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PLEXdb Frequently Asked Questions






1.1. What is PLEXdb?

PLEXdb is a MIAME/Plant-compliant database which serves as a public repository for raw and normalized expression data. PLEXdb also provides annotation for the Affymetrix plant microarrays and for other important microarrays.

1.2. How is  PLEXdb funded?

PLEXdb is funded by USDA-NRI grant no. 2002-35300-12619.

1.3. Does PLEXdb only store Affymetrix barley GeneChip data?

No. PLEXdb accepts data obtained with all of the plant GeneChips provided by Affymetrix. Now PLEXdb also supports array platforms from NimbleGen (Maize NimbleGen array) and Affymetrix Whole Transcript arrays. We regard this diversity in microarray data as essential ingredient for comparative genomics analysis at expression level.

1.4. How is PLEXdb integrating expression data with other genomic data

PLEXdb is collaborating with PlantGDB and Gramene. This allows PLEXdb users to perform EST alignments and gene prediction using the Barley1 GeneChip exemplar sequences or cross-species comparison at the genome level. We plan to add links to dictionaries of cereal terminology and other databases in the future. If you have suggestions, please contact the PLEXdb development team.

1.5. Some vocabulary is not familiar; where can I find word definitions?

For the experiment submission process please see the help for each field. Information on the different types of GeneChip normalization and data processing is available on the data set query page. You may consult the glossary.

1.6. How do I cite PLEXdb?

To cite PLEXdb use the Dash et al 2012 Nucleic Acids Research article:
PLEXdb: gene expression resources for plants and plant pathogens.
Dash S, Van Hemert J, Hong L, Wise RP, Dickerson JA. 2012. PLEXdb: gene expression resources for plants and plant pathogens. Nucleic Acids Research 40 (D1): D1194-D1201.

In addition to citing the Dash et al paper listed above for general use of PLEXdb, if applicable, you should cite the original paper and the accession number used to identify the experiment(s) in PLEXdb. That way the original generators of the data sets will get credit and allow readers to locate the source. This will also add value to the original data. That is one of the goals of the PLEXdb database.

Publications for experiment data made available by PLEXdb are listed on the publications page as well as on the individual experiment pages.

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2.1. What's the submission interface for PLEXdb?

PLEXdb features a web-based experiment submission tool, PLEX Express, which allows users to manage their experiment descriptions, array design, and expression analysis information, either individually or as a group. This interface organizes the experiment by experimental factors and defines a organized submission table.

2.2. Is the submission tool, PLEXdb, consistent with the MIAME/Plant standards?

Yes. PLEX Express follows the guidelines set out by the MIAME working group as well as the MAIME/Plant whitepaper

2.3. What is needed before I start my submission?

The basic requirements for making a submission are:

1. Registration with PLEXdb as an official user.
2. Your experimental design.
3. Your protocols.
4. The raw data from Affymetrix MAS 5.0 Suite. *.CEL and *.EXP files are required for each hybridization.

2.4. Which operating systems can be used for making submissions?

Windows, MAC and Linux all work, provided you have a compatible browser installed. PLEXdb has been tested successfully with all popular browsers.

2.5. Which browser works best for the submission process?

Any popular browser should work fine for the submission process. You will be safest if you use Firefox, Safari, Mozilla, or Internet Explorer.

2.6. Why does PLEX Express require experiment factor and factor levels?

PLEX Express needs the experiment factors and their levels explicitly specified. This is essential for other users to understand the experiment, as well as helping PLEXdb to analyze and present the data in a more meaningful and easy-to-understand way. As more experiments are added to PLEXdb, this will also help users to compare results across experiments.

2.7. Must I finish a submission in one sitting? Can I stop at some point and resume submission later?

Yes, you may stop at any time point and resume submission later.

2.8. Can I add more experiment factors or factor levels to my finished submission?

No, this is one of the few fields that cannot be changed without resubmission. You can rename fields and values however (see section 2.9)

2.9. Can I change the names of the experiment factors/level?

Changing the names of factors or factor levels is allowed before finalizing your experiment submission, provided that this change will not change the numbers of factors and levels.

2.10. Any recommendations for a smooth submission?

Submission requires careful checking before presenting your results to other researchers in PLEXdb. Some things to keep in mind are:

  1. Specify the number of factors and the levels of each factor carefully. Once submitted, this information can't be changed without re-doing the entire submission. The only allowable modifications are typo-corrections or renaming the factors and levels.
  2. CAREFULLY check your file name association and sample association with the treatment before finalizing your submission. Complete all fields in the "Plant Sample Description" page that you have information for.
  3. Any revisions, except for text changes, after "Finalize" will incur much effort at both sides from submitter and administrator, and greatly delay the processing of your data in the best situation. Significant revisions may require re-submission.

2.11. I have many samples and they are very similar; how can I submit them quickly?

Specifiying pllant sample information is the most time-consuming part for experiment submission. To help ease this process, the submitter an copy existing plant sample records for editing. This means the submitter will need to just fill in one plant sample record completely, and for all subsequent samples, use this first record as a "template", changing the name and any other field that differ from one sample to the next.

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3.1. Why register with PLEXdb? How to register with PLEXdb?

Only registered users can submit their experimental data, access non-public data, and perform batch downloads of data.

3.2. What is the purpose of group management?

Group management lets users grant data access to their collaborators before the data is released to the public. For example, a user could create a group consisting of consortium members worldwide then give that group permission to view experiment data submitted by that user.

3.3. Will my experiment data be visible to the public immediately? Can I control who will be able to access my submission before my results are published?

PLEXdb encourages data sharing with the whole community. But we understand your need for keeping data private until your results are published. To make your data visible ONLY to users that you select, please designate your submission as "Private" or "Group Consortium" when you submit your experiment using PLEX Express. Then you can use group management to grant access to people you select.

3.4. How can I grant access to my private data to other users? Can I delete users from the access list?

Under the "Your Account" menu, select "Group Management", then you can create, edit, or remove groups. You can also add or delete users from your own groups.

To grant access to an experiment to a given group, under the "Your Account" menu, select "Experiment Management", follow the link Associate groups with the experiments.

3.5. What if I designated my data as private when making my submission, but later on I need to let selected people to access it?

You can create groups, and associate experiments with the groups as explained in 3.4.

3.6. Can I get all data for an experiment with batch download? What types of data will be downloadable?

Yes, we make