Tab | Section | Sources | Use of sources |
---|---|---|---|
Structure | Structures | RSCB PDB, Pfam | Structural predictions are made with the help of experimentally verified protein structures downloaded from the RSCB PDB. In the process of creating the structural predictions, we use the HMM database from Protein Families (Pfam) to help us identify domains found in protein sequences in the RSCB PDB database (which we use as templates) as well as the protein sequences of putative structures we want to predict |
TFBS | TFBS logos | PAZAR | The logo in this section is generated with the Perl module MEME and its dependencies, using binding site data from PAZAR |
 | Binding site profiles | PAZAR | The logo and position frequency matrix in this section are generated with the Perl module MEME and its dependencies, using binding site data from PAZAR |
Targets | Targets (author curated) | Gene Ontology (NCBI) | While the author provides the gene ID, TF complex, effect, and reference, biological process GO terms associated with each target gene in this section are imported from gene-to-GO annotations from NCBI |
 | Targets (automatically populated) | PAZAR, Gene Ontology (NCBI) | Target gene, TF complex, and reference data are imported from PAZAR. The author supplies effect data. Biological process GO terms associated with each target gene in this section are imported from GO annotations provided by NCBI |
Interactions | Ligands (author curated) | PubChem (NCBI) | While ligand IDs, experiment types, natures of interaction and references are supplied by the author, the ligand common name and image are provided from PubChem |
 | Interactions (automatically populated) | BioGRID | Interactor names, experiment types, and references are imported from BioGRID. Natures of interaction are provided by the author |
 | Transcriptional regulators (automatically populated) | PAZAR, Gene Ontology (NCBI) | Regulating TF complex, regulating TF, genomic links, and reference information are provided by PAZAR. Biological process GO terms associated with each target regulator in this section are imported from GO annotations provided by NCBI |
Genetics | MeSH cloud (automatically populated) | MeSH (NCBI), Entrez Gene, GeneRIF | MeSH term associations and Fisher's exact P-values are generated using data from NCBI MeSH, Entrez Gene, and GeneRIF |
Expression | Expression (automatically populated) | UCSC Genome Browser, Allen Brain Atlas | Expression data in this section are imported from the UCSC Genome Browser database, GNF Expression Atlas 2 dataset, and the Allen Brain Atlas |
Ontologies | Gene Ontology (automatically populated) | Gene Ontology (NCBI) | GO terms associated with the transcription factor in this section are imported from GO annotations provided by NCBI |
 | MeSH cloud (automatically populated) | MeSH (NCBI), Entrez Gene, GeneRIF | MeSH term associations and Fisher's exact P-values are generated using data from NCBI MeSH, Entrez Gene, and GeneRIF |
Papers | Papers | PubMed | Detailed information on relevant papers such as authors, titles, journals, and publication dates are imported from NCBI PubMed. |