Digital cloning: Identification of human cDNAs homologous to novel kinases through expressed sequence tag database searching

Chen, Hua Chien; Kung, Hsing Jien; Robinson, Dan R.

doi:10.1007/bf02258361

Cited by 10 publications

(5 citation statements)

References 48 publications

(29 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This approach requires sophisticated optical equipment and assembly of non-redundant gene transcripts. Another approach is presented by Chen et al [2], where they described their attempt in digital cloning of new kinases from the EST database. Other approaches, such as differential display [13], SAGE [21] and RDA [16], are also intended to give an overall differential expression profile.…”

Section: Additional Approaches and Concluding Remarksmentioning

confidence: 99%

“…When fully developed, this is a powerful method which is aimed to describe the expression of all human genes in a single screen. The approaches described by Chen et al [2] and Chou et al [4] appear to be rewarding, and extension of these strategies to identify other novel kinases seems worthwhile. The kinase display method described here is complemen-tary to these approaches and focuses on a specific, perhaps the largest, family of genes involved in growth and tumorigenesis.…”

Section: Additional Approaches and Concluding Remarksmentioning

confidence: 99%

See 1 more Smart Citation

Molecular profiling of tyrosine kinases in normal and cancer cells

Kung

Chen²,

Robinson

1998

J Biomed Sci

Self Cite

View full text Add to dashboard Cite

As the post-genome era is approaching, with vast amount of sequence information available and new technology developed, scientists are presented with opportunities to explore in simple analysis the structure and expression pattern of not just a single gene, but of an entire family of genes, if not the entire genome. The concept of 'molecular profiling' or 'expression array' has thus emerged. The need to simultaneously 'see' all genes in the same family is obvious under the precept of the combinatorial process being an underlying principle of complex biological systems: no gene exists in isolation, for virtually every molecule participates in intermolecular interactions. The activation of receptor tyrosine kinases through homo or hetero-dimerization is the prototypic example. In this review, a tyrosine kinase profile technique and its application to studying the expression of tyrosine kinases and the identification of novel kinases will be discussed. This serves as an introduction to the several interesting papers published in this special 'kinase' issue of the Journal of Biomedical Sciences, using this technique. A new simplified approach, kinase display, which is an extension of the profiling method and requires only restriction digestion and gel analysis will also be introduced.

show abstract

Section: Additional Approaches and Concluding Remarksmentioning

confidence: 99%

Section: Additional Approaches and Concluding Remarksmentioning

confidence: 99%

Molecular profiling of tyrosine kinases in normal and cancer cells

Kung

Chen²,

Robinson

1998

J Biomed Sci

Self Cite

View full text Add to dashboard Cite

show abstract

“…ESTs which overlap with the coding sequence of the transcript may help to prioritize novel members of that protein family, if they share sequence similarity with the group of genes of interest. This strategy has been used to clone, for instance, novel members of the G-protein-coupled receptor family (3,4) and new kinases (5,6). …”

Section: Introductionmentioning

confidence: 99%

Beyond tissueInfo: functional prediction using tissue expression profile similarity searches

Aguilar

Skrabanek

Gross

et al. 2008

Nucleic Acids Research

View full text Add to dashboard Cite

We present and validate tissue expression profile similarity searches (TEPSS), a computational approach to identify transcripts that share similar tissue expression profiles to one or more transcripts in a group of interest. We evaluated TEPSS for its ability to discriminate between pairs of transcripts coding for interacting proteins and non-interacting pairs. We found that ordering protein–protein pairs by TEPSS score produces sets significantly enriched in reported pairs of interacting proteins [interacting versus non-interacting pairs, Odds-ratio (OR) = 157.57, 95% confidence interval (CI) (36.81–375.51) at 1% coverage, employing a large dataset of about 50 000 human protein interactions]. When used with multiple transcripts as input, we find that TEPSS can predict non-obvious members of the cytosolic ribosome. We used TEPSS to predict S-nitrosylation (SNO) protein targets from a set of brain proteins that undergo SNO upon exposure to physiological levels of S-nitrosoglutathione in vitro. While some of the top TEPSS predictions have been validated independently, several of the strongest SNO TEPSS predictions await experimental validation. Our data indicate that TEPSS is an effective and flexible approach to functional prediction. Since the approach does not use sequence similarity, we expect that TEPSS will be useful for various gene discovery applications. TEPSS programs and data are distributed at http://icb.med.cornell.edu/crt/tepss/index.xml.

show abstract

“…Ten new kinases are revealed in their search, focusing on MAPK and cdk families of kinases. The approaches described by Chen et al [2] and Chou et al [4] appear to be rewarding, and extension of these strategies to identify other novel kinases seems worthwhile.…”

Section: Additional Approaches and Concluding Remarksmentioning

confidence: 99%

“…As shown in that publication [4], this strategy worked well and several new kinases have been identified. Another approach is presented by Chen et al [2], where they described their attempt in digital cloning of new kinases from the EST database. This method relies on 'hybridization' of a query sequence (probe) with the EST sequences (cDNA library) in the database.…”

Section: Additional Approaches and Concluding Remarksmentioning

confidence: 99%

Molecular Profiling of Tyrosine Kinases in Normal and Cancer Cells

Kung

Chen²,

Robinson

1998

J Biomed Sci

Self Cite

View full text Add to dashboard Cite

As the post-genome era is approaching, with vast amount of sequence information available and new technology developed, scientists are presented with opportunities to explore in simple analysis the structure and expression pattern of not just a single gene, but of an entire family of genes, if not the entire genome. The concept of ‘molecular profiling’ or ‘expression array’ has thus emerged. The need to simultaneously ‘see’ all genes in the same family is obvious under the precept of the combinatorial process being an underlying principle of complex biological systems: no gene exists in isolation, for virtually every molecule participates in intermolecular interactions. The activation of receptor tyrosine kinases through homo or hetero-dimerization is the prototypic example. In this review, a tyrosine kinase profile technique and its application to studying the expression of tyrosine kinases and the identification of novel kinases will be discussed. This serves as an introduction to the several interesting papers published in this special ‘kinase’ issue of the Journal of Biomedical Sciences, using this technique. A new simplified approach, kinase display, which is an extension of the profiling method and requires only restriction digestion and gel analysis will also be introduced.

show abstract

Digital cloning: Identification of human cDNAs homologous to novel kinases through expressed sequence tag database searching

Cited by 10 publications

References 48 publications

Molecular profiling of tyrosine kinases in normal and cancer cells

Molecular profiling of tyrosine kinases in normal and cancer cells

Beyond tissueInfo: functional prediction using tissue expression profile similarity searches

Molecular Profiling of Tyrosine Kinases in Normal and Cancer Cells

Contact Info

Product

Resources

About