1. The Rice Functional Genomics Program of China cDNA microarray database (RIFGP-CDMD) consists of complete datasets, including the probe sequences, microarray images, raw data, and experiment description. The main goal of this database is to provide different users to download the microarray datasets and search the expression profiling for some interest genes. Also, this database makes available for people to do some sequence analysis for the genes presented in the cDNA microarray. RIFGP-CDMD homepage includes four parts of information: 1.Microarray experiment explorer: list the rice cDNA microarray data by projects and experiment information; 2.Analysis of cDNA clones: search the cDNA information by clone ID and blast sequences against local cDNA database and other databases; 3.Search data by sample information: download the data for specific experimental conditions; 4.Experiment data submission: submit the sample information and raw data for the new experiments RIFGP cDNA Microarray Database

2. Experiment explorer Project name and PI Table of experiments for project Download expression data (tif, gpr, exp files) Advance search for the expression profiling for selected probes and experiments Rice cDNA Microarray database 1. cDNA sequence: link to the NCBI database 2. Full-length cDNA: link to Japanese KOME database and TIGR OSA1 sequence database 3. Annotation 4. GO information search Analysis of cDNA clone cDNA information by Clone Id Blast sequences against the local cDNA database and other database Search Data by Sample information Search by sample keywords Advanced search by multiple keywords Data Submission Single experiment submission Group experiment submission

3. Click here to database structure and demo

4. Download slides for the instruction

5. Login or register here

6. Please login here If you are new user, please click here for asking login name and password

7. Click here to explore the microarray data Four parts of content in the database Introduction of the cDNA microarray database

8. The table lists the project name and PI. Click here for the experiment data of the project about the gene expression profiling in the normal developmental stages.

9. Click here to show the microarray image

10. ratio image (JPG file): 5DAP (f635) vs. 10EM (f532) Array ID Zoom Red: higher expression in Cy5-f635; Green: higher expression in Cy3-f532; Yellow: equally expression in both sample

11. Click here to show the microarray data

12. These rows provide the basic information about the microarray data generation.

13. Microarray raw data Position of the probes cDNA clone ID, NCBI Accession number and GenBank ID Median Intensity Mean Intensity Flags for unsure spots in the microarray Gene description for the probes in the microarray

14. Click here to show the microarray experiment information

15. Experiment information for the microarray

17. Click here to explore the microarray data List clone IDs here Click here to get the advanced search results Advance search: expression profiling for selected experiments and clones

18. Advance search result:

19. Click here to search and analyze the cDNA clones in the mcroarray

20. List clone IDs here Click here to get the sequencing results

21. Click here to get the NCBI information for the clone sequence

22. The clone information available in NCBI web

23. Click here to get the possible full-length cDNA sequence information List clone IDs here

24. Note: this research result was based on the annotation table for the cDNA clones in the microarray. The cDNA clones were blasted against two sequence databases, TIGR OSA1 and KOME rice full-length cDNA database. Click here to get the cDNA sequence

26. Click here to get the information in KOME

27. KOME information for the cDNA

28. Click here to get the sequence annotation

30. Click here to get the GO information

31. GO information for sequence p747d07p3; the other two sequences with no GO information

32. Search the clone ID for sequences Click here to do blast against cDNA clone database

33. Click here to get the detail blast result Note: this page shows the top hit for the blast result

35. Click here to search microarray data based on key words of sample information

36. Enter the key words of sample information Click here to search

38. Enter the key words of sample information Click here to search

40. Click here to submit microarray data in the web

41. Enter the general information for a microarray Enter the information for the microarray experiment design Enter the sample information and target preparation protocols used

42. Browse the microarray image and raw data Put the software information here Briefly add the information about the microarray design Click here to submit the microarray data information To submit a group of microarray experments’ information here. For the image and raw data, the FTP will be used for transferring data.