Help

  
 

 

About SAMMD

  • sammd is a meta-database. All the information in this database comes from manually curating the papers published on Staphylococcus aureus microarray studies.

  • ORF IDs in the curated papers are mapped on to their corresponding counterpart N315 ORF IDs for standard comparison purposes.
  • For more details about the back-end and the programming involved in this database please refer to the following reference.
  • If you find out a reference that is not included in sammd, please let us know so that we can include it in the database.

Search

You can search  sammd using an ORF ID or using a Gene Name or using an ORF Product Name.

Search using an ORF ID

  1. You can search sammd using ORF IDs from S. aureus strains N315 (eg., SA1007) or COL (eg., SACOL2737) or MW2 (eg., MW0848) or Mu50 (eg., SAV1433).
  2. Enter the ORF ID in the given text box. ID could be entered in any case (both sa1007 and SA1007 are valid queries and would return the same results)
  3. Select the ORFID option.
  4. Click the Search button.
  5. sammd maps your ORF ID to N315 ID and returns the expression status of your query ID under different experimental conditions.
  6. Remember to select the option ORF ID before searching.

Search using a Gene Name

  1. You can search sammd using a Gene name from S. aureus like agr or agrA or ure or ureA etc.,
  2. Enter the Gene name in the given text box. Gene name could be entered in any case ( for example, both agr and AGR are valid queries and would return the same results)
  3. Select GeneName option.
  4. Click the Search button.
  5. sammd lists all the hits that match your query Gene Name.
  6. Click an ORF ID from the results to know its expression status.
  7. Remember to select the option GeneName before searching.

Search using a ORF Product Name or Function

  1. sammd lets you search using the ORF Product name or by function like "accessory gene regulator" or urease or gyrase or "dna polymerase" etc.,
  2. Enter the ORF or Gene product name in the given text box.
  3. Make sure to select the ORFFunction option.
  4. Click the Search button.

  5. For ORFFunction option, users can query sammd using Boolean operators AND, NOT, * and "".

EXAMPLE searches using ORFFunction option

 

Search Term

Result

without any operator

urease gamma subunit

Returns any name that contains 'urease' and 'gamma' or 'subunit',      like;

urease alpha subunit

urease accessory protein, in addition to

urease gamma subunit

 

Without any operators (AND or NOT), 'gamma', 'subunit' becomes optional, in other words, urease gamma subunit returns results similar to urease OR gamma OR subunit

within double quotes ""

"urease gamma subunit"

Returns only

 

urease gamma subunit

with AND operator

urease gamma AND subunit

Returns all names containing both urease AND subunit, like;

 

urease alpha subunit

urease beta subunit

urease gamma subunit

with NOT and AND operator

urease NOT gamma AND subunit

Returns all names containing both urease AND subunit, but NOT gamma, like;

 

urease alpha subunit

urease beta subunit

with * wild card operator

transport*

Returns all names containing words like;

 

transport

transporter

transporting

Advanced Search

Your input for the advanced search, could be in any one of these formats:

N315 orf ids separated by a new line character

SA0107
SA0153
SA0253
SA0271
SA0899
SA0900
SA1007
SA1628
SA1630
SA1631
SA1842
SA1843
SA1844

N315 orf ids separated by a space

SA0107 SA0153 SA0253 SA0271 SA0899 SA0900 SA1007 SA1628 SA1630 SA1631 SA1842 SA1843

N315 orf ids separated by a comma

SA0107,SA0153,SA0253,SA0271,SA0899,SA0900,SA1007,SA1628,SA1630,SA1631,SA1842,SA1843

Compare Datasets

You can analyze the differences and similarities between any two or three transcriptomes that are present in SAMMD, using "Compare Datasets" option, using the following procedure:

  1. Select the number of datasets you want to compare. By default "Three" is the selected option. Click on the drop-down list to select "Two" if you want to compare only TWO datasets.

  2. If you want to compare TWO datasets, select the first dataset by clicking on the "click here to select FIRST dataset" drop-down list and choose the dataset of your choice.

 

 

  3. For every dataset there is an upregulated gene list and a downregulated gene list. You can choose either one of them for comparison by selecting the Up or Down option from the drop-down list adjacent to each dataset selection drop-down list.  By default Up regulation is selected.

  4. Follow the same procedure to select the second dataset and the third dataset (if you choose to compare three datasets).

  5. Click the button "Submit" to do the comparison.

 

 

  6. Set operations are performed on the submitted datasets and the result is displayed as a

"Venn Diagram".

 

 

  7. The Sets are labeled according to the dataset name, in the bottom of the Venn Diagram, with their corresponding Up or Down regulation type. The dataset labels are linked to the corresponding experiment details (clicking pops up  experimental details).

 

 

  8. Clicking the numbers in the Venn Diagram pops up the corresponding list of ORF IDs. The ORF IDs are linked to their respective NCBI Gene entries.

  9. You can Right click on the picture (click just outside the circles in the white space) and either copy or save it.

 

Database Schema

 

Implementation Scheme