当前位置： SCI文献检索 > NUCLEIC ACIDS RESEARCH期刊下所有文献 > MAGNET: MicroArray Gene expression and Network Evaluation Toolkit.

MAGNET: MicroArray Gene expression and Network Evaluation Toolkit.

Abstract：

:MicroArray Gene expression and Network Evaluation Toolkit (MAGNET) is a web-based application that provides tools to generate and score both protein-protein interaction networks and coexpression networks. MAGNET integrates user-provided experimental measurements with high-throughput proteomic datasets, generating weighted gene-gene and protein-protein interaction networks. MAGNET allows users to weight edges of protein-protein interaction networks using a logistic regression model integrating tissue-specific gene expression data, sub-cellular localization data, co-clustering of interacting proteins and the number of observations of the interaction. This provides a way to quantitatively measure the plausibility of interactions in protein-protein interaction networks given protein/gene expression measurements. Secondly, MAGNET generates filtered coexpression networks, where genes are represented as nodes, and their correlations are represented with edges. Overall, MAGNET provides researchers with a new framework with which to analyze and generate gene-gene and protein-protein interaction networks, based on both the user's own data and publicly available -omics datasets. The freely available service and documentation can be accessed at http://gurkan.case.edu/software or http://magnet.case.edu.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Linderman GC,Chance MR,Bebek G

doi

10.1093/nar/gks526

subject

Has Abstract

pub_date

2012-07-01 00:00:00

pages

W152-6

issue

Web Server issue

eissn

0305-1048

issn

1362-4962

pii

gks526

journal_volume

40

pub_type

杂志文章

相关文献

NUCLEIC ACIDS RESEARCH文献大全
  • Oncogene activation of HIV-LTR-driven expression via the NF-kappa B binding sites.

    abstract：:The Raf-1 proto-oncogene product is a highly regulated serine/threonine kinase that functions in signal transduction downstream from growth factor receptors and upstream from nuclear proto-oncogene products. Using a transient cotransfection assay we have found that activated Raf-1 activates expression from the HIV-LTR...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/21.22.5229

    authors： Bruder JT,Heidecker G,Tan TH,Weske JC,Derse D,Rapp UR

    更新日期：1993-11-11 00:00:00

  • Structural insights into target DNA recognition by R2R3-MYB transcription factors.

    abstract：:As the largest group of MYB family transcription factors, R2R3-MYB proteins play essential roles during plant growth and development. However, the structural basis underlying how R2R3-MYBs recognize the target DNA remains elusive. Here, we report the crystal structure of Arabidopsis WEREWOLF (WER), an R2R3-MYB protein...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkz1081

    authors： Wang B,Luo Q,Li Y,Yin L,Zhou N,Li X,Gan J,Dong A

    更新日期：2020-01-10 00:00:00

  • Nucleosome positioning as a critical determinant for the DNA cleavage sites of mammalian DNA topoisomerase II in reconstituted simian virus 40 chromatin.

    abstract：:We have assessed the ability of nucleosomes to influence the formation of mammalian topoisomerase II-DNA complexes by mapping the sites of cleavage induced by four unrelated topoisomerase II inhibitors in naked versus nucleosome-reconstituted SV40 DNA. DNA fragments were reconstituted with histone octamers from HeLa c...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/18.15.4553

    authors： Capranico G,Jaxel C,Roberge M,Kohn KW,Pommier Y

    更新日期：1990-08-11 00:00:00

  • Antisense inhibition of gene expression in cells by oligonucleotides incorporating locked nucleic acids: effect of mRNA target sequence and chimera design.

    abstract：:Use of antisense oligonucleotides is a versatile strategy for achieving control of gene expression. Unfortunately, the interpretation of antisense-induced phenotypes is sometimes difficult, and chemical modifications that improve the potency and specificity of antisense action would be useful. The introduction of lock...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkf651

    authors： Braasch DA,Liu Y,Corey DR

    更新日期：2002-12-01 00:00:00

  • The use of oligodeoxynucleotide probes in chaotrope-based hybridization solutions.

    abstract：:Hybridization solutions containing chaotropes may be used to modulate the thermal stability (Tm or Td) of oligodeoxynucleotide (ODN) duplexes or hybrids over a 90 degrees C range. Modulation of Td allows formulation of hybridization solutions that permit ambient temperature hybridization using most combinations of pro...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/19.19.5143

    authors： Van Ness J,Chen L

    更新日期：1991-10-11 00:00:00

  • Assays for DNA double-strand break repair by microhomology-based end-joining repair mechanisms.

