Expression Level Polymorphism Project



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ELP finder

This tool allows you to easily check if your genes of interest are differentially expressed between pairs of Arabidopsis accessions (Col-0, Cvi-1, Est, Kin-0, Mt-0, Tsu-1, Van-0). The values obtained with this tool are based on the control treatment GeneChip samples from the experiment described in our publication "Genomic survey of gene expression diversity in Arabidopsis thaliana" (PubMed link PubMed - National Library of Medicine). The results we provide for each gene and accession are the average expression value with the standard error, and the results of pairwise t-tests between the accessions selected.

Before using this tool you should read:
Experiment description and data processing.
Acknowledgment of Data Use and Disclaimer.




Step 1. Enter your gene(s) of interest.
  • You can enter either Affymetrix ATH1 GeneChip probeset IDs (e.g. 245612_at) or Arabidopsis gene codes (e.g. At4g14440).
  • Multiple entries on separate lines.
  • Limited to 50 probesets/genes (download entire data set here)


Step 2. Select the accessions of interest.


A) Do the 6 pairwise comparisons with Col-0.

OR

B) Do all pairwise comparisons with the accessions you select below:
Col-0 Kin-0 Van-0
Cvi-1 Mt-0
Est Tsu-1

You must select at least 2 accessions if you choose option B.
Step 3.




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Experiment description and data processing

Materials, experimental design and conditions.
See detailed description in Kliebenstein et al. (2005) PubMed link PubMed - National Library of Medicine.
Seeds of seven Arabidopsis thaliana accessions (Col-0, Cvi-1, Est, Kin-0, Mt-0, Tsu-1, and Van-0) were provided by J. Chory, Salk Institute, San Diego, CA. These accessions can be obtained from NASC (http://arabidopsis.info) and TAIR (http://www.arabidopsis.org). A factorial experiment was conducted with the seven accessions, using three biological replications for each of the two treatments and the three time points. Due to space limitations in the growth chambers, these replications were performed on different dates. For each biological replicate, multiple plants (~30) per accession were grown in a growth chamber under short day conditions (8 hr light at 100-120 µEi, 20° C day/20° C night) to maintain plants in the vegetative phase for six to seven weeks. Plants with 25 to 30 rosette leaves (rosette diameter 60 to 70 mm) were selected and control plants were sprayed with 0.02% Silwet L77, a surfactant, alone. Plants from each accession were harvested at 4, 28, and 52 hours post-treatment. RNA was purified and labeled cRNA was prepared and hybridized to Affymetrix ATH1 GeneChips, containing 22,810 Arabidopsis genes, according to the manufacturer’s guidelines (Affymetrix, Santa Clara, CA, USA).

Data processing
The GeneChips were scanned with an Affymetrix GeneArray 2500 Scanner and data acquired via the Microarray Suite software MAS 5.0. In order to allow comparisons of gene expression values across GeneChips, global scaling was used to adjust the trimmed mean signal of each GeneChip probe array to a target signal value of 600 (GeneChip Operating Software User’s Guide, Version 1.3, http://www.affymetrix.com/support/technical/index.affx). For each accession in the control treatment, the scaled expression values per gene of 9 samples (3 time points × 3 biological replicates) were used to calculate the average expression value for each probeset and the standard error of the average expression value per gene for these 9 samples. For all the pairwise combinations of the 7 accessions, we calculated the t-test probability values using the Microsoft Excel ttest function for a two-tailed distribution and type 'paired'. These t-tests have not been adjusted for multiple comparison correction since each researcher is requesting different numbers of tests. If a large number of tests are requested, appropriate multiple corrections should be applied.



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Acknowledgment of Data Use and Disclaimer

Data and information released from the Expression Level Polymorphism (ELP) Project website are provided on an "as is" basis, without warranty of any kind, including without limitation the warranties of merchantability, fitness for a particular purpose and non-infringement. Data and/or information may contain errors or be incomplete.

Availability of this data and information does not constitute scientific publication. We request that information derived from it not be published prior to our publication without permission (see below) or 12 months from the time of display (November 1, 2005 or later as indicated on individual data sets) whichever is the sooner.

Our policy is to release data in a timely and prompt manner to aid the progress of science in general and research in Arabidopsis in particular. However, it is not intended to allow others to preempt our scientific publications by rushing to publication in advance of our own efforts.

Therefore, written permission should be obtained from one of the project's Principal Investigators in writing in advance of submitting any articles containing data or figures primarily derived from this website prior to our publication or within 12 months of the data being displayed whichever is the sooner.

In accordance with scientific protocol, appropriate acknowledgment of the ELP Project should be made in any publications or other disclosures concerning data or information made available by the ELP Project. The data used for the 'ELP finder' tool can be referenced with the publication by Kliebenstein et al. (2005) PubMed link PubMed - National Library of Medicine. This project was supported in part by the Arabidopsis 2010 project, NSF Division of Molecular and Cellular Biosciences, award 0115109.

Except as expressly described above, please do not reproduce, redistribute, transfer, or publish any information or data from the ELP Project web site in whole or in part without the prior written permission of a Principal Investigator of the ELP Project.



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Download expression values entire data set

This data file contains the scaled expression values for the 22810 probesets for all control treatment GeneChip samples used for the 'ELP finder' tool. The file is in tab-delimited format. The first row contains the accession code, the second row contains the time point, the third row contains the biological replicate number and the fourth row contains the GeneChip sample code. The first column contains the 22810 probeset codes.

Before downloading the data set you should read:
Experiment description and data processing.
Acknowledgment of Data Use and Disclaimer.


Download data set (tab delimited text file; 8 MB)


Authors 'ELP finder': Hans van Leeuwen, Daniel J. Kliebenstein.




Contact information.

last modified on June 8, 2006