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Table 1 Sources of automatically populated content

From: The Transcription Factor Encyclopedia

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.
  1. Eight out of ten tabs in TFe articles contain one or more subheadings of automatically populated content. This table lists the direct sources of automatically populated content by tab and subheading ('section'). GO, Gene Ontology; RSCB, Research Collaboratory for Structural Bioinformatics.