    abstract：:DNA double stranded breaks (DSBs) are one of the most deleterious types of DNA lesions. The main pathways responsible for repairing these breaks in eukaryotic cells are homologous recombination (HR) and non-homologous end-joining (NHEJ). However, a third group of still poorly characterized DSB repair pathways, collect...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkv1349

    authors： Kostyrko K,Mermod N

    更新日期：2016-04-07 00:00:00

  • jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1.

    abstract：:Detecting recombinations in the genome sequence of human immunodeficiency virus (HIV-1) is crucial for epidemiological studies and for vaccine development. Herein, we present a web server for subtyping and localization of phylogenetic breakpoints in HIV-1. Our software is based on a jumping profile Hidden Markov Model...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkl255

    authors： Zhang M,Schultz AK,Calef C,Kuiken C,Leitner T,Korber B,Morgenstern B,Stanke M

    更新日期：2006-07-01 00:00:00

  • An ARS element from Drosophila melanogaster telomeres contains the yeast ARS core and bent replication enhancer.

    abstract：:We have sequenced the 0.7-kb-long fragment of Drosophila DNA which ensures the autonomous replication of plasmids in yeast. Deletion mapping has shown the ARS element to consist of at least two domains: the core having the consensus 11-bp sequence TAAATATAAAT and the enhancer which is no more than 90 bp long and is lo...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/16.3.1169

    authors： Gragerov AI,Danilevskaya ON,Didichenko SA,Kaverina EN

    更新日期：1988-02-11 00:00:00

  • Automatic assessment of alignment quality.

    abstract：:Multiple sequence alignments play a central role in the annotation of novel genomes. Given the biological and computational complexity of this task, the automatic generation of high-quality alignments remains challenging. Since multiple alignments are usually employed at the very start of data analysis pipelines, it i...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gki1020

    authors： Lassmann T,Sonnhammer EL

    更新日期：2005-12-16 00:00:00

  • Invadolysin acts genetically via the SAGA complex to modulate chromosome structure.

    abstract：:Identification of components essential to chromosome structure and behaviour remains a vibrant area of study. We have previously shown that invadolysin is essential in Drosophila, with roles in cell division and cell migration. Mitotic chromosomes are hypercondensed in length, but display an aberrant fuzzy appearance....

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkv211

    authors： Rao SG,Janiszewski MM,Duca E,Nelson B,Abhinav K,Panagakou I,Vass S,Heck MM

    更新日期：2015-04-20 00:00:00

  • The pR UV+ plasmid, transfected into mammalian cells, enhances their UV survival.

    abstract：:It has been recently reported that the pR plasmid enhances the UV survival in E.coli c600. In order to test whether this function may be expressed also in mammalian cells, LTA (tk- aprt-) mouse cells were cotransformed with pR plasmid DNA and ptk1 plasmid as selectable marker. Tk+ transformants were analyzed for their...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/11.11.3679

    authors： Elli R,Marcucci L,Bosi R,Oppi C,Battaglia PA,Gigliani F

    更新日期：1983-06-11 00:00:00

  • Developmentally regulated cleavage of tRNAs in the bacterium Streptomyces coelicolor.

    abstract：:The ability to sense and respond to environmental and physiological signals is critical for the survival of the soil-dwelling Gram-positive bacterium Streptomyces coelicolor. Nutrient deprivation triggers the onset of a complex morphological differentiation process that involves the raising of aerial hyphae and format...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkm1096

    authors： Haiser HJ,Karginov FV,Hannon GJ,Elliot MA

    更新日期：2008-02-01 00:00:00

  • Ligation of oligonucleotides to nucleic acids or proteins via disulfide bonds.

    abstract：:We have developed general methods for joining together, via cleavable disulfide bonds, either two unprotected polynucleotides or a polynucleotide and a peptide or protein. To join two oligonucleotides, each is first converted to an adduct in which cystamine is joined to the 5'-terminal phosphate of the oligonucleotide...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/16.9.3671

    authors： Chu BC,Orgel LE

    更新日期：1988-05-11 00:00:00

  • Characterization of L1 retrotransposition with high-throughput dual-luciferase assays.

    abstract：:Recent studies employing genome-wide approaches have provided an unprecedented view of the scope of L1 activities on structural variations in the human genome, and further reinforced the role of L1s as one of the major driving forces behind human genome evolution. The rapid identification of novel L1 elements by these...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkq1076

    authors： Xie Y,Rosser JM,Thompson TL,Boeke JD,An W

    更新日期：2011-02-01 00:00:00

  • Distribution of 5-methylcytosine in the DNA of somatic and germline cells from bovine tissues.

