 100 issue 26 pages 15776 81 pmid 14663149 doi 10.1073 pnas.2136655100 url http www.pnas.org content 100 26 15776 title Cap analysis gene expression for high throughput analysis of transcriptional starting point and identification of promoter usage pmc 307644 ref CAGE has been extensively used with in the FANTOM research projects. Analysis The output of CAGE is a set of short nucleotide sequences often called tags with their observed counts. Using a reference genome a researcher can usually determine, with some confidence, the original mRNA and therefore which gene the tag was extracted from. Copy numbers of CAGE tags provide an easy way of digital quantification of the RNA transcript abundances in biological samples. Unlike a similar technique Serial Analysis of Gene Expression SAGE, superSAGE in which tags come from other parts of transcripts, CAGE is primarily used to locate an exact transcription genetics transcription start sites in the genome. This knowledge in turn allows a researcher to investigate promoter biology Promoter elements promoter structure necessary for gene expression. However, the CAGE protocol has a known bias with a nonspecific G at the most 5 end of the CAGE tags, which is attributed to the template free ... homepage at the RIKEN Omics Science Center. DEFAULTSORT Cap Analysis Gene Expression Category Molecular biology Category Gene expression ...   more details



  1. Serial analysis of gene expression

    Serial analysis of gene expression SAGE is a technique used by molecular biologist s to produce a snapshot of the messenger RNA population in a sample of interest in the form of small tags that correspond to fragments of those transcripts. The original technique was developed by Dr. Victor Velculescu at the Oncology Center of Johns Hopkins University and published in 1995. ref name SAGE cite journal journal Science volume 270 issue 5235 pages 484&ndash 7 year 1995 author Velculescu VE, Zhang L, Vogelstein B, Kinzler KW. title Serial analysis of gene expression url http www.sciencemag.org cgi pmidlookup?view long&pmid 7570003 pmid 7570003 doi 10.1126 science.270.5235.484 ref Several variants have been developed since, most notably a more robust version, LongSAGE, ref name Saha cite journal journal Nat Biotechnol volume 20 issue 5 pages 508&ndash 12 year 2002 author Saha S et al. title Using ... technique at the Science Creative Quarterly DEFAULTSORT Serial Analysis Of Gene Expression Category ... method for gene discovery and transcriptome analysis url http www.plantphysiol.org cgi pmidlookup ... of a source gene. Overview Briefly, SAGE experiments proceed as follows Isolate the mRNA of an input ..., the original mRNA and therefore which gene the tag was extracted from. Statistical methods can be applied to tag and count lists from different samples in order to determine which gene s are more ... a corresponding tumour to determine which gene s tend to be more or less active. Applications Although ... to be known a priori , so genes or gene variants which are not known can be discovered. DNA microarray .... Quantifying gene expressions is more exact in SAGE because it involves directly counting the number ... 22nt segments of RNA which have been found to play a crucial role in gene regulation. One of the most ... then be sequenced to identify the miRNA present, as well as analysing expression levels of a given ... fr Analyse en s rie de l expression des g nes ja SAGE ...   more details



  1. Protein A

    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. ref name pmid10754313 cite journal author Idusogie EE, Presta LG, Gazzano Santoro H, Totpal K, Wong ... 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 56 Atomic mass unit kDa MSCRAMM surface protein originally found in the cell wall of the bacterium Staphylococcus aureus . It is encoded by the spa gene and its regulation ... 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 IgM ... or IgD , nor will it react to mouse IgM, IgA or IgE. The capacity of protein A to bind antibodies with such high .... 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 are all ... 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 ...   more details



  1. Protein S

    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 binding protein C4BP . In humans, protein S is encoded by the PROS1 gene . ref name pmid2944113 cite journal author Lundwall A, Dackowski W, Cohen E, Shaffer M, Mahr A, Dahlb ck B, Stenflo J, Wydro R title Isolation and sequence of the cDNA for human protein S, a regulator ... doi cite journal author Maillard C, Berruyer M, Serre CM, et al. title Protein S, a vitamin K dependent ... PH, van der Logt CP, Bertina RM title Intron exon organization of the active human protein S gene ... Primary structure of bovine vitamin K dependent protein S journal Proc. Natl. Acad. Sci. U.S.A. volume ... author Watkins PC, Eddy R, Fukushima Y, et al. title The gene for protein S maps near the centromere ... cite journal author Long GL, Marshall A, Gardner JC, Naylor SL title Genes for human vitamin K ... url ref In 1979, researchers in Seattle , Washington first discovered protein S and arbitrarily ... X Stuart factor , and protein S journal Biochemistry volume 16 issue 4 pages 698 706 year 1977 ... RG, Davie EW title Characterization of protein S, a gamma carboxyglutamic acid containing protein ... March pmid 420821 doi 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 .... ref name pmid18695379 cite journal author Castoldi E, Hackeng TM title Regulation of coagulation by protein ... 18695379 doi 10.1097 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 ... such as macrophages . 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 ...   more details



  1. Protein

    sequence of a gene genetic code encodes the amino acid sequence of a protein. Proteins are assembled from amino acids using information encoded in gene s. Each protein has its own unique amino acid sequence that is specified by the nucleotide sequence of the gene encoding this protein. The genetic ... in the protein. ref name Standley2008 Many more gene sequences are known than protein structures ... linked to a reporter gene reporter such as green fluorescent protein GFP . ref name Stepanenko2008 ... width 10em column width 10em Cdx protein family Expression cloning Intein List of proteins List of recombinant ... cite journal author Plewczy ski D, Ginalski K title The interactome predicting the protein ...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 ... folded into a globular protein globular or fibrous protein fibrous form, facilitating a biological ... . The peptide sequence sequence of amino acids in a protein is defined by the DNA sequence sequence of a gene , which is encoded in the genetic code . In general, the genetic code specifies 20 standard ... archaea pyrrolysine . Shortly after or even during synthesis, the residues in a protein are often ... to form stable protein complex es. Like other biological macromolecules such as polysaccharide ... acid s from food. Through the process of digestion , animals break down ingested protein into free amino acids that are then used in metabolism. Proteins may be protein purification purified from ... made possible a number of methods to facilitate purification. Methods commonly used to study protein ... 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



