We developed a user-friendly, interactive program to simultaneously cluster and visualize omics data, such as DNA and protein array profiles. This program provides diverse algorithms for the hierarchical clustering of two-dimensional data. The clustering results can be interactively visualized and optimized on a heatmap. The present tool does not require any prior knowledge of scripting languages to carry out the data clustering and visualization. Furthermore, the heatmaps allow the selective display of data points satisfying user-defined criteria. For example, a clustered heatmap of experimental values can be differentially visualized based on statistical values, such as p-values. Including diverse menu-based display options, QCanvas provides a convenient graphical user interface for pattern analysis and visualization with high-quality graphics.
DNA ; Genomics ; Protein Array Analysis

Animals ; Humans ; Protein Array Analysis ; classification ; trends

Genomics ; Humans ; Oligonucleotide Array Sequence Analysis ; Plants, Medicinal ; chemistry ; genetics ; Protein Array Analysis ; Quality Control

Drug Design ; Genomics ; methods ; Oligonucleotide Array Sequence Analysis ; Protein Array Analysis ; Proteomics ; Technology, Pharmaceutical

Recently, in situ protein microarrays have been developed for large scale analysis and high throughput studies of proteins. In situ protein microarrays produce proteins directly on the solid surface from pre-arrayed DNA or RNA. The advances in in situ protein microarrays are exemplified by the ease of cDNA cloning and cell free protein expression. These technologies can evaluate, validate and monitor protein in a cost effective manner and address the issue of a high quality protein supply to use in the array. Here we review the importance of recently employed methods: PISA (protein in situ array), DAPA (DNA array to protein array), NAPPA (nucleic acid programmable protein array) and TUSTER microarrays and the role of these methods in proteomics.
Cell-Free System ; DNA ; metabolism ; Oligonucleotide Array Sequence Analysis ; Protein Array Analysis ; Proteins ; metabolism ; RNA ; metabolism

The adsorption of proteins on the surface of glass slides is essential for construction of protein chips. Previously, we prepared a nickel-coated plate by the spin-coating method for immobilization of His-tagged proteins. In order to know whether the structural factor is responsible for the immobilization of His-tagged proteins to the nickel-coated glass slide, we executed a series of experiments. First we purified a His-tagged protein after expressing the vector in E. coli BL21 (DE3). Then we obtained the unfolding curve for the His-tagged protein by using guanidine hydrochloride. Fractions unfolded were monitored by internal fluorescence spectroscopy. The delta G(H20) for unfolding was 2.27 kcalmol +/- 0.52. Then we tested if unfolded His-tagged proteins can be adsorbed to the nickel-coated plate, comparing with Ni2+ -NTA (nitrilotriacetic acid) beads. Whereas unfolded His-tagged proteins were adsorbed to Ni2+ -NTA beads, they did not bind to the nickel-coated plate. In conclusion, a structural factor is likely to be an important factor for constructing the protein chips, when His-tagged proteins will immobilize to the nickel-coated slides.
Adsorption ; Fibrinogen ; Glass* ; Guanidine ; Immobilization ; Protein Array Analysis ; Spectrometry, Fluorescence

A protein microarray biosensor based on imaging ellipsometry has been developed as a high-throughput and fast technique for protein analysis. As an automatic technique, it has advanced properties such as label-free, multi-protein simultaneous detection, static or kinetic analysis for protein interaction, and qualitative or quantitative analysis. It has been used for the biomedical applications including tumor markers detection, hepatitis B test, protein competitive adsorption and kinetic visualization for protein interactions. It have demonstrated promising potential for further applications in biomedicine.
Biosensing Techniques ; methods ; trends ; Humans ; Protein Array Analysis ; methods ; trends

The rapid screening of tumor markers is a challenging task for early diagnosis of cancer. This study aims to use highly sensitive chemiluminescent protein microarray technology to efficiently screen a variety of low abundance tumor related markers. A new material, termed integrated polydimethylsiloxane modified silica gel (iPDMS), was obtained by adding a surface polymerization initiator with olefin end to the conventional polydimethylsiloxane, and fixing into the three-dimensional structure of polydimethylsiloxane by thermal crosslinking through silicon hydrogen bonding. In order to make the iPDMS material resistant to non-specific protein adsorption, a poly(OEGMA) polymer brush was synthesized by surface-initiated atom transfer radical polymerization at the active initiation site. Finally, 20 tumor-related antigens were printed into the specific areas of the microarray by high-throughput spray printing technology, and assembled into 48-well detection microtiterplates of the iPDMS microarray. It was found the VEGFR and VEGF121 autoantibodies that obtained from 8 common tumors (breast cancer, lung cancer, colon cancer, gastric cancer, liver cancer, leukemia, lymphoma and ovarian cancer) can be used as potential tumor markers. The chemiluminescence labeled iPDMS protein microarray can be used for the screening of tumor autoantibodies at early stage.
Adsorption ; Autoantibodies ; Dimethylpolysiloxanes ; Protein Array Analysis ; Silica Gel ; Surface Properties

Objective To obtain the protein expression profile of rat liver tissue after death by the 2100 bioanalyzer combined with protein chip, and infer the relationship between protein expression profile and postmortem interval. Methods Rats were killed by abdominal anesthesia and placed at 16 ℃. Water-soluble proteins in liver tissues were extracted at 14 time points after death. The expression profile data of proteins with relative molecular weight of 14 000-230 000 were obtained using protein chip, and principal component analysis （PCA）, partial least squares-discriminant analysis （PLS-DA） and Fisher discriminant were used to analyze the data. Results According to the changes of protein expression profile, the postmortem interval was divided into group A （0 d）, group B （1-9 d）, group C （12-30 d） according to the result of PLS-DA. The prediction accuracy of the training set and test set of the model were all 100.0%, and the internal cross-validation of the training set was 100.0% according to Fisher discriminant. The Fisher discriminant model at each time point of group B and C was established to narrow the time window of postmortem interval estimation. The prediction accuracy of the training set and test set were all 100.0%, and the internal cross-validation accuracy of the training set was 100.0% in group B. The prediction accuracy of the training set and test set were respectively 95.2% and 78.6% in group C, and the internal cross-validation of the training set was 88.1%. Conclusion Protein chip detection technology can quickly and easily obtain the expression profile of water-soluble proteins of rat liver tissue with a relative molecular weight of 14 000-230 000 at different time points after death. PLS-DA and Fisher discriminant models are established to classify and predict the postmortem interval, in order to provide new ideas and methods for postmortem interval estimation.
Animals ; Autopsy ; Discriminant Analysis ; Least-Squares Analysis ; Postmortem Changes ; Protein Array Analysis ; Rats ; Technology

The major bottle-neck in the way of constructing high density protein microarray is the availability and stability of proteins. The traditional methods of generating protein arrays require the in-vivo expression, purification and immobilization of hundreds or thousands of proteins. The cell-free protein array technology employs cell-free expression systems to produce proteins directly onto surface from co-distributed or pre-arrayed DNA or RNA, thus avoiding the laborious and often costly processes of protein preparation in the traditional approach. Here we provide an overview of recently developed novel technology in cell free based protein microarray and their applications in protein interaction analysis, in antibody specificity and vaccine screening, and in biomarker assay.
Cell-Free System ; DNA ; genetics ; Humans ; Protein Array Analysis ; methods ; Protein Biosynthesis ; Protein Interaction Mapping ; Proteins ; analysis ; genetics ; metabolism