|Gene expression analysis of CD14+ monocytes immunomagnetically separated directly from whole blood: adaptation of protocols towards clinical trial requirements|
Gregor Winkels1, Ines Dischinger1, Katharina Bublitz1, Evert Luesink2, Nanguneri R. Nirmala2, Frank Staedtler2, Keith J. Johnson2, Alena Fitz1, Sabrina Schmitz1, Dirk Dietrich1, Sonja Balzer1, Sabine Classen1, Silvia Rüberg1, Uwe Janssen1, and Bernhard Gerstmayer1
Peripheral blood is widely used as starting material for biomarker discovery and validation using molecular biology technologies. The vast majority of currently published transcriptome data is based on RNA derived either from stabilized whole blood or peripheral blood mononuclear cells (PBMCs). Here, gene expression profiling studies and SOPs for fast, easy and specific manual or automated isolation of monocytes directly from whole blood are being described.
|Integrated In Silico Analysis of NGS Prostate Cancer Data via High-Resolution RNA-Seq Analysis|
Sandeep Sanga , Antoaneta Vladimirova, Aubree Hoover
The goal: To get novel insights into the mechanisms of prostate adenocarcinoma by leveraging next generation sequencing (NGS) data, particularly human transcriptome data, through in silico data analysis and interpretation by Ingenuity’s IPA® software. CLC Genomics Workbench and CLC Genomics Server helped us assess short read RNA-Seq data.
|Gene Expression Profiling of Archived FFPE Samples|
Silvia Rüberg, Sabine Classen, Jana Ciomperlik, Dirk Dietrich, Ines Dischinger, Alena Böttcher, Sabrina Schmitz and Bernhard Gerstmayer
According to the BBMRI (Biobanking and Biomolecular Resources Research Infrastructure) about 8,000,000 formalin-fixed paraffin-embedded (FFPE) samples derived from a multitude of different diseases have been collected in medical centers and biobanks all over Europe during the last decades.
|Differential Expression and Localization of Dicer1 and Ovarian Steroid Hormone Receptors in Human Fallopian Tubes|
Ruijin Shao et al.
Dicer1 expression is upregulated in cell-specific fashion in human Fallopian tubes during ovulation. The stage-dependent expression of Dicer1 and its correlation with ERa, ERß2, and PRB mRNA suggests that tubal Dicer1 helps regulate tubal expression of steroid hormone receptors in a cycle-dependent manner and may contribute to tubal transport in humans.
|An improved data processing pipe-line for comprehensive H-NMR and X/MS -omics data|
R. J. O. Torgrip, K. M. Åberg, E. Alm
In the post acqusition analysis of comprehensive -omics data the pre-processing pipe-line is crucial to extract the maximum possible amount of information from the data. Here we show a processing pipe-line for (1D)H-NMR and (2D)X/MS data comprising; feature detection, inter-sample feature alignment and internal-standard free normalization that outperforms today’s state-of-the-art processing schemes.
|Alignment of 1H-NMR data using a Generalized Fuzzy Hough Transform|
Erik Alm, Leonard Csenki, Ralf J.O. Torgrip, K. Magnus Åberg, Lars I. Nord, Ina Schuppe-Koistinen and Johan Lindberg
In metabolic profiling, multivariate data analysis techniques are used to interpret 1D 1H–NMR data. Multivariate data analysis techniques require that peaks are located in the same variables in every spectrum – this requirement is not met in native NMR spectra. Current state-of-the-art alignment algorithms are unable to align peaks when the spatial order of the peaks changes. We present the Fuzzy Generalized Hough Transform alignment which solves the alignment problem.
|ROLE OF IRF-8 IN THE INTERFACE OF MELANOMA TUMOR CELL-IMMUNE SYSTEM INTERACTION.|
Fabrizio Mattei, Giovanna Schiavoni, Massimo Spada, Francesca Spadaro and Lucia Gabriele
Interferon-regulatory factor-8 is essential for differentiation and function of dendritic cells and thus for the induction of competent immune responses. Here, we investigated the role of IRF-8 in affecting immune response against melanoma. Our results reveal a critical role of IRF-8 in controlling melanoma growth and suggest that IRF-8-mediated antitumor activity is the result of a coordinated action between DC-mediated immune response and the tumor suppressor function of IRF-8.
|Software for Genomic/Epigenomic Research|
A.S.Tanas, V.V.Shkarupo, E.B.Kuznetsova, D.V.Zaletayev, V.V. Strelnikov
We present two computer programs: 1) AIMS in silico - a suggestion tool for Amplification of Intermethylated Sites experimental design and results analysis; and 2) PeakPick – a tool to view & analyse capillary electrophoregrams Our computer software is intended to standardize AIMS applications and to turn it into one of the principal approaches towards cancer methylomes studies as well as towards diagnostics in oncology, including early screening.
|Geneset-based cancer survival analysis: On the non-uniform distributiuon of p-values under the null hypothesis|
Esteban Czwan, Benedikt Brors, David Kipling
Although null p-values are assumed to be uniformly distributed in gene expression experiments, the actual distribution often deviates from the assumed distribution. This can incorrectly associate the biology of a geneset with cancer prognosis in geneset-based survival studies. To assess the implications of this, a geneset-based method was developed. This method empirically approximates the distribution of null p-values and tests whether predefined sets of biologically-related genes are associate