Searching proteins by identifier in TcoF-DB requires the selection of the desired type of protein. Proteins can be searched by three different identifiers using the 'Search by identifier' tab on the home page of TcoF. These identifiers are Uniprot identifiers like e.g. 'BRCA1_HUMAN', Uniprot accession number like e.g. 'P51587' and the recommended protein name as given in the Uniprot/SwissProtKB like e.g. 'Breast cancer type 2 susceptibility protein'. A result is returned if the given search string is contained as a substring in the respective database field. Entering an empty search string will result in all proteins being returned.

The search results are presented in form of a table. If there are more than 20 results, they are given page by page in a browsable format. The left three columns contain the main identifiers of the protein in question. The three columns on the right contain the classification of the given protein as 'TF', 'TcoF', 'TF binding protein' or 'Other protein', the number of interactions that was found for a given protein and a link to details for the protein. For TcoFs the classification of the TcoFs according to the available evidence in GO is also given.

The details page for transcription factors consists of two parts. The upper section contains a table with all details for the protein in question including all names, annotations, tissues and protein sequence. This section also contains the 'status evidence' statement that contains the justification for this protein to be considered a TF. At the top of the lower section the total number of proteins that interact with the TF in questions is given. These proteins are divided into three parts: Transcription factors that interact with the one in question, the transcription co-factors that are reported to interact with it, and its interactions with other proteins. All of these can be listed by clicking on the small magnifying glass. The interaction between a TF and another protein can be reported a number of times (e.g. by several reference databases or by several experiments within the same reference database). A horizontal line is used to divide lines referring to the same interacting protein. The interacting TcoFs are divided into sections according to their TcoF class. Detailed information for each interaction is given in all cases. This information comprises source reference database (e.g. EBI's IntAct), type of interaction, name of experiment, reference (as link to PubMed or DOI) and a link to the interaction in the source reference database.

The details page for transcription co-factors equally consists of two parts. The upper section contains a table with all details for the protein in question including all names, annotations, tissues and protein sequence. This section also contains information about why this protein is regarded as a TcoF and details about the GO annotations used to make this assessment are given. The class of the TcoF is also given here. The class of a TcoF depends on the typenof evidence that was used to annotate the protein as 'involved in transcription regulation' and 'nuclear'. The lower section contains information about the transcription factors that are reported to interact with the given co-factor. It can be accessed by clicking on the small magnifying glass. The interaction between a TcoF and another protein can be reported a number of times (e.g. by several reference databases or by several experiments within the same reference database). A horizontal line is used to divide lines referring to the same interacting protein. The interacting TcoFs are divided into sections according to their TcoF class. Detailed information for each interaction is given in all cases. This information comprises source reference database (e.g. EBI's IntAct), type of interaction, name of experiment, reference (as link to PubMed or DOI) and a link to the interaction in the source reference database.

The details page for other TF interacting proteins also consists of two parts. The upper section contains a table with all details for the protein in question including all names, annotations, tissues and protein sequence. Other TF interacting proteins are proteins that are neither TF not TcoF, but nevertheless interact with at least one TF. The lower section contains information about the transcription factors that are reported to interact with the given protein. It can be accessed by clicking on the small magnifying glass. The interaction between a proteni and a TF can be reported a number of times (e.g. by several reference databases or by several experiments within the same reference database). A horizontal line is used to divide lines referring to the same interacting protein. The interacting TcoFs are divided into sections according to their TcoF class. Detailed information for each interaction is given in all cases. This information comprises source reference database (e.g. EBI's IntAct), type of interaction, name of experiment, reference (as link to PubMed or DOI) and a link to the interaction in the source reference database.