It's a pleasure to announce that new releases of a range of our products are now available. The new releases offer a number of new features and improvements specific for each of the products.
For more details on the updates, please visit the latest improvements/statistics pages for the products of your interest:
Biomedical Genomics Workbench 3.0
CLC Genomics Workbench 9.0
CLC Main Workbench 7.7
CLC Drug Discovery Workbench 3.0
CLC Sequence Viewer 7.7
CLC Genomics Server 8.0
CLC Server Command Line Tools 3.0
CLC Bioinformatics Database 4.7
CLC Developer Kit 9.0
CLC Genomics Developer Kit 9.0
CLC Developer Kit Server 9.0
TRANSFAC is a unique knowledge-base containing published data on eukaryotic transcription factors and miRNAs, their experimentally-proven binding sites, and regulated genes. Here we've identified a few papers referencing the use of TRANSFAC.
The handedness-associated PCSK6 locus spans an intronic promoter regulating novel transcripts
Shore et al.
Following up on their previously published GWAS study which looked at genetic signatures of handedness in individuals with dyslexia, the authors performed a detailed analysis of the PCSK6 locus and specifically SNP rs11855145. TRANSFAC was used for in silico analysis of transcription factor binding at this site, predicting an allelic effect on binding of several HOX transcription factors which have been shown to be involved in anterior/posterior developmental patterning. In vitro EMSA confirmed an allelic difference for transcription factor binding site affinity.
Erosion of conserved binding sites in personal genomes points to medical histories
Guturu et al.
The authors of this study used matrices from TRANSFAC to perform an analysis of variants that fall within conserved predicted transcription factor binding sites and are predicted to significantly decrease transcription factor binding affinity compared to the ancestral reference nucleotide. Their work suggests that these variants, which they call conserved binding site eroding loci (CoBELs), tend to congregate near functionally related genes and influence heritable phenotypes providing new insight into disease penetrance.
Antagonistic effects of IL-17 and D-resolvins on endothelial Del-1 expression through a GSK-3β-C/EBPβ pathway
Maekawa et al.
In this study, the authors sought to characterize the mechanism of regulation of Del-1, an endothelial cell-secreted anti-inflammatory protein whose expression is inversely related to IL-17 expression. Based on prior knowledge of IL-17 stimulation resulting in phosphorylation and inactivation of the transcription factor C/EBPβ, coupled with parallel knowledge that IFNγ stimulation simultaneously enhances transcriptional activity of C/EBPβ and increases Del-1 expression, the authors hypothesized that C/EBPβ may in fact be a regulator of Del-1 expression. Promoter analysis of the Del-1 encoding gene (EDIL3) using TRANSFAC identified two predicted binding sites for C/EBPβ. The relevance of these binding sites was confirmed using ChIP-seq data provided within TRANSFAC suggesting that C/EBPβ is indeed a positive regulator of Del-1 expression.
A novel, dynamic pattern-based analysis of NF-κB binding during the priming phase of liver regeneration reveals switch-like functional regulation of target genes
Cook et al.
The authors of this study sought to characterize the role of transcriptional regulation by NF-κB during liver regeneration. They used ChIP-chip analysis to isolate NF-κB binding sites, followed by de novo motif discovery to identify other transcription factors associated with transcriptional regulation during this process. TRANSFAC was used to analyze the de novo motifs, identifying potential co-regulators including AP-1, AP-2, SMAD3, TAL1 and more. Validation of NF-κB targets was performed by ChIP qPCR with primers designed using TRANSFAC.
Activation of the Nrf2 response by intrinsic hepatotoxic drugs correlates with suppression of NF-κB activation and sensitizes toward TNFα-induced cytotoxicity
Herpers et al.
The aim of this study was to better understand Nrf2 and NF-κB signaling in the context of response to drug-induced liver injury. Common sources for protein-protein interaction data were used to assemble the list of genes involved in these two pathways. TRANSFAC was used to uniquely provide the set of genes bound by the terminal NFE2L2 and RELA transcription factors at the end of the respective signaling cascades. The resulting list of genes was analyzed for differential expression upon exposure to compounds associated with drug-induced liver injury.
