Frequently Asked Questions

What species are stored in the database?

The current version of ORTRD houses human olfactory receptor (OR) TF/Gene dataset.

Why might web pages load slowly?

ORTRD uses advanced storage technology and has sufficient bandwidth for fast web page loading. However, a few users may experience slow loading times due to their network conditions.

What Information is available in the ORTRD?

ORTRD is a database for human genes, and has information on olfactory receptor genes, their transcription factors (TFs), and regulatory mechanisms.

Is the service provided by ORTRD free?

The service is provided free to academic non-profit institutions.

How can I get TF-Gene pairs for a particular search entry?

TF-Gene pairs for human olfactory receptors can be freely obtained by downloading the datasets in the information page.

Why does my search term return 'no results available'?

Your search term returns 'no results available' because our database lacks corresponding regulatory annotations or significant annotation results for this TF/gene.

How can I find the specific function of a gene in ORTRD?

In ORTRD, human genes are linked to the NCBI database, and transcription factors (TFs) are linked to the UniProt database. When users click on a gene NCBI ID or TF UniProt ID, it automatically searches the relevant database and displays detailed information and functions of the gene or TF.

What does the positive and negative value of log2FC means?

Log2FC > 0 means gene is down-regulated, log2FC < 0 means gene is up-regulated. Log2FC values represent the comparison between knocked-down transcription factors (TF) and control samples. When a transcription factor is upregulated in the control sample and downregulated in the knocked-down sample, the transcription factor's effect is inversely correlated with the logFC value.
If the log2FC value is negative, it means the gene is more active (upregulated) in the control condition, where the transcription factor is present.
If the log2FC value is positive, it means the gene is less active (downregulated) in the control condition, where the transcription factor is present.

Why some regulation information is "conflicting/activation" or "conflicting/repression"?

Information where the Biological process terms do not have the word "negative" or "repressor" have the "conflicting" tag. This means when biological process do not have a proper indication of whether it is positive or negative regulation, or instances where Biological processes and Log2(FC) values do not match, such instances were marked as conflicting in both activation and repression.
For example, Gene symbol : "OR10A5" and TF symbol : "BCL6"

What criterion is used to prioritize one transcription factor (TF) over others in the list? Does the server-side determine which TF is prioritized? While the regulatory network displays multiple TFs, what is the basis for selecting one TF over the others for additional information?

There is no predefined criterion on the server-side for prioritizing one Transcription Factor (TF) over others in ORTRD. The appearance of a specific TF in the result is solely dependent on the data collection process.
During data integration, ORTRD compiles information from multiple sources, including GTRD, ENCODE, GEO, and KnockTF. The association between an olfactory receptor (OR) gene and a TF is determined by the order in which the data was processed and stored rather than any ranking or prioritization mechanism. While the gene regulatory network (GRN) visually represents all TFs linked to a specific OR gene, the display of a particular TF over others is incidental. It is not influenced by any server-side prioritization algorithm but rather by the sequence in which the TF-OR interactions were retrieved and integrated into the database.

What are the search tips?

To search a gene entity type its gene symbol into the search bar and select the gene symbol radio button while for a TF search type their symbol and select on the transcription factor symbol radio button.

How often does ORTRD update?

We will be continuously updating ORTRD in the future. Once we curate, process, and analyze new dataset, the related gene regulatory network information will be available in the ORTRD. The updated information will be displayed in the Home webpage.