How to look for temporal patterns of expression of genes or gene predictions

1. Click the Temporal Expression Pattern link to go to the expression query page.

For a single gene query, enter the 5 digits of a GLEAN number and click Submit. The next page is the 5-stage histogram pattern summarized from 5 oligomer probes. On this page,
  • Click Probe Sequences to see all probe sequences to evaluate the pattern.
    • Click each sequence to compare the sequence with all GLEAN predictions by BLAST. A single hit is usually a unique probe. Two matches nearly always indicate alleles or duplicates. Check the E value because we found that a perfect match for a 60-mer oligo is e-27 or e-26. A mismatched probe with E value over 5 orders difference (≥e-22) does not contribute to the pattern.
    • Click Pattern to see the pattern of expression for that probe. If similar patterns are seen for most probes, the summarized pattern is reliable.
    • Please read the notes on these two pages.

  • Click SPU_0xxxxx Sequences to retrieve the prediction's sequence. There are other tools on this site to analyze the sequence. For example, you can BLAST search the Supertig (Scaffold), EST, GLEAN3, Scaffold V2.0 and other databases.
You can also enter a common name (omit the preceding "Sp-") as a query. The next could be a pattern page if the output is a single gene or a list if the output is multiple genes. If the output is a list, click one of the names, which will lead to the individual pattern page.

If you have a list of GLEAN numbers, you can do a batch search to get a list of expression values. Enter comma-separated GLEAN numbers or copy/paste from an Excel spreadsheet and click Submit. The return page is a table with GLEAN numbers, common names and signal intensities for the five stages listed. At the bottom of the page, a link leads to a Comma Separated Version display for you to save for further analysis.

2. If you have a DNA sequence but there is no GLEAN number, you can query by clicking the Supertigs/EST/GLEAN3/Scaffold v2.0 link. From the Database drop list, select Array Probes, from the Blast Method drop list, select blastn. The matching probes will be listed. Click the probe name to see the expression pattern of that probe. At the bottom of the probe expression pattern page, a link leads to the summarized pattern for the prediction from which the probe was obtained. The probe name format is SPUR01Pxxxxxxyyyy. The xxxxxx part is the scaffold number (ignore the preceding 0s) or GLEAN number.