1. Forthcoming… Molecule Pages –
Mutations ---
Sequence Alignments & Structure Display
Tracking of Molecular State Changes
Connection to Signaling Pages
Signaling Database Infrastructure & Display of Biochemical Networks
Complex Query Tools and Engines ---
“Context-specific” Parts Lists – The precursor to reconstruction of signaling maps

2. Molecule Page Search Function

6. Forthcoming… Molecule Pages –
Mutations ---
Sequence Alignments & Structure Display
Tracking of Molecular State Changes
Connection to Signaling Pages
Signaling Database Infrastructure & Display of Biochemical Networks
Complex Query Tools and Engines ---
“Context-specific” Parts Lists – The precursor to reconstruction of signaling maps

7. The Parts-List: AfCS Strategy

8. This is the “front door” to the database, and also serves as the launching point for searching all information by gene name. The “Limit to experimental match” option will be redundant once all data types have their own special search pages, I think. Note the highlighted experiment type: the Agilent-Operon chip. This is a hyperlink to its special “parts list” page.

9. This is a result of a gene search for “Bcap”
This is a result of a gene search for “Bcap”. Note all the experimental data that appears for it, with hyperlinks to the molecule pages (via AfCS ID), LocusLink (via the gene name), and Affymetrix and Agilent cDNA annotation (via the cloneID). The “D” button shows all related protein database records and extended synonym information, the “E” link goes to experimental results of that datatype for this gene, the “S” link zeroes in on a summary like this one for those genes, the “B” link goes to Yeast 2-hybrid bait information (in the DataCenter), and the “I” link goes to the Y2H Interaction summary for that bait.

10. This is what you get when you select the “E” link for the Agilent-Operon oligo microarray. The expression calls were from Yi-Xiong’s analysis.

11. This is the setup page for the Agilent-Operon “parts list” building page.

12. This is a small part of a parts list built from the Agilent-Operon microarray set. This particular list was built from all genes showing any expression. The 4th column are synonyms, and the 5th column shows all clones on the chip which *could* be related to the particular gene. The number in parentheses is sort of an alignment measure of the oligo to the gene – 1 is a perfect match. Any times listed after that are those where expression of the gene was seen.

13. The AfCS Molecule Pages
Joshua Li
Yuhong Ning
Warren Hedley
Brian Saunders
Andrea Maer
Yongsheng Chen
Timo Hannay (NPG)
Nicole Tindill (NPG)
& Dallas AfCS Team
The “alpha-beta” testers
AfCS
2002