  1. Structural Biochemistry/ Kiss Gene Expression

    to demonstrate that the Kiss 1 gene expression is sexually differentiated in rats Analyzing the sex ... of Kiss 1 mRNA in the AVPV, however there appeared to be no difference in the Kiss 1 expression in the ARC between male and female rats. Their research suggests that sex differences in kiss 1 gene expression in the AVPV region of the brain might play a role in regulating the GnRH LH levels of male ... strands of interest. Examining the effects of sex differences in Kiss I mRNA expression ... 1 mRNA expression between male and female rats during their neonatal period time period between ... Roa, Alisa C. Byquist, Angelena Crown, Don K. Clifton, Gloria E. Hoffman, Robert A. Steiner and Manuel ...   more details



  1. Wellcome Trust Centre for Gene Regulation and Expression

    The Wellcome Trust Centre for Gene Regulation and Expression , located within the University of Dundee , pioneers new approaches in the field of gene expression and chromosome biology. Previously part of the Dundee Biocentre and receiving significant Wellcome Trust funding from 1995 onwards, it was awarded Wellcome Trust Centre status in 2008. Professor Angus Lamond is the Centre s Director. The Centre aims to enhance our understanding of how genes are regulated at both the single cell and whole organism level. Researchers use a wide range of advanced techniques, including live cell fluorescent imaging disambiguation needed date November 2011 and mass spectrometry based proteomics , to explore the functions of key proteins and molecular mechanisms in cell biology. Research and discoveries Live cell imaging and proteomic studies have allowed researchers at the Centre to gain fresh understanding of protein function and cell behaviour. The Centre is studying many aspects of the cell cycle , including the way in which chromosomes replicate and separate during cell division and how DNA damage is detected. Failure of these events can lead to major faults within a genome , potentially leading to the rise of cancerous cells. The Centre is also investigating how DNA is tightly wound and compacted so that it can fit into the nuclei of eukaryotic cells, as well as the protein DNA complexes that are involved in this packaging. The controlled unravelling of DNA is an important step in the regulation of gene function. Researchers Researchers at the Centre include Professor Angus Lamond a Wellcome Principal Research Fellow, studies the composition and function of organelles and multiprotein complexes ref cite journal pages 1153 9 doi 10.1002 pmic.201000548 title Mass spectrometry based ... Wellcome Trust Centre for Gene Regulation and Expression website http www.wellcome.ac.uk ... Kingdom Category Gene expression Category University of Dundee ...   more details



  1. Critical Reviews in Eukaryotic Gene Expression

    Italic title Critical Reviews in Eukaryotic Gene Expression ISSN 1045 4403 is a quarterly scientific journal published by Begell House publishing reviews on topics related to gene regulation , organization, and structure within contexts of biological control and diagnosis treatment of disease. According to the Journal Citation Reports , its 2009 impact factor is 2.949. The Editor in chief editors in chief are Gary S. Stein , Janet L. Stein , and Jane B. Lian . External links Official http www.begellhouse.com journals 6dbf508d3b17c437.html Category Publications established in 1991 Category English language journals Category Genetics journals Category Quarterly journals Category Begell House academic journals ...   more details



  1. Repression of heat shock gene expression (ROSE) element

    Infobox rfam Name Repression of heat shock gene expression ROSE element image RF00435.jpg width caption Predicted secondary structure and sequence conservation of ROSE Symbol ROSE AltSymbols Rfam RF00435 miRBase miRBase family RNA type Cis regulatory element Cis reg thermoregulator Tax domain Bacteria GO SO SO 0000204 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData NOTOC Image PDB 2gio EBI.png thumb 200px left A representation of the 3D structure of the microROSE RNA. This derived from a solution NMR structure of the microROSE element. ref name pmid16710302 cite journal doi 10.1038 sj.emboj.7601128 author Chowdhury S, Maris C, Allain FH, Narberhaus F title Molecular basis for temperature sensing by an RNA thermometer journal EMBO J volume 25 issue 11 pages 2487 97 year 2006 pmid 16710302 pmc 1478195 ref The repression of heat shock gene expression ROSE element is an cis regulatory element RNA element found in the 5 UTR of some heat shock protein s mRNA s. The ROSE element is an RNA thermometer that negatively regulates heat shock gene expression . The secondary structure is thought to be altered by temperature, thus it is an RNA thermometer. This structure blocks access to the Shine Dalgarno sequence ribosome binding site at normal temperatures. During heat shock however, the structure changes freeing the ribosome binding site and allowing expression to occur. ref cite journal last Nocker first A coauthors Hausherr T, Balsiger S, Krstulovic NP, Hennecke H, Narberhaus F year 2001 title A mRNA based thermosensor controls expression of rhizobial heat shock genes journal Nucleic Acids Res volume 29 pages 4800&ndash 4807 pmid 11726689 doi 10.1093 nar 29.23.4800 issue 23 pmc 96696 ref ref cite journal last Balsiger first S coauthors Ragaz ... gene expression ROSE element DEFAULTSORT Repression Of Heat Shock Gene Expression Rose Element Category ... S, Krstulovic NP, Hennecke H, Narberhaus F title A mRNA based thermosensor controls expression ...   more details




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