the rice functional genomics program of china cdna microarray database (rifgp-cdmd) consists of...
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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
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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
Ric
e cD
NA
Mic
roar
ray
dat
abas
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
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Click here to database structure and demo
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Download slides for the instruction
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Login or register here
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Please login hereIf you are new user, please click here for asking login name and password
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Click here to explore the microarray data
Four parts of content in the database
Introduction of the cDNA microarray database
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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.
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Click here to show the microarray image
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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
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Click here to show the microarray data
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These rows provide the basic information about the microarray data generation.
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Microarray raw data
Pos
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Median IntensityMean Intensity
Flags for unsure spots in the microarray Gene description for the
probes in the microarray
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Click here to show the microarray experiment information
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Experiment information for the microarray
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Cli
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data
List clone IDs here
Click here to get the advanced search results
Advance search: expression profiling for selected experiments and clones
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Advance search result:
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Click here to search and analyze the cDNA clones in the mcroarray
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List clone IDs here
Click here to get the sequencing results
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Click here to get the NCBI information for the clone sequence
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The clone information available in NCBI web
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Click here to get the possible full-length cDNA sequence information
List clone IDs here
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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
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Click here to get the information in KOME
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KOME information for the cDNA
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Click here to get the sequence annotation
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Click here to get the GO information
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GO information for sequence p747d07p3; the other two sequences with no GO information
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Search the clone ID for sequences
Click here to do blast against cDNA clone database
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Click here to get the detail blast result
Note: this page shows the top hit for the blast result
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Click here to search microarray data based on key words of sample information
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Enter the key words of sample information
Click here to search
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Enter the key words of sample information
Click here to search
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Click here to submit microarray data in the web
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Enter the general information for a microarray
Enter the information for the microarray experiment design
Enter the sample information and target preparation protocols used
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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.
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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