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Collins, John; Wright, Charmain L; Edwards, Carol A.; Davis, Matthew P; Grinham, James; Cole, Charlotte G.; Goward, Melanie E.; Aguado, Begoña; Mallya, Meera; Mokrab, Younes; Huckle, Elizabeth J.; Beare, David; Dunham, Ian

doi:10.1186/gb-2004-5-10-r84

Cited by 39 publications

(15 citation statements)

References 24 publications

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“…For gene amplification, a previously described nested PCR strategy was used [20]. For the first PCR (PCR1), outer primers isolated the target DNA flanked by 30–40 nucleotides at both ends.…”

Section: Methodsmentioning

confidence: 99%

Generation of anti-Notch antibodies and their application in blocking Notch signalling in neural stem cells

Falk

Dyson

et al. 2012

Methods

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Section: Methodsmentioning

confidence: 99%

Generation of anti-Notch antibodies and their application in blocking Notch signalling in neural stem cells

Falk

Dyson

et al. 2012

Methods

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“…These cDNAs were cloned from either existing MGC clones or amplified from mixed-tissue human cDNA essentially as described (Collins et al 2004). Within this set of proteins are published negative interactions (Martin et al 2001;Kumaresan et al 2002;Falco et al 2004;Flaig et al 2004;Romero et al 2005), outlined with black circles in Figure 1D.…”

Section: Avexis Validationmentioning

confidence: 99%

Large-scale screening for novel low-affinity extracellular protein interactions

Söllner²,

et al. 2008

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Extracellular protein-protein interactions are essential for both intercellular communication and cohesion within multicellular organisms. Approximately a fifth of human genes encode membrane-tethered or secreted proteins, but they are largely absent from recent large-scale protein interaction datasets, making current interaction networks biased and incomplete. This discrepancy is due to the unsuitability of popular high-throughput methods to detect extracellular interactions because of the biochemical intractability of membrane proteins and their interactions. For example, cell surface proteins contain insoluble hydrophobic transmembrane regions, and their extracellular interactions are often highly transient, having half-lives of less than a second. To detect transient extracellular interactions on a large scale, we developed AVEXIS (avidity-based extracellular interaction screen), a high-throughput assay that overcomes these technical issues and can detect very transient interactions (halflives Յ 0.1 sec) with a low false-positive rate. We used it to systematically screen for receptor-ligand pairs within the zebrafish immunoglobulin superfamily and identified novel ligands for both well-known and orphan receptors. Genes encoding receptor-ligand pairs were often clustered phylogenetically and expressed in the same or adjacent tissues, immediately implying their involvement in similar biological processes. Using AVEXIS, we have determined the first systematic low-affinity extracellular protein interaction network, supported by independent biological data. This technique will now allow large-scale extracellular protein interaction mapping in a broad range of experimental contexts.

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“…One strategy is for researchers to focus on (a) meaningful subset(s) of genes for functional studies relevant to the biological questions they wish to address. For a human ORF collection the criteria for selecting genes are mostly driven by researchers' interest and clone availability, resulting often in either collections of special interest [4] [5] , or more ‘random’ lists of genes in collections (RZPD, Invitrogen).…”

Section: Introductionmentioning

confidence: 99%

A Biomedically Enriched Collection of 7000 Human ORF Clones

Rolfs

Ebert

et al. 2008

PLoS ONE

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We report the production and availability of over 7000 fully sequence verified plasmid ORF clones representing over 3400 unique human genes. These ORF clones were derived using the human MGC collection as template and were produced in two formats: with and without stop codons. Thus, this collection supports the production of either native protein or proteins with fusion tags added to either or both ends. The template clones used to generate this collection were enriched in three ways. First, gene redundancy was removed. Second, clones were selected to represent the best available GenBank reference sequence. Finally, a literature-based software tool was used to evaluate the list of target genes to ensure that it broadly reflected biomedical research interests. The target gene list was compared with 4000 human diseases and over 8500 biological and chemical MeSH classes in ∼15 Million publications recorded in PubMed at the time of analysis. The outcome of this analysis revealed that relative to the genome and the MGC collection, this collection is enriched for the presence of genes with published associations with a wide range of diseases and biomedical terms without displaying a particular bias towards any single disease or concept. Thus, this collection is likely to be a powerful resource for researchers who wish to study protein function in a set of genes with documented biomedical significance.

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Cited by 39 publications

References 24 publications

Generation of anti-Notch antibodies and their application in blocking Notch signalling in neural stem cells

Generation of anti-Notch antibodies and their application in blocking Notch signalling in neural stem cells

Large-scale screening for novel low-affinity extracellular protein interactions

A Biomedically Enriched Collection of 7000 Human ORF Clones

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