RhodoBase
What is RhodoBase?
Collection of analytical tools designed to help reconstructing of transcriptional network modules in Rhodobacter sphaeroides on a genome-wide scale:
Recommended analysis pipeline:
While the system is fully functional without need to login, creating of a personal account is strongly encouraged: the modularity of the system allows to store job resulats and intermedate objects (such as gene lists and networks) in your personal account with possibility to use them later in further analysis.
Collection of analytical tools designed to help reconstructing of transcriptional network modules in Rhodobacter sphaeroides on a genome-wide scale:
- Advanced visualization of gene-centric transcriptional correlation networks based on meta-analysis of pooled transcriptome profiles
- Adaptive cross-genome transcription factor binding site pattern matching
Recommended analysis pipeline:
- Generation of the Gene Set:
- Input of a custom Gene Set generated with ArrayExplorer module (coming soon) or taken from other sources. GeneChip IDs, common names and gene names are recognized. -> Enter Gene List
- Generating of the Transcriptional Neighbours Gene Set around any Gene Of Interest (GOI) by Rhodobase system using Global Co-Expression Analysis -> Gene-Centric List
- Gene Set analysis:
- Visualizing network relationships between the Gene Set members -> Gene Network Visualization
- Searching for overrepresented transcription Factor Binding Site (TFBS) motifs within regulatory regions of the gene set members -> Motif Search
- Viewing the results (multiple views supported) -> Results
While the system is fully functional without need to login, creating of a personal account is strongly encouraged: the modularity of the system allows to store job resulats and intermedate objects (such as gene lists and networks) in your personal account with possibility to use them later in further analysis.