Biomedical Resources Browse by Title: T

Resource Name About this Resource
TOXNET

Toxnet is a collection of databases on toxicology, hazardous chemicals, environmental health, and toxic releases. Among the most popular included databases are the Hazardous Substances Data Bank, TOXLINE, and ChemlDplus. 

Transcription Factor Binding Sites (TRANSFAC)

About this Resource

Transcription Factor Binding Sites (TRANSFAC) is a knowledge-base containing published data on eukaryotic transcription factors and miRNAs, their experimentally-proven binding sites, and regulated genes.  The same data also forms the basis of derived positional weight matrices which can be used with the included Match™ tool to search DNA sequences for putative transcription factor binding sites. Integrated transcription factor ChIP-Seq, DNase hypersensitivity and histone methylated intervals from the ENCODE project complement the curated and predicted binding site data. All data, including the transcription factor – gene interactions, matrix library and command line Match™ program are available for download.

 

TRANSFAC

TRANSFAC is a knowledge-base containing published data on eukaryotic transcription factors (and miRNAs), their experimentally-proven binding sites, and regulated genes. The same data also forms the basis of derived positional weight matrices which can be used with the included tools (Match/FMatch/CMsearch) to search DNA sequences for putative transcription factor binding sites. Transcription factor ChIP-Seq, DNase hypersensitivity and histone methylated intervals from the ENCODE project have been mapped to promoter sequences and complement the binding site data curated from the literature.

Key Capabilities

  • Predict TF binding sites or composite elements within single DNA sequences with Match and CMsearch, using matrices (PWMs) from TRANSFAC or your own
  • Analyze microarray, ChIP-seq and RNA-seq data for over-represented TF-binding sites (FMatch/Step-by-step analysis)
  • Find de novo motifs in sequence sets with the DECOD algorithm and compare them against TRANSFAC matrices
  • Analyze gene sets for the presence of shared miRNA target sites
  • Build custom transcription regulatory networks from experimentally demonstrated factor-DNA and factor-factor interactions
  • Explore detailed reports for transcription factors, their experimentally-characterized binding sites, regulated genes and promoters with mapped regulatory features
  • Download binding fragments and best scoring sites from individual ChIP experiments in FASTA or BED format, or lists of nearest genes, for analysis

Access for database search does not require a personal username and password. But users will need to create a personal account to save data and to use the included tools.

A Yale email address is required to create an account. Register to use TRANSFAC®  

TRANSFAC + PROTEOME (formerly Biobase)

TRANSFAC  and PROTEOME (containing the HumanPSD and TRANSPATH databases) combine data on gene regulation, pathways, drugs and diseases. The data are assembled from the scientific literature by subject matter experts and organized in an accessible and easily searchable manner that enables the users to identify connections between disparate pieces of information and to apply that knowledge to their specific topic of interest. Integration of TRANSFAC and PROTEOME under one interface allows seamless analysis with the included tools and functionalities.

Access for database search does not require a personal username and password. But users will need to create a personal account to save data and to use the included tools.

TRIP Database

Simultaneously searches evidence-based sources of systematic reviews, practice guidelines, and critically appraised topics and articles. Also searches MEDLINE's Clinical Queries, medical image databases, e-textbooks, and patient information leaflets. [TRIP = Turning Research into Practice]