PubMed Health⌕ Search
Home/Archive/PubMed

PubMed · 16859521

A method for high-throughput gene expression signature analysis.

David Peck·Emily D Crawford·Kenneth N Ross·Kimberly Stegmaier·Todd R Golub·Justin Lamb
View original source ↗Export metadata ↓

Abstract

Genome-wide transcriptional profiling has shown that different biologic states (for instance, disease and response to pharmacologic manipulation) can be recognized by the expression pattern of relatively small numbers of genes. However, the lack of a practical and cost-effective technology for detection of these gene expression 'signatures' in large numbers of samples has severely limited their exploitation in important medical and pharmaceutical discovery applications. Here, we describe a solution based on the combination of ligation-mediated amplification with an optically addressed microsphere and flow cytometric detection system.

Explore related subjects

Base SequenceDNA PrimersGene Expression ProfilingHL-60 CellsHumansNucleic Acid HybridizationOligonucleotide Array Sequence AnalysisRNA, MessengerReproducibility of ResultsTranscription, GeneticJournal ArticleResearch Support, Non-U.S. Gov't

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

David Peck, Emily D Crawford, Kenneth N Ross, Kimberly Stegmaier, Todd R Golub, Justin Lamb. 2006. A method for high-throughput gene expression signature analysis.. https://doi.org/10.1186/gb-2006-7-7-r61

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2016

miR-503-3p promotes epithelial-mesenchymal transition in breast cancer by directly targeting SMAD2 and E-cadherin.

Although progress in clinical and basic research has significantly increased our understanding of breast cancer, little is known about the molecular mechanism underlying breast cancer metastasis. Identification of effective therapeutic targets to prevent breast cancer metastasis is urgently needed. The function of miR-503-3p has been investigated in other cancers, but its role in breast cancer remains undefined. Here, we found that miR-503-3p was overexpressed in breast cancer tissue and plasma compared with adjacent normal breast tissue and with plasma from healthy individuals. Moreover, we identified miR-503-3p to be an oncogene of breast cancer cell proliferation, migration and invasion. Upregulation of miR-503-3p in breast cancer cells inhibited expression of epithelial-mesenchymal transition (EMT)-related protein SMAD2 and the epithelial marker protein E-cadherin by directly binding to their mRNA 3' untranslated region, whereas increased expression of mesenchymal marker proteins, including vimentin and N-cadherin. Taken together, our findings support a critical role for miR-503-3p in induction of breast cancer EMT and suggest that plasma miR-503-3p may be a useful diagnostic biomarker for breast cancer.

Base Sequence↗
PubMed2007

MS-KIF18A, a kinesin, is associated with estrogen receptor.

The study of MS-KIF18A kinesin protein is focused on its cellular distribution and association with a cargo protein. Indirect immunofluorescence (IF) analyzed the intracellular distribution of endogenous MS-KIF18A and the transfected enhanced green fluorescence protein (eGFP)-MS-KIF18A in osteogenic cells. In both cases, the proteins were localized at the plasma membrane, cytosol, and nucleus. Bioinformatics analysis suggested interactions between MS-KIF18A and estrogen receptor (ERalpha) which were further elucidated by immunoprecipitation (IP). We identified interaction between endogenous MS-KIF18A with 66 and 46 kDa isoforms of ERalpha in MBA-15 cells. Moreover, MS-KIF18A and 66 kDa ERalpha complex has been demonstrated between ectopically expressed proteins in COS-7 cells. We have shown that anti-MS-KIF18A antibody immunoprecipitated the ERalpha and pERK in cells challenged with 17beta-estrogen (17beta-E2). The hormone activation induced mitogen-activated protein kinases (MAPK) pathway and increased p-ERK. The activation was interfered when cells were pre-treated with either ICI-182,780 or MAPK inhibitor PD98059 prior the challenge with 17beta-E2 that resulted in a decrease in association between MS-KIF18A and p-ERK1/2. The obtained results suggest a role for the proteins in a non-genomic response of MBA-15 cells challenged with 17beta-E2. This study presents a novel interaction between MS-KIF18A and ER that may have important physiological and pharmacological implications for estrogen action in various cells.

Base Sequence↗
PubMed2007

Investigating the in vivo activity of the DeaD protein using protein-protein interactions and the translational activity of structured chloramphenicol acetyltransferase mRNAs.

Here, we report the use of an in vivo protein-protein interaction detection approach together with focused follow-up experiments to study the function of the DeaD protein in Escherichia coli. In this method, functions are assigned to proteins based on the interactions they make with others in the living cell. The assigned functions are further confirmed using follow-up experiments. The DeaD protein has been characterized in vitro as a putative prokaryotic factor required for the formation of translation initiation complexes on structured mRNAs. Although the RNA helicase activity of DeaD has been demonstrated in vitro, its in vivo activity remains controversial. Here, using a method called sequential peptide affinity (SPA) tagging, we show that DeaD interacts with certain ribosomal proteins as well as a series of other nucleic acid binding proteins. Focused follow-up experiments provide evidence for the mRNA helicase activity of the DeaD protein complex during translation initiation. DeaD overexpression compensates for the reduction of the translation activity caused by a structure placed at the initiation region of a chloramphenicol acetyltransferase gene (cat) used as a reporter. Deletion of the deaD gene, encoding DeaD, abolishes the translation activity of the mRNA with an inhibitory structure at its initiation region. Increasing the growth temperature disrupts RNA secondary structures and bypasses the DeaD requirement. These observations suggest that DeaD is involved in destabilizing mRNA structures during translation initiation. This study also provides further confirmation that large-scale protein-protein interaction data can be suitable to study protein functions in E. coli.

Base Sequence↗