Read more about TRANSFAC
The AACR Annual Meeting 2016 will be held in New Orleans, Louisiana, on April 16-20.
The theme this year is "Delivering Cures Through Cancer Science" and we're very much looking forward to presenting our solutions for data analysis and interpretation.
During the conference you can find us at booth #741 and on April 19, we'll host a presentation on transcriptome analysis of pancreatic cancer exomes.
Presentation
Transcriptome analysis of Kupffer cells after uptake of pancreatic cancer exosomes reveal pathways and biological processes involved in metastatic progression
Speaker: Jean-Noel Billaud, Ph.D., Principal Scientist, QIAGEN
Date and time: Tuesday, April 19 at 3:00 PM – 4:00 PM
Location: Spotlight Theater B – Hall J (enter through Lobby I)
There will be a video shoot at the presentation
Posters
Gene expression signatures in circulating tumor cells are prognostic for metastatic lesions in breast cancer patients and correlate with response to therapy
Presentation time: Sunday, April 17 at 1:00 PM - 5:00 PM
Location: Section 23, poster board #19
Our solutions have been used for this research and there will be a video shoot at the presentation
The presence and persistence of ERCC1 positive circulating tumor cells predicts worse prognosis in primary ovarian cancer patients
Presentation time: Sunday, April 17 at 1:00 PM - 5:00 PM
Location: Section 21, poster board #24
Our solutions have been used for this research
Development of a quantitative targeted RNA-Seq methodology for use in differential gene expression analysis
We have developed a new digital targeted RNA-Seq technology for differential gene expression analysis - grab a copy of our poster at poster board.
Presentation time: Monday, April 18 at 1:00 PM - 5:00 PM
Location: Section 3, poster board #13
Identification of potential immune targets in controlling endometrioid endometrial carcinoma metastatic progression
Presentation time: Wednesday, April 20 at 8:00 AM -12:00 PM
Location: Section 22, poster board #23
We're looking forward to seeing you in New Orleans!
You can get additional updates on the Biomarker Insights blog
Get more information about AACR
Webinar
Studies of differential gene expression patterns using micro-array and RNA-seq technologies provide insight into the molecular mechanisms responsible for changes in gene expression. TRANSFAC, a unique knowledge-base containing published data on eukaryotic transcription factors and miRNAs, binding sites, and regulated genes can be leveraged to perform comparative promoter analyses of such high-throughput data, identifying the transcription factors most likely to have induced the experimentally observed pattern of gene expression.
In this webinar, we’ll discuss TRANSFAC’s method of virtual TSS calculation for defining promoter sequences and explore the impact that promoter assignments have on differential expression analysis results.
TRANSFAC 2015.3 release
Get a brief overview of the new features for easier and more specific data analysis:
Read more about TRANSFAC and the new updates.
At ISMB in Dublin it became clear: computational biology is quickly changing from an innovation field to an excellence field. While we are still far from knowing it all, we are certainly moving in the right direction.
A testimony to that is the fact that scientists are focusing more and more on issues as data compression and filtering instead of data collection.
At QIAGEN Bioinformatics we are, however, not intimidated by big data. Our colleague, Alex Kaplun, held Technical Track and introduced TRANSFAC, which is a knowledge-base for transcription factor binding sites, and the way it handles data and identifies the best supported promoters for a gene.
If you are interested in the topic, you can learn more about TRANSFAC, it’s features and capabilities, or get a trial on BIOBASE’s website.
Besides TRANSFAC, we featured two more products focusing on computational biology at ISMB 2015.
The first one was Ingenuity Pathway Analysis, which is a solution helping you to reveal potential causal associations hidden in your datasets of differentially expressed genes.
It has been widely adopted by the life science research community and perfected over the last 12 years. Right now we are proud to announce that a new major feature has been integrated into the software via the IPA 2015 summer release.
Read more about IPA 2015 summer release
The second product we presented was Ingenuity Variant Analysis, a leading application within human sequencing generated with next generation sequencing (NGS). Among many features, we highlighted the user friendliness of the interface, which makes it possible for people with no bioinformatic skills to use the software.
If this caught your interest and you want to learn more, please find product details, trials, access to webinars, training and more here: info, training and downloads