    abstract：:Genomic DNA of calf thymus contains 1.5 times as much 5-methylcytosine as similar sperm DNA, but the major EcoRI repeat fragment from satellite I of thymus contains ten times as much 5-methylcytosine as the corresponding fragment from sperm DNA. Restriction enzyme analyses of the total DNA and the satellite I fragment...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/9.18.4537

    authors： Sturm KS,Taylor JH

    更新日期：1981-09-25 00:00:00

  • A chicken middle-repetitive DNA sequence which shares homology with mammalian ubiquitous repeats.

    abstract：:We have identified and sequenced two members of a chicken middle repetitive DNA sequence family. By reassociation kinetics, members of this family (termed CRl) are estimated to be present in 1500-7000 copies per chicken haploid genome. The first family member sequenced (CRlUla) is located approximately 2 kb upstream f...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/9.20.5383

    authors： Stumph WE,Kristo P,Tsai MJ,O'Malley BW

    更新日期：1981-10-24 00:00:00

  • TropGeneDB, the multi-tropical crop information system updated and extended.

    abstract：:TropGeneDB (http://tropgenedb.cirad.fr) was created to store genetic, molecular and phenotypic data on tropical crop species. The most common data stored in TropGeneDB are molecular markers, quantitative trait loci, genetic and physical maps, genetic diversity, phenotypic diversity studies and information on genetic r...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gks1105

    authors： Hamelin C,Sempere G,Jouffe V,Ruiz M

    更新日期：2013-01-01 00:00:00

  • Discovery of protein-DNA interactions by penalized multivariate regression.

    abstract：:Discovering which regulatory proteins, especially transcription factors (TFs), are active under certain experimental conditions and identifying the corresponding binding motifs is essential for understanding the regulatory circuits that control cellular programs. The experimental methods used for this purpose are labo...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkp554

    authors： Zamdborg L,Ma P

    更新日期：2009-09-01 00:00:00

  • Metal-binding, nucleic acid-binding finger sequences in the CDC16 gene of Saccharomyces cerevisiae.

    abstract：:The CDC16 gene is involved in the process of chromosome segregation in mitosis and a cdc16ts mutant accumulates the predominant microtubule-associated protein at the nonpermissive temperature. We find that the CDC16 gene open reading frame (ORF) is capable of encoding a protein whose calculated molecular weight and pI...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/15.20.8439

    authors： Icho T,Wickner RB

    更新日期：1987-10-26 00:00:00

  • Metal sensing and regulation of adaptive responses to manganese limitation by MtsR is critical for group A streptococcus virulence.

    abstract：:Pathogenic bacteria encounter host-imposed manganese (Mn) limitation during infection. Herein we report that in the human pathogen Streptococcus pyogenes, the adaptive response to Mn limitation is controlled by a DtxR family metalloregulator, MtsR. Genes upregulated by MtsR during Mn limitation include Mn (mtsABC) and...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkz524

    authors： Do H,Makthal N,Chandrangsu P,Olsen RJ,Helmann JD,Musser JM,Kumaraswami M

    更新日期：2019-08-22 00:00:00

  • Studies on transfer ribonucleic acids and related compounds. 8(1). Further studies on aromatic phosphoramidates as a protecting group for phosphomonoesters.

    abstract：:Stability of aromatic phosphoramidates was studied using 2',3'-O-dibenzoyluridine 5'-phosphoramidates and N,2',3'-O-tribenzoylcytidine 5'-phosphate. The effect of dicyclohexylcarbodiimide in this mixture was investigated. Decomposition of the anilidate was slower in the presence of DCC. Substituted anilidates of uridi...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/1.2.223

    authors： Otsuka E,Honda A,Shigyo H,Morioka S,Sugiyama T

    更新日期：1974-02-01 00:00:00

  • Cell cycle-dependent changes in conformation and composition of nucleosomes containing human histone gene sequences.

    abstract：:Unfolding of the nucleosomes in transcriptionally active chromatin uncovers the sulfhydryl groups of histone H3 and permits the selective recovery of the unfolded nucleosomes by mercury-affinity chromatography. This new technique has been used to compare the nucleosomal proteins and their postsynthetic modifications i...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/15.11.4375

    authors： Sterner R,Boffa LC,Chen TA,Allfrey VG

    更新日期：1987-06-11 00:00:00

  • GOBASE: an organelle genome database.

