Tutorial

From Ytpdb

Contents 1 Free text edition 2 Modify gene data 2.1 Modify / create and edit gene data 2.1.1 Create a new gene 2.1.2 Modify gene report 2.1.3 Delete a gene 2.2 Add / modify / delete a protein post-translational modification 2.2.1 Add a new post-translational modification 2.2.2 Modify / complete a post-translational modification 2.2.3 Delete a post-translational modification 2.3 Add / modify / delete a protein Km value 2.3.1 Add a new Km value 2.3.2 Delete or modify Km value 2.4 Add or delete a reference about a gene 2.4.1 Add a new reference 2.4.2 Delete a reference

Free text edition

There are two distinct types of data in YTPdb : free text and tabular data. Almost any page (gene, substrate, substrate class, transporter class, this page, etc) can contain free text. To add or edit the free text data in a page (or add a picture), click on the "create" (in case there is already free text) or the "edit" tab that is on top of the page.

If the wiki syntax seems to tricky, you can simply click on the [Rich Editor] link that is displayed on top of the text field (see next figure).

Modify gene data

Modify / create and edit gene data

Create a new gene

1. Click on the link "Add a new gene" in the left menu

   

2. Fill the fields (see figure and description under the figure)

   

   1. Names
      1. Main synonym : specify the usual name of the gene
      2. ORF : specify the ORF name of the gene (something of the form YMR088C)
      3. Uniprot : specify the uniprot id (something of the form P12345)
      4. Synonyms : specify ALL the denominations of the gene with the main synonym, the orf and the uniprot id you have just entered together with other names. All the names must be separated by a vertical line (pipe) character : |
   2. Description : enter a small description
   3. Known function : specify whether the function of this protein is known or not
   4. Sublocation : choose the sublocation in the list
   5. Substrates : enter the substrates. The substrate must come from this [Browse_by_substrate_name|list], if the substrate you are looking for does not exist, you will have to create a new substrate (see the dedicated section). All substrates must be separated by a pipe character : | (vertical line).
   6. Discovery year : enter the year this gene has been identified (0 if uknown)
   7. TC family and YTP family : choose the family of the protein
   8. Sequences : peptidic and nucleotidic sequences
3. Click on Save

Modify gene report

1. Go on the gene of interest page
2. Click the link "Modify GENENAME data" on top of the page. A web form opens.

   

3. Fill the fields described in the previous section and click "Save"

Delete a gene

1. Follow the two first step of the previous section
2. Click on "Delete" button below.

Add / modify / delete a protein post-translational modification

Add a new post-translational modification

1. Starting from the gene report page of a gene you are interested in, click on the link See modifications and domains

   

   This page displays all post-translational mutations encoded in YTPdb for the transporter of interest. You also have access to a map of the protein that shows these modifications together with the PFAM domains.

2. Click on the Add a new post-translational modification link

   

3. A web form opens. In this form, you have to specify for each modification you want to enter :
   1. Residue : The type of amino acid to which the modification is applied. If this information is unknown, choose Undetermined
   2. Position : The position of the amino acid. If this information is unknown, the field must be emptied.
   3. Modification : Enter the modification type (phosphorylation, ubiquitylation, ...)
   4. Protein : The name of the protein which undergoes the modification
   5. Comments : Any interesting supplementary comment
   6. References : the pubmed id of the paper(s) describing this modifications. More than one pubmed id can be indicated, in this case, they must be separated by vertical bars (pipe) characters (|).

   

4. Click the Save button.

Modify / complete a post-translational modification

1. Starting from the post-translational modification page of the protein of interest (after executing point 1 of the previous section), click on the pencil icon next to the post-translational modification you want to edit.

   You are redirected to a form similar to the one described in the previous section that you can edit as explained previously.

Remember that to add a reference, you have to use the pipe character. If you overwrite the previous pubmed id, you will remove it.

Delete a post-translational modification

1. See point 1 of previous section
2. Click on the Delete button in the post-translational modification form.

Add / modify / delete a protein Km value

Add a new Km value

1. Starting from the gene report page of a gene you are interested in, click on the link See modifications and domains

   

   This page displays the Km values encoded in YTPdb for the transporter of interest.

   

   

2. Click on the Add a Km value for this protein link
3. A web form opens. In this form, you have to specify for each Km value :
   1. Compound : The substrate for which the entered Km applies
   2. The Km value or the Km range : If there is only one Km value, then only fill the first field. Don't forget to specify the unit in which this Km is expressed.
   3. Protein : Specify the protein to which this Km applies.
   4. References : Indicate the related references pubmed id. More than one pubmed id can be indicated, in this case, they must be separated by vertical bars (pipe) characters (|).
   5. Comments : Specify any interesting comment
4. When the form is filled, click on save.

Delete or modify Km value

1. Following the instructions given in the previous section, go to the page enumerating the Km values of the interest protein.
2. Click on the pencil icon, next to the Km value you want to suppress or edit.

   

3. If you want to delete the Km value, click on the "Delete" button, below the form that opened.
4. If you want to edit the Km value, fill the form according to the indications detailed in the previous section and click on the Save button.

Add or delete a reference about a gene

Add a new reference

1. Starting from the gene report page of a gene you are interested in, click on the link Add a new reference

   

2. You are redirected to a form that you have to fill this way
   1. Pubmed ID : the pubmed Id of the paper you would like to include as reference for this gene.
   2. Genes : the name of the gene that are concerned by this paper. There may be more than one gene, in this case they must be separated by the pipe (|) (vertical bar)
   3. Reference type : Id of the type of reference separated by a pipe (|) character. The id are described in the table in the bottom of the page.

   

3. Click on the Save button.

Delete a reference

1. Starting from the gene report page of a gene you are interested in, click on the link See list of curated references
2. You are redirected to the list of references for this gene. Click on the pencil next to the reference you want to remove.

   

3. In the form that opens and that summarizes the reference data, click on the Delete button