How to use Glycan Microarray DB

You can either upload your microarray data in a spreadsheet file or search the microarray data in our database.

Upload Microarray Spreadsheet File

  1. Click the "Browse" button to locate your microarray spreadsheet file. If you have the protein sequence information, you can copy and paste it in the text box. Please use the FASTA format. With the protein sequence infromation available, we will try to match PDB files.

    The uploaded spreadsheet file should contain at least three columns: Glycan Number, Glycan Structure and RFU (signal intensity), like the one shown in the following example. The glycan structure should be represented in the format of CFG (Consortium Functional Glycomics) text nomenclature.
  2. Select the criterion for binders and non-binders. We provide two options. For the first option, the z-score is calculated for each glycan, where z-score = (RFU - mean(RFU))/StDev(RFU). It is then converted to p-value. You can choose a threshold for the p-value (between 0 and 1). For the second option, the threshold is a certain percentage of the maximum RFU (between 0 and 100).
  3. View binders and non-binders. The binders and non-binders are sorted by either glycan number or signal intensity. Click the "View Binders / Non-Binders" button and you can see the signal intensity as well as the text and symbol nomenclature of each glycan.

    You can sort the list of binders / non-binders by glycan number or signal intensity.
  4. Match PDB Files (if you have uploaded the protein sequence information). You can choose the sequence identity (between 0 and 100), and the minimum length of glycan ligands in the PDB files.

    You can sort the list of PDB files by glycan ligand length, protein sequence identity or PDB resolution.
    Click the "View Structure" buttom to see the structure of the PDB file.

Search Database

  1. Search glycan microarray database by protein name, sequence or PDB Id.
    • Search by protein name. We provide some autocomplete options, however, you do not need to limit your search to these options. Please use double quotation marks for exact match. For example, "Concanavalin A" search for protein names containing "Concanavalin A", while Concanavalin A search for protein names containing "Concanavalin" and "A". Check the option "Microarray Sample with Protein Sequence information" if you want to include only the microarray samples with protein sequence information available in the search result.
    • Search by protein sequence. Copy and paste the protein sequence in the text box, and select the threshold of sequence identity for protein sequence alignment. Please use the FASTA format.
    • Search by PDB Id. Fill in the text box, and select the threshold of sequence identity for protein sequence alignment.

    You can use the following filters to narrow your search criteria.
  2. Select the microarray sample and criterion for binders and non-binders. The underlined samples have protein sequence information available. You can click to view the microarray sample information. We provide two options for the binder / non-binder criterion. For the first option, the z-score is calculated for each glycan, where z-score = (RFU - mean(RFU))/StDev(RFU). It is then converted to p-value. You can choose a threshold for the p-value (between 0 and 1). For the second option, the threshold is a certain percentage of the maximum RFU (between 0 and 100).
  3. View binders and non-binders. The binders and non-binders are sorted by either glycan number or signal intensity. Click the "View Binders / Non-Binders" button and you can see the signal intensity as well as the text and symbol nomenclature for each glycan.

    You can sort the list of binders / non-binders by glycan number or signal intensity.
  4. Match PDB Files (if the microarray sample you selected has protein sequence information available). You can choose the sequence identity (between 0 and 100), and the minimum length of glycan ligands in the PDB files.

    You can sort the list of PDB files by glycan ligand length, protein sequence identity or PDB resolution.
    Click the "View Structure" buttom to see the structure of the PDB file.