Out now !
- TRANSFAC® 2023.1
- TRANSPATH® 2023.1
- HumanPSD™ 2023.1
New workflows and methods
- The platform now provides a new section called “Combinatorial regulation”, which provides tools for analysis of combinations of TF binding sites in promoters, enhancers and silencers, and other regulatory genomic regions. In this section, in addition to our traditional Composite Module Analyst, we introduce a completely new branch of site search combinatorial analysis methods based on the sparse logistic regression (MEALR).
- The new workflow Combinatorial regulation analysis of genomic or custom sequences scans input sequences for tissue and cell type- specific transcription factor binding regions using the newly created library of MEALR models delivered with the TRANSFAC® database.
- The new method MEALR combinatorial regulation analysis applies combinatorial regulatory models (CRMs) based on the MEALR affinity score to classify or scan sequences for occurrences of combinations of transcription factor binding sites represented by TRANSFAC® PWMs.
- The new method Extract TRANSFAC(R) PWMs from combinatorial regulation analysis extracts TRANSFAC® PWMs from a result table generated by the MEALR combinatorial regulation analysis. The PWMs represent transcription factor binding motifs for the TF in focus and its co-factors that constitute the combinatorial module predicted by the MEALR model.
New import possibility
- The files from the Sequence Read Archive (SRA) can be now uploaded to the geneXplain platform directly by the SRR ID.