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ErythronDB FAQ

Here are some questions and answers about the Erythron Database Website. If you do not find the information you are looking for, please contact us to submit your question.

What gene identifiers can I use in my searches?

Our gene identifier searches are case-insensitive and accept EntrezGene, MGI, or ENSEMBL Identifers, Official Gene Symbols and Gene Synonyms.

 

In what format should a gene list be provided in a search, either in a text box or uploaded file?

If a search allows a list of genes to be entered in a text box or uploaded from a file, the list may be separated by commas, semicolons or new-lines. For uploaded files tab separators work as well.

 

How do I find potential binding targets of a certain transcription factor?

Click on the "Search" tab. There is a section on Transcriptional Regulation. These inlcude manually curated target gene lists pulled from published ChIP studies and targets for key regulators of erythropoiesis computationally inferred using a positional weight matrix (PWM) sequence matching approach.

 

What is a Strategy?

Strategies are a graphical user interface (GUI) designed to make advanced searching and set operations (e.g., AND, OR, NOT) on search results easy for all users. The use of strategies facilitates the exploration of relationships across related datasets through the use of Venn Diagrams to detail a strategy's flow. For more details on the Strategy Framework, see Fischer et al. (2011). Database..

 

How can I view more information in the summary result table?

On the "My Strategies" page, above the table containing the results of your search, you will find a "Select Columns" button. Clicking this button will open a pop-up window that will allow you to select additional information about each gene.

 

How can I view the expression profile for the fetal definitive lineage in the result table?

On the "My Strategies" page, above the table containing the results of your search, you will find a "Select Columns" button. Clicking this button will open a pop-up window. Select "Fetal Expression" in the "Expression Profile" section.

 

How can I download a search result?

On the "My Strategies" page, above the table containing the results of your search, you will find a "Download..." link. If you follow this, you will be prompted to choose the format of the report and the columns to include.