TRANSFAC versus JASPAR
|
Feature |
TRANSFAC |
JASPAR |
|---|---|---|
|
Database statistics |
Factors – 48,258 DNA Sites – 50,892 Factor-DNA Site Links – 68,900 Genes – 102,973 Matrices – 10,706 References – 45,130 |
– No DNA Sites -2,000 profiles (Matrices) in JASPAR core (2024 release) |
|
Database statistics (miRNA) |
miRNAs – 1,772 mRNA Sites- 67,703 miRNA-mRNA Site Links – 74,553 |
No miRNA data |
|
Database statistics |
Distinct transcription factors in Chip-seq experiment : 1,171 TF-TG associations : 15,639,406 ChIP TFBS : 95,867,624 |
No Chip-seq data. |
|
Data Depth |
Genome annotation of experimentally validated TF binding sites Genome annotation of enhancers, genome conserved regions. |
Limited to binding motifs |
|
Data Quality |
Combines public and proprietary datasets, enhancing dataset completeness. |
Restricted only to open-access data. |
|
Data Integration |
Links TF binding site data with additional omics data, including epigenetic modifications and expression profiles. Supports multi-layered analyses that combine DNA-protein interactions and gene expression. |
Focuses on TF motifs and provides limited integration with other datasets. |
|
Integrated Pathway Analysis |
Supports integrated promoter and pathway analysis allowing to identify Master Regulators of the studied processes, which in their turn can serve as prospective disease mechanism-based biomarkers and drug targets |
Limited exclusively to promoter analysis with no further pathway analysis extensions supported |
|
Additional tools |
Offers tools like MATCH™ for TFBS prediction and analysis., Click and Run pipelines integrating TRANSFAC for identifying enriched binding sites, composite modules, combinatorial analysis |
No own tools. Linked to third-party tools for motif scanning and sequence analysis |
|
AI-based extensions |
Includes AI and ML based methods for prediction of TFBS combinations, including construction of composite modules based on a genetic |
Limited to standard approached towards motif scanning and sequence analysis |
|
Clinical Relevance |
Annotated for disease-related transcription factors and binding sites. In addition to biomarker info, includes annotations for drug-disease-clinical trials relations |
Minimal disease annotations |
|
Species |
Includes data on multiple species of vertebrates, nematodes, yeast, insects, plants. TRANSFAC is integrated with geneXplain platform and provides flexibility to integrate new custom genomes and identify transcription factor binding sites |
Includes TF binding motifs for six organism classes. Integration of new custom genomes is not provided |
|
Customer Support |
Regular updates, Prompt customer support with technical assistance by experts in the industry |
Open-source platform, assistance through documentation |
|
Accessibility |
Flexible, affordable and customized packages available to access total TRANSFAC functionality |
Freely accessible for academic and non-commercial research |