4 Workflow
Here, we present TTSBBC to serve as a valuable resource for researchers investigating the role of TTSs in cancer and other genetic diseases. It offers an accessible platform for analyzing and visualizing TTSs.
There are 2 ways to use the app:
- query by region to find TTSs (findTTS)
- query by TTS to find their mapping locations and features (myTTS)
4.1 findTTS
4.1.1 findTTS input
TTSBBC has been designed to support multiple region queries to cater to a range of potential use cases. Users can input either a gene symbol (gene- or signature-level) or defined genomic regions (site-level), either individually or in batches. The users are also able to input amplified segments from CCLE cell lines. The app also allows users to query any custom genomic region to find TTSs.
4.1.2 findTTS: Biomarker
The Biomarker module analyzes TTS accuracy and precision for input query region(s). This allows users to find TTSs that accuratly and precisely target their query region(s). TTSBBC calculates accuracy and precision of a TTS to the input region set and visualizes it in a scatter plot. The most accurate and precise TTS will automatically be selected for network visualization to find on and off target locations for given TTSs. The user can select from the scatter plot which TTSs they want visualized in a network and to use in the Barcode module.
4.1.3 findTTS: Barcode
The Barcode module allows for a deeper exploration of TTS sequence features, spatial locations, and sequence-level motif clustering. This allows users to assess factors that affect TTS binding. From the selected TTSs in Biomarker, we have implemented a heatmap to summarize and filter by barcodes. We generate a circos plot to illustrate the targeted regions by the selected TTSs. We have employed unsupervised clustering to detect TTSs with high G-contents and proper length. The clustering is able to support pairwise features clustering for the numeric TTS sequence features such as G content, Length, and number of mappings.