PlateletWeb - Systems Biology Workbench

5. How to optimally use advanced search options?

The advanced options search gives the opportunity to combine different types of search regarding a specific protein or a group of platelet proteins characterized by a specific feature, such as Gene Ontology terms, physical characteristics or drugs that target a set of proteins.

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A. Search Using Specific Identifier
	Search for a specific protein by its exact name (VASP, which retrieves VASP) or similar name (VASP, which retrieves VASP and EVL), or using the swissprot accession number or the NCBI gene id.
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B. Search for Drug Targets
	This search block is intended for searching a specific drug of interest and retrieving a list of "protein targets" associated with it. A list of suggestions is dynamically shown when entering the name of the drug. Clicking on the link "Drug ID: xxxxx " retrieves the DrugBank webpage with detailed information about the drug. The navigation to a target's description is simply achieved by clicking on the protein in the list of targets.
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C. Search for a specific term
	In this block, proteins can be searched according to specific words, found in their summary. A search for GO-ontology terms is also available and it provides a list of similar terms to the one entered in the search field. It is recommended to use a more specific term to get the best results and the results are limited to a maximum of 50.
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D. Combined Search
	It is possible to narrow down the search by using this combined search where a Gene Ontology term is required and this can be optionally complemented with the protein domains, level of detection and phosphorylation state. In order to make the search more easier, the suggestions are provided for both GO Terms and the protein domains. In the protein detection level, a drop down box is provided which lists multiple options for selection. ALL Levels: Proteins found on trancriptome level OR on proteome level OR on both transcriptome and proteome level. Only Proteome: Proteins found exclusively on proteome level and NOT on transcriptome level. Only SAGE: Proteins found exclusively on transcriptome level and NOT on proteome level. Full Proteome: Proteins found on proteome level, which might also have transcriptome data. Full SAGE: Proteins found on transcriptome level, which might also have proteome data. Both SAGE and Proteome: Proteins found on BOTH proteome and transcriptome level. In the phosphorylations, a check box is provided which can be combined for an optimal results. Platelet ST: Platelet proteins phosphorylated on Serine or/and Threonine residues. The phosphosites are detected in platelets. Platelet Y: Platelet proteins phosphorylated on Tyrosine residues. The phosphosites are detected in platelets. Human ST: Proteins phosphorylated on Serine or/and Threonine residues. The phosphosites are detected in human cells. Human Y: Proteins phosphorylated on Tyrosine residues. The phosphosites are detected in human cells. None: Proteins, which are not phosphorylated (This will uncheck all the other options). A list of all platelet proteins having these characteristics is easily retrieved and detailed information about the protein is then available.
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E. Search using Physical Properties
	Search using physical properties is a useful tool when looking for a set of platelet proteins having a similar length, molecular weight or isoelectric point range. In order to further minimize the results, a combined search is helpful.
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