Table 1

Sources of automatically populated content

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.


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.

Yusuf et al. Genome Biology 2012 13:R24   doi:10.1186/gb-2012-13-3-r24

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