Link: https://portal.genexplain.com/cgi-bin/transfac_factor/search.cgi
It seems the database might have severe issues. They either reused information from different transcription factors than the one some pages are about or they have wrongly tagged some TF pages.
EG I am searching some C/EBP transcription factor binding site hits and out of 4 different C/EBP hits with different accession numbers, all pages link to a different TF in a different host.
For example: if you search T0138, then in the search results page, as well as in Alggen promo, it says T01386 is C/EBP from Aplysia californica; but if you click on it, you go to a page about protein X from HBV and it is not a link issue since it clearly displays 1386 in the url in browser.
I know it is a free version; but how can this happen?
Here are a few potential reasons why these issues might be happening and steps you can take to address them:
### 1. **Database Versioning Issues**:
- The **TRANSFAC public database** may be using an outdated or free version of the platform that hasn’t been updated to include recent corrections or adjustments. This could lead to mismatched transcription factor data and link issues.
- **Solution**: Contact the database administrators at geneXplain or check if they have a more up-to-date, paid version that may not have these issues.
### 2. **Incorrect or Mixed Metadata**:
- It is possible that some of the transcription factors, such as C/EBP, have incorrect metadata attached to their entries, leading to wrong accession numbers being linked to incorrect transcription factors or species. This can happen in large datasets where information is continuously updated.
- **Solution**: Report the issue to geneXplain support. They may not be aware of the problem with these specific TF entries and can investigate further.
### 3. **Free vs. Paid Database Versions**:
- Sometimes, the free versions of databases are more prone to errors or may have limitations compared to full paid versions, which are often more rigorously maintained. The paid versions may include more complete and corrected data.
- **Solution**: If your work is dependent on accurate TF data, consider investing in the full version or finding alternative databases like **JASPAR** for transcription factor binding sites.
### 4. **Browser or Interface Glitches**:
- It’s possible that the issue you’re experiencing with the URL displaying the correct TF accession but loading a different page could be a browser or interface glitch, though this seems less likely given your detailed description.
- **Solution**: Clear your browser cache or try accessing the database through another browser or device to see if the issue persists. If it does, it’s likely a backend problem with the database.
### 5. **Alternative Databases**:
- If the issues with TRANSFAC persist, you might want to consider other transcription factor databases that could provide similar information, such as:
- **JASPAR**: A high-quality, curated database for transcription factor binding profiles.
- **HOCOMOCO**: A collection of human transcription factor binding models.
- **TFClass**: A classification of eukaryotic transcription factors based on structural features.
### 6. **Contact Support**:
- **geneXplain** provides technical support and feedback channels. Reporting the issue might help them fix it faster, and they might provide insights into whether the problem is a temporary glitch or a known issue.
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