TY  - JOUR
A1  - Ankenbrand, Markus J.
A1  - Weber, Lorenz
A1  - Becker, Dirk
A1  - Förster, Frank
A1  - Bemm, Felix
T1  - TBro: visualization and management of de novo transcriptomes
JF  - Database
N2  - RNA sequencing (RNA-seq) has become a powerful tool to understand molecular mechanisms and/or developmental programs. It provides a fast, reliable and cost-effective method to access sets of expressed elements in a qualitative and quantitative manner. Especially for non-model organisms and in absence of a reference genome, RNA-seq data is used to reconstruct and quantify transcriptomes at the same time. Even SNPs, InDels, and alternative splicing events are predicted directly from the data without having a reference genome at hand. A key challenge, especially for non-computational personnal, is the management of the resulting datasets, consisting of different data types and formats. Here, we present TBro, a flexible de novo transcriptome browser, tackling this challenge. TBro aggregates sequences, their annotation, expression levels as well as differential testing results. It provides an easy-to-use interface to mine the aggregated data and generate publication-ready visualizations. Additionally, it supports users with an intuitive cart system, that helps collecting and analysing biological meaningful sets of transcripts. TBro’s modular architecture allows easy extension of its functionalities in the future. Especially, the integration of new data types such as proteomic quantifications or array-based gene expression data is straightforward. Thus, TBro is a fully featured yet flexible transcriptome browser that supports approaching complex biological questions and enhances collaboration of numerous researchers.
KW  - database
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-147954
VL  - 2016
ER  - 
TY  - JOUR
A1  - Bemm, Felix
A1  - Becker, Dirk
A1  - Larisch, Christina
A1  - Kreuzer, Ines
A1  - Escalante-Perez, Maria
A1  - Schulze, Waltraud X.
A1  - Ankenbrand, Markus
A1  - Van de Weyer, Anna-Lena
A1  - Krol, Elzbieta
A1  - Al-Rasheid, Khaled A.
A1  - Mithöfer, Axel
A1  - Weber, Andreas P.
A1  - Schultz, Jörg
A1  - Hedrich, Rainer
T1  - Venus flytrap carnivorous lifestyle builds on herbivore defense strategies
JF  - Genome Research
N2  - Although the concept of botanical carnivory has been known since Darwin's time, the molecular mechanisms that allow animal feeding remain unknown, primarily due to a complete lack of genomic information. Here, we show that the transcriptomic landscape of the Dionaea trap is dramatically shifted toward signal transduction and nutrient transport upon insect feeding, with touch hormone signaling and protein secretion prevailing. At the same time, a massive induction of general defense responses is accompanied by the repression of cell death-related genes/processes. We hypothesize that the carnivory syndrome of Dionaea evolved by exaptation of ancient defense pathways, replacing cell death with nutrient acquisition.
KW  - Dionaea-muscipula ellis
KW  - Plant utricularia-gibba
KW  - Programmed cell-death
KW  - Genomics data sets
KW  - RNA-SEQ data
KW  - Arabidopsis-thaliana
KW  - Jasmonate perception
KW  - Action potentials
KW  - Stress responses
KW  - Wonderful plants
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-188799
VL  - 26
IS  - 6
ER  -