The High Priority list consists of genes with specific, biochemically testable predictions of molecular function that have been nominated by registered COMBREX users to have high priority for experimental validation. This High Priority status implies that their biochemical characterization would be of great benefit to the scientific community. The list is not ranked, and as a result it can be sorted by species name, gene name, and functional assignment.

Instructions on how to nominate a gene for the High Priority are shown below. Registered COMBREX users who wish to apply for funding to experimentally validate a High Priority gene may do so either through the appropriate gene page, or directly from the High Priority list (instructions can be found how to submit a bid document). If you have any questions regarding the top 100 list please contact us at: help-desk@combrex.bu.edu.

Instructions for Nominating a Gene for the High Priority List

Finding Your Gene of Interest

You must be a registered COMBREX user to nominate genes for the High Priority list, submit predictions, apply for funding, or submit annotations (instructions on setting up a COMBREX account can be found in the Guide for Navigating COMBREX REGISTERING AND LOGGING IN documentation).

To nominate a gene for the High Priority list, you must first search for your gene of interest in COMBREX and go to its dedicated gene page.

To find a gene of interest in the COMBREX gene database, enter information about the gene into the search field within the COMBREX homepage.

home_page_isomerase_example

In COMBREX, information about a gene is stored within its gene detail page. In order to locate the appropriate gene page, search for it using the search tools on the main page. COMBREX supports searching for a gene using keywords, Entrez gene id, protein GI, RefSeq protein accession id, Uniprot id, and gene symbol.

Examples of search terms accepted for a COMBREX query:

Entrez GeneIDs are typically of the form:

RefSeq protein accessions are typically of the form:

Uniprot IDs are typically of the form: Gene Symbols are typically of the form: NCBI Protein Cluster accession numbers are typically of the form: and Gene names and keywords can take a variety of forms:   

In general, the more specific the information used in your search, the easier it is to locate a specific gene of interest. Therefore, whenever possible, we advise that you search for a specific gene using its Entrez gene ID or protein GI.

The advanced search functionality can be used to specify your query and consequently limit your search results, allowing you to more easily find your gene of interest. Advanced search can be used to specify the organism, the experimental validation status of the gene, and/or the experimental validation status of the cluster.

advanced search

Currently, COMBREX organizes proteins within the context of NCBI protein clusters. Therefore, once you have submitted your search terms, COMBREX will return one or more appropriate NCBI protein clusters. If you search using an Entrez gene ID or protein GI, you should see only one cluster. Below this cluster, your gene of interest will be listed. Clicking on this gene link will bring you directly to the appropriate gene page.

search_results

If you search using keywords, COMBREX will in most cases return multiple protein clusters. You must then go through each protein cluster page until you find the appropriate gene link. Once you have located this link, clicking on it will bring you to the appropriate gene page.

If for some reason, your search does not return any results or the results do not contain your gene of interest, please review the search help documentation located in the COMBREX help center. If you still have questions, contact us at: help-desk@combrex.bu.edu.

Accessing the High Priority List submission form

On the gene page, scroll down to the Predicted Functions section and click on the “Submit” button to “Submit annotation/prediction/comment/gold gene set” as shown in the figure below. (This single button can initiate any of those actions.)

Submit

If you are not currently logged in, you will be asked to log in at this point.

Login Prompt

Filling out the High Priority List submission form

Once you have logged in, the “Submit Bid” page will appear with the prediction ID, gene ID, gene name, cluster ID, cluster name, organism, phylogenetic score, percent homology, prediction, and priority score of your gene of interest already filled in.

Top Priority List

In the provided text box marked "Annotation or Comment", please describe the predicted molecular function of the gene and, briefly, the reasons why this gene should be considered of High Priority for experimental validation.

You can also upload documents relevant to your nomination by clicking on the “Choose File” button , as shown below.

Choose File Button

If possible, please include any references relevant to your nomination.

In the box marked "Type" you must select “TOP 100_LIST” from the drop down menu.

Press “Submit” to send your form. Your submission will be reviewed before integration into the COMBREX database.

After submitting your nomination, you will receive an email confirming that your submission has been received. Your nomination will be reviewed before integration into the COMBREX database.

You can access all of your nominations for the High Priority list as well as submitted bids, annotations, and predictions through your user portal. If logged in, you can access your user portal by clicking on your user name, displayed as your email address, in the top right corner of any page in COMBREX.

My Nominations

In your user portal, click on “My Nominations” to access a list of your nominations for the High Priority list.