    abstract：:The organelle genome database GOBASE, now in its 21st release (June 2008), contains all published mitochondrion-encoded sequences (approximately 913,000) and chloroplast-encoded sequences (approximately 250,000) from a wide range of eukaryotic taxa. For all sequences, information on related genes, exons, introns, gene...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkn819

    authors： O'Brien EA,Zhang Y,Wang E,Marie V,Badejoko W,Lang BF,Burger G

    更新日期：2009-01-01 00:00:00

  • Roles of yeast eIF2α and eIF2β subunits in the binding of the initiator methionyl-tRNA.

    abstract：:Heterotrimeric eukaryotic/archaeal translation initiation factor 2 (e/aIF2) binds initiator methionyl-tRNA and plays a key role in the selection of the start codon on messenger RNA. tRNA binding was extensively studied in the archaeal system. The γ subunit is able to bind tRNA, but the α subunit is required to reach h...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gks1180

    authors： Naveau M,Lazennec-Schurdevin C,Panvert M,Dubiez E,Mechulam Y,Schmitt E

    更新日期：2013-01-01 00:00:00

  • A short 5' region of the long terminal repeat is required for regulation by hormone and heat shock of Drosophila retrotransposon 1731.

    abstract：:1731, a Drosophila retrotransposon was first described as having a transcription activity which was negatively regulated by 20-hydroxyecdysone (20-OH), the steroid molting hormone of insects. Using constructions expressing the bacterial chloramphenicol-acetyltransferase (CAT) gene under the control of the entire or de...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/19.20.5689

    authors： Ziarczyk P,Best-Belpomme M

    更新日期：1991-10-25 00:00:00

  • How 'arm-twisting' by the inducer triggers activation of the MalT transcription factor, a typical signal transduction ATPase with numerous domains (STAND).

    abstract：:Signal transduction ATPases with numerous domains (STAND) get activated through inducer-dependent assembly into multimeric platforms. This switch relies on the conversion of their nucleotide-binding oligomerization domain (NOD) from a closed, ADP-bound form to an open, ATP-bound form. The NOD closed form is stabilized...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkv158

    authors： Danot O

    更新日期：2015-03-31 00:00:00

  • Targeted correction of a thalassemia-associated beta-globin mutation induced by pseudo-complementary peptide nucleic acids.

    abstract：:Beta-thalassemia is a genetic disorder caused by mutations in the beta-globin gene. Triplex-forming oligonucleotides and triplex-forming peptide nucleic acids (PNAs) have been shown to stimulate recombination in mammalian cells via site-specific binding and creation of altered helical structures that provoke DNA repai...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkp217

    authors： Lonkar P,Kim KH,Kuan JY,Chin JY,Rogers FA,Knauert MP,Kole R,Nielsen PE,Glazer PM

    更新日期：2009-06-01 00:00:00

  • Sequence dependent phase separation of protein-polynucleotide mixtures elucidated using molecular simulations.

    abstract：:Ribonucleoprotein (RNP) granules are membraneless organelles (MLOs), which majorly consist of RNA and RNA-binding proteins and are formed via liquid-liquid phase separation (LLPS). Experimental studies investigating the drivers of LLPS have shown that intrinsically disordered proteins (IDPs) and nucleic acids like RNA...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkaa1099

    authors： Regy RM,Dignon GL,Zheng W,Kim YC,Mittal J

    更新日期：2020-12-16 00:00:00

  • FIDEA: a server for the functional interpretation of differential expression analysis.

    abstract：:The results of differential expression analyses provide scientists with hundreds to thousands of differentially expressed genes that need to be interpreted in light of the biology of the specific system under study. This requires mapping the genes to functional classifications that can be, for example, the KEGG pathwa...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkt516

    authors： D'Andrea D,Grassi L,Mazzapioda M,Tramontano A

    更新日期：2013-07-01 00:00:00

  • High-level transgene expression by homologous recombination-mediated gene transfer.

    abstract：:Gene transfer and expression in eukaryotes is often limited by a number of stably maintained gene copies and by epigenetic silencing effects. Silencing may be limited by the use of epigenetic regulatory sequences such as matrix attachment regions (MAR). Here, we show that successive transfections of MAR-containing vec...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkr436

    authors： Grandjean M,Girod PA,Calabrese D,Kostyrko K,Wicht M,Yerly F,Mazza C,Beckmann JS,Martinet D,Mermod N

    更新日期：2011-08-01 00:00:00