Search   for 
Find Your Gene ·  Publications ·  Tools ·  Gene List Suite ·  Expression Atlases ·  About PLEXdb ·  Feedback
Login ID:
Password:
Plants
Arabidopsis
Barley
Brachypodium
Citrus
Cotton
Grape
Maize
Medicago
Poplar
Rice
Soybean
Sugarcane
Tomato
Wheat
Pathogens & Symbionts
Search Experiments
Download Data
Gene List Suite
Tools
Your Account
Documentation
News
Personnel
Links
 Data Release Policy 
PLEXdb is committed to making expression data publicly available to researchers world-wide...
complete policy
 

Browse SoyPLEX Experiment Data

Choose an experiment:
Transcript profiling of common bean using the Soybean Genome Array: optimizing analysis by masking biased probes
Sam Yang, USDA, ARS, St Paul, Minnesota (sam.yang@ars.usda.gov)
Experiment design (18 hybridizations)
species
•soybean •common bean
organism part name
•leaf •nodule •root

This experiment has been imported by PLEXdb from NCBI GEO (GSE18822) Series_summary: Common bean (Phaseolus vulgaris) and soybean (Glycine max...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

Show
Experiment Name: Transcript profiling of common bean using the Soybean Genome Array: optimizing analysis by masking biased probes
Accession No: GM30
Microarray: Soybean
Visibility: public
Experiment Type:
Experiment Factor(s):
species
•soybean   •common bean
organism part name
•leaf   •nodule   •root
Quality Control: biological replicates
Treatment summary:
 species  organism part name  # replicates
 soybean  leaf  3
 soybean  nodule  3
 soybean  root  3
 common bean  leaf  3
 common bean  nodule  3
 common bean  root  3
Total hybridizations: 18
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE18822)

Series_summary:
Common bean (Phaseolus vulgaris) and soybean (Glycine max) both belong to the Phaseoleae tribe and share significant coding sequence homology. To evaluate the utility of the soybean GeneChip for transcript profiling of common bean, we hybridized cRNAs purified from nodule, leaf, and root of common bean and soybean in triplicate to the soybean GeneChip. Initial data analysis showed a decreased sensitivity and specificity in common bean cross-species hybridization (CSH) GeneChip data compared to that of soybean. We employed a method that masked putative probes targeting inter-species variable (ISV) regions between common bean and soybean. A masking signal intensity threshold was selected that optimized both sensitivity and specificity. After masking for ISV regions, the number of differentially-expressed genes identified in common bean was increased by about 2.8-fold reflecting increased sensitivity. Quantitative RT-PCR analysis of a total of 20 randomly selected genes and purine-ureides pathway genes demonstrated an increased specificity after masking for ISV regions. We also evaluated masked probe frequency per probe set to gain insight into the sequence divergence pattern between common bean and soybean. The results from this study suggested that transcript profiling in common bean can be done using the soybean GeneChip. However, a significant decrease in sensitivity and specificity can be expected. Problems associated with CSH GeneChip data can be mitigated by masking probes targeting ISV regions. In addition to transcript profiling CSH of the GeneChip in combination with masking probes in the ISV regions can be used for comparative ecological and/or evolutionary genomics studies.

Series_overall_design:
We hybridized cRNA purified from nodule, leaf, and root of common bean and soybean in, triplicate, to the soybean GeneChip (18 GeneChip hybridizations = 2 species x 3 organs x 3 replicates).
Publication: 'Transcript profiling of common bean (Phaseolus vulgaris L.) using the GeneChip Soybean Genome Array: optimizing analysis by masking biased probes.', Yang SS, Valdés-López O, Xu WW, Bucciarelli B, Gronwald JW, Hernández G, Vance CP.
BMC Plant Biol 2010 May 7;10:85.
pubmed: 20459672
Created: 2011-04-21 13:24:55
Last Update: 2011-06-02 13:24:41
Released: 2011-06-02
GEO Accession GSE18822
Submitter: PLEXdb Curator
Name: Sam Yang
Institution: USDA, ARS, St Paul, Minnesota
Head of Laboratory: Sam Yang
email(s):
Homepage:

 
Copyright@2001-2013 The PLEXdb Group
All rights reserved.

For problems with the webpages contact PLEXdb webmasters