|2-DE Analysis of Breast Cancer Cell Lines MDA-1833 and MDA-4175 with Distinct Metastatic Organ-Specific Potentials and Comparison with Parental Cell Line MDA-MB-231|
Irena Selicharová, Miloslav Šanda, Lucia Svitekova, Sujata Suraswat Ohri, Aruna Vashishta, Martin Fusek and Václav Vetvicka
Breast cancer has diverse metastatic behavior. Subpopulations of cells with enhanced metastatic abilities either to bone (1833) or to lung (4175) have been isolated by the group of J. Massague by in vivo selection of MDA-MB-231 cells. We performed the 2-DE analysis of the cell lines. We have found and identified 11 differentially expressed protein spots.
|Expression Profiling of CD34+ of Peripheral Blood of Patients with Lymphoma During ex vivo Granulocytic Differentiation|
Irena Koutna, Lenka Tesarova, Martin Klabusay, Petr Krontorad, Michal Strehovsky, Martina Peterkova and Viera Hrabcakova
On the basis of global expression data analysis we have concluded that population of CD34+ cells from patients with lymphoma shows different expression status during ex-vivo differentiation. And thus we assume that CD34+ population is not suitable for autologous transplantation. We have used cDNA microarrays technology to obtained precise expression profiles.
|MS-Xelerator™: Advanced Algorithms for LC/MS Data Processing Applied to Biomarker Discovery, Differential Analysis and Quantitative Proteomics|
LC-MS based proteomic experiments are used to compare complex biological samples across multiple conditions. Fast, powerful computational tools are needed to explore and detect differences in the areas of Expression Proteomics and Biomarker Discovery. In general, specialized steps are necessary to solve these difficult problems (binning, alignment & normalization, peak picking, relative quantitation, etc.). MS-Xelerator is a collection of software tools dedicated to all of the above tasks.
|Caveolin-1 Expression as a Possible Biomarker in Pancreatic Cancer Diagnosis|
C. Tanase, E. Raducan, L. Albulescu, E. Codorean, M.I. Nicolescu, D.I. Popescu, M.L. Cruceru and A.C. Popa
Caveolin1 (Cav-1) function either as a tumor supressor or as a promoter of metastasis. Overexpresion of cav-1 was correlated with: tumoral grading, proliferration markers (Ki67, p53), serum tumor markers (CEA, CA19.9) and angiogenic markers (VEGF, bFGF).
|In silico Screening for Signalosome Inhibitors|
Melanie Füllbeck, Wolfgang Dubiel, Cornelius Frömmel, Andrean Goede and Robert Preissner
The COP9 signalosome (CSN) is involved in cell cycle regulation, possesses kinase activity and is therefore an interesting therapeutic target for anti-tumor drugs. Known inhibitors of the kinase activity exhibit low binding constants. Using them a 3D similarity screening for our in-house database is performed. The superposition algorithm enables the explicit consideration of conformers reflecting the structural flexibility.
|EuroGentest: Reference Materials for Genetic Testing|
David E Barton, David Gancberg, Philippe Corbisier, Sarah Berwouts, Elisabeth Dequeker and Christine Brady
The lack of reference materials (RMs) for most genetic tests causes difficulties in validating and developing new assays, and results in tests being run without proper quality controls. EuroGentest and the EU-funded network for Medical Genetics, is addressing this issue by defining the present and future needs for RMs, setting priorities for and supporting the development of new RMs and building an enduring network involving all stakeholders in RM development.
|Prediction of Genes with U12-Dependent Introns in the Human Genome|
Alioto, T.S. and Guigó R.
We enhanced the gene prediction program GeneID with a framework for detecting U12-dependent introns without appreciable loss in gene prediction sensitivity or specificity. We present statistics on the performance of the U12-enhanced GeneID on a test set of known U12-intron-possessing genes as well as results for scans of both the ENCODE regions and the entire human genome.
|Large-scale Microarray Analysis of Protein and mRNA Level Changes in HL-60 Cells|
Pavel Simara, Irena Koutna, Stanislav Stejskal, Martina Peterkova, Petr Krontorad, Zdenek Rucka
In this study we compare methods for large-scale microarray analysis of protein and RNA level changes in HL-60 cells, responding to differentiation stimuli. Using microarrays we have found, that level of several proteins was either up- or down-regulated after cell differentiation. In some cases there was significant correlation with appropriate genes.
|PRIMe: Platform for RIKEN Metabolomics|
Atsushi Fukushima, Miyako Kusano, Kenji Akiyama, Takeshi Obayashi, Takayuki Tohge, Masami Yokota Hirai, Shigehiko Kanaya, Masanori Arita, Yoko Shinbo, Kazuo Shinozaki, Tetsuya Sakurai and Kazuki Saito
We have developed a web-based database, "PRIMe (Platform for RIKEN Metabolomics)," which contains powerful tools for researchers to analyze gene co-expression data and mass spectral data. PRIMe has been developed with the main aim of facilitating integrated analysis for transcriptomics and metabolomics.