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

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

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dat

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e 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 SubmissionSingle experiment

submission

Group experiment submission

Click here to database structure and demo

Download slides for the instruction

Login or register here

Please login hereIf you are new user, please click here for asking login name and password

Click here to explore the microarray data

Four parts of content in the database

Introduction of the cDNA microarray database

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.

Click here to show the microarray image

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

Click here to show the microarray data

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

Microarray raw data

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Median IntensityMean Intensity

Flags for unsure spots in the microarray Gene description for the

probes in the microarray

Click here to show the microarray experiment information

Experiment information for the microarray

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List clone IDs here

Click here to get the advanced search results

Advance search: expression profiling for selected experiments and clones

Advance search result:

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

List clone IDs here

Click here to get the sequencing results

Click here to get the NCBI information for the clone sequence

The clone information available in NCBI web

Click here to get the possible full-length cDNA sequence information

List clone IDs here

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

Click here to get the information in KOME

KOME information for the cDNA

Click here to get the sequence annotation

Click here to get the GO information

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

Search the clone ID for sequences

Click here to do blast against cDNA clone database

Click here to get the detail blast result

Note: this page shows the top hit for the blast result

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

Enter the key words of sample information

Click here to search

Enter the key words of sample information

Click here to search

Click here to submit microarray data in the web

Enter the general information for a microarray

Enter the information for the microarray experiment design

Enter the sample information and target preparation protocols used

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.

Development stage

experiment PI Expermenter materials descriptionybxue lefu lan root 7 days oldybxue lefu lan shoot 7 days oldybxue lefu lan anther matureybxue ying lai UP pistil in the stage of 1-2 days before anthesisybxue ying lai 5hP pistil in the stage of 0-5 hours after anthesisybxue lefu lan 5DAP seed of 5 days oldybxue lefu lan 10EM embyro of 10-day old seedybxue lefu lan 10EN emdosperm of 10-day old seedNote: ying lai' work include the UP vs. 5hP,UP vs. shoot,5hP vs.shoot hybridization (the materials ,that is ,UP and 5hP are collected by lefu lan and wei chen in hangzhou)5DAP, 10EM and 10EN are col l ected by xi ansheng zhang

Hormone treament

experiment PI Expermenter materials descriptionkang chong zheng wang GA rice callus cell suspension culture under GA treatedkang chong zheng wang JA rice callus cell suspension culture under JA treatedkang chong zheng wang ck ri ce cal l us cel l suspensi on cul ture

Mutant

experiment PI Expermenter materials descriptionybxue ying lai S6 rice spikes derived from development stage 6 (meiotic division of pollen mother cells) in a floral mutant-1ybxue ying lai CK rice spikes derived from development stage 6 in wild type

ybxue ying lai S7 rice spikes derived from development stage 7 (filling stage of pollen) in the mutant-1ybxue ying lai CK rice spikes derived from development stage 7 in wild type

ybxue ying lai PM rice spikes derived from development stage 5 (formation of the pollen mother cells) in a floral mutant-2ybxue ying lai CK rice spikes derived from development stage 5 in wild type

Stress treamnet

experiment PI Expermenter materials descriptionybxue lefu lan w woundingybxue lefu lan(2hr,6hr(one slide done by meina li),12hr) and meina li(ck vs ck,30min,ck vs. 24hr)dr dehydrationybxue meina li re rehydrationybxue meina li treated Drought treated with no rehydrationNote: all the materials used in wounding and dehydration are derived from 14-day old shoot of rice