Tools for Expression Analysis

This tool extracts up to four possible SAGE tags and orientalion signals from a sequence. Orientation signals aMowlhs most likely tag to be chosen (sequences are usually written in the 5 -3 [+) or 3 -5 (-) orienlions), 

Follow the tag hotlinks in the output table to find out its expression level in different SAGE libraries and how it is represented in the rest of the sequences in GenBank and UnlGene. 

Enter mRlWcDNA sequence here and press stibimi ] 

2531 stcccatttt tatategatc tctt tttta cabtaaaaet tt tgccaaa aaaaataa aa 

Q[ientatiQns SA Etag Tjq position PolyA gnjI position PclycA tdil7 

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Kain, S. R. Mai, K. Sinai, P. Human multiple tissue western blots a new immunological tool for the analysis of tissue-specific protein expression. Biotechniques 1994, 17(5), 982-987. 

The ff-moment approach has proved to be a very robust and valuable tool for the analysis of the partitioning of compounds between most diverse phases. A typical application is logi oc, the logarithmic soil sorption coefficient, which is of crucial importance in environmental exposition and distribution models. Since the experimental measurement of Koc is difficult, expensive, and often unreliable, good prediction models are especially important here. On the basis of a training set of 387 compounds collected by Winget et al. [110], we derived a COSMO-KOC model expressed as... 

In a study of the Qa-2-expression regulation by the transporter associated with antigen processing (TAP) protein, Ke and Warner [14] reported the monitoring of preimplantation embryos from TAP-1 knockout and normal mice by IPCR and RT-PCR. IPCR was carried out as described by McElhinny et al. [17]. Again, IPCR proved its potential as a valuable tool for the analysis of protein expression on the cell surface from small numbers (2-20) of one-cell and two-cell embryos, as well as blastocystes. 

Large-scale gene expression studies, especially microarray technologies, have rapidly become a significant part of bioinformatics. There are many excellent sites focusing on microarray databases and tools for data analysis. The following sites are simply some examples. 

Facchiano A, A Weisz Internet tools for the analysis of gene expression by database integration, Proceedings of the NETTAB 2001 Workshop CORBA and XML—Toward a bioinformatics integrated network environment , Italy, 2001, pp. 99-102. 

The interest of the consortium in developing and testing new tools for proteome analysis was directed to solutions for particular technical problems concerning sample preparation, the 2D PAGE system, protein quantification, and the development of UniClone sets (nonredundant cDNA expression library) from the adult human brain to be used for creating clinically relevant biochips. These... 

Several public databases serve mieroarray data and include tools for mieroarray analysis, including the Stanford Mieroarray Database [165], the RIKEN Expression Array Database [166], and Array Express at the European Bioinformatics Institute [167]. 

Exploratory methods are used not to test hypotheses but rather to get an overview of data. Various clustering methods and ordination are excellent tools for exploratory analysis of microarray data. These unsupervised methods do not require external class or group information. Clusters are generated purely based on the intrinsic similarity of the gene or sample expression profiles. No null hypothesis can be rejected, and p values are not generated to test statistical significance. Methods that... 

Knocking-Down the Expression of TLS Polymerases using Small Interfering RNA Provides a useful Tool for the Analysis of TLS using the Gapped Plasmid Assay... 

The ability to knock down the expression of specific genes using small interfering RNA (siRNA) revolutionized the ability to manipulate mammalian cells and provided a powerful tool for the analysis of various cellular processes. We adapted our assay to be used with cells in which the expression of specific DNA polymerases... 

Srinivas S, Goldberg MR, Watanabe T, D Agati V, al-Awqati Q, Costantini F. 1999. Expression of green fluorescent protein in the ureteric bud of transgenic mice a new tool for the analysis of ureteric bud morphogenesis. Dev Genet 24(3 ) 241-251. 

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