КРОС-ПЛАТФОРМНЕ ОБ’ЄДНАННЯ ДАНИХ МІКРОМАСИВ-ЕКСПЕРИМЕНТІВ ТА ЙОГО ВПЛИВ НА ЗНАЧЕННЯ ГЕННОЇ ЕКСПРЕСІЇ ПРИ АНАЛІЗІ ЗРАЗКІВ РАКОВИХ ПУХЛИН МОЛОЧНОЇ ЗАЛОЗИ ЛЮДИНИ

Introduction. Currently advances in different fields of biology and medicine accumulated large amount of high-throughput microarray datasets. It allows comparing, merging and analyzing such data in order to get more informative and statistically significant results. However, the process of cross-platform microarray data integration is complicated by different platform designs, that is the kind of probes used, the hybridization paradigm, the labeling and production methods. Such characteristics of microarray platforms should be considered when analyzing datasets from one study and even more when merging datasets.В различных областях биологии и медицины накопилось значительное количество данных широкомасштабных исследований генной экспрессии с использованием микромасив-технологий. Поэтому возникает насущная необходимость в сравнении, объединении и анализе этих данных с целью повышения информативности и статистической достоверности результатов анализа.У різних галузях біології та медицини накопичилася значна кількість даних широкомасштабних досліджень генної експресії за використання мікромасив-технологій. Тому виникає нагальна потреба в порівнянні, об'єднанні й аналізі цих даних з метою підвищення інформативності та статистичної достовірності результатів аналізу. Однак, процес об'єднання результатів мікромасив-експериментів на базі крос-платформного аналізу ускладнений існуванням багатьох мікроарей-платформ, різних за технологією виготовлення, методикою нанесення проб на чип і різновидністю дизайну проб. Ці особливості кожного з досліджень повинні бути враховані при обробленні та аналізі результатів мікромасив-експериментів, отриманих як на однакових, так і на різних платформах

Structure and functions of glutathione S-transferase Pl-1

Glutathione S-transferase Pl-1 (GSTP1-1) is a multifunctional enzyme which protects the cell from the influence of genotoxic factors and apop-tosis. Contemporary knowledge about the GSTP1 molecule structure and the enzyme functions are summarized in this review. Also PI isoform is compared to other glutathione S-transferases and structure-function relationships are emphasized. Novel functions of GSTP1 in cell signaling modulation, NO storage and metabolism are highlighted in this paper

Evaluation criteria of rat hepatocytes transcriptome analysis under the influence of interferon alpha by DNA microarray

The changes induced in transcriptome of rat hepatocytes treated with interferon alpha (IFN) during three and six hours were analyzed by DNA microarray. Aim. To conduct a stepwise analysis of the results of microarray experiment and to determine whether they meet/fail to the conventional requirements. Methods. The files obtained after scanning microarrays were subjected to the analysis in statistical environment R by Bioconductor’s packages «affy», «simpleaffy», «affyPLM» and BRB Array Tools software for paired T-test. Results. All microarrays had quality metrics lying within recommended ranges, passed quality control, were normalized and are comparable with each other. The T-test revealed 28 and 124 differentially expressed genes after three and six hours of cells cultivation with IFNα , respectively. Conclusions. The obtained data meet the conventional criteria of quality and are applicable for further evaluation of their biological significance. The R-codes used in this study can be used for the analysis of the microarrays data

Transcription regulation in differential expression of the human GSTP1 gene in breast and choriocarcinoma cells

Glutathione S-transferase P1 is a major phase II detoxification enzyme in most cell types. Aberrant expression of GSTP1 is associated with carcinogenesis and development of multidrug resistance. GSTP1 gene transcription is regulated by promoter methylation and by transcription factors. To elucidate the mechanisms responsible for the different levels of GSTP1 expression observed in Hbl-100 and BeWo cells we utilized truncated promoter constructs to compare the functional role of different promoter elements. We also identified transcription factors binding the responsive elements by electrophoretic mobility shift assay. The applied approaches provided the evidence that binding of transcription factors to ARE, CRE and NF-kappaB sites are responsible for the cell specific levels of GSTP1 expression in Hbl-100 and BeWo cells. It was also indicated that partial promoter methylation occurs in BeWo cells

Some aspects of glutathione S-transferase P1-1 gene transcription regulation in human placenta

Glutathione S-transferase P1-1 is the main phase II xenobiotic metabolism enzyme in human placenta. Low level of its gene expression and corresponding ineffective protection of fetus from toxic compounds is associated with pregnancy disorders such as preeclampsia and abnormalities of fetus development. It was previously reported that environmental radioactive contamination caused down-regulation of GSTP1 transcription in human placenta, but mechanisms responsible for such changes were unclear. In the present study we have found that observed changes in transcription of this gene are not caused by promoter methylation because GSTP1 promoter was not methylated in any of analyzed 91 placental samples. Regulation of GSTPl by methylation or transcription factors was not previously studied in human placenta. Using "Gene Expression Atlas" online software the placental expression profile of transcription factors known to interact with GSTP1 promoter in other cell types, was identified. According to computer analysis the genes coding for GATA2, GATA3, Fos-B, Nrf3 and MafK transcription factors are highly expressed in human placenta, while genes coding for c-Fos, Juns, Mafs, ERβ, RARα and NF-κB factors have moderate level of expression. Competitive EMSA provided the evidence that ARE and NF-κB-like sites specifically interacted with placental nuclear proteins. Among these proteins transcription factors AP-1 and NF-κB were identified using corresponding consensus oligonucleotides as competitors in EMSA