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RIFGP cDNA Microarray Database PowerPoint Presentation
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RIFGP cDNA Microarray Database

RIFGP cDNA Microarray Database

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RIFGP cDNA Microarray Database

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  1. RIFGP cDNA Microarray Database • 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: • Microarray experiment explorer: list the rice cDNA microarray data by projects and experiment information; • Analysis of cDNA clones: search the cDNA information by clone ID and blast sequences against local cDNA database and other databases; • Search data by sample information: download the data for specific experimental conditions; • Experiment data submission: submit the sample information and raw data for the new experiments

  2. Download expression data (tif, gpr, exp files) Table of experiments for project Experiment explorer Project name and PI Advance search for the expression profiling for selected probes and experiments 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 cDNA information by Clone Id Analysis of cDNA clone Blast sequences against the local cDNA database and other database Rice cDNA Microarray database Search by sample keywords Search Data by Sample information Advanced search by multiple keywords Single experiment submission Data Submission Group experiment submission

  3. Click here to database structure and demo

  4. Download slides for the instruction

  5. Login or register here

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

  7. Introduction of the cDNA microarray database Click here to explore the microarray data Four parts of content in the 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. Red: higher expression in Cy5-f635; Green: higher expression in Cy3-f532; Yellow: equally expression in both sample ratio image (JPG file): 5DAP (f635) vs. 10EM (f532) Zoom Array ID

  11. Click here to show the microarray data

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

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

  14. Click here to show the microarray experiment information

  15. Experiment information for the microarray

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

  17. Advance search result:

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

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

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

  21. The clone information available in NCBI web

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

  23. Click here to get the cDNA sequence 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.

  24. Click here to get the information in KOME

  25. KOME information for the cDNA

  26. Click here to get the sequence annotation

  27. Click here to get the GO information

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

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

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

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

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

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

  34. Click here to submit microarray data in the web

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

  36. Put the software information here Browse the microarray image and raw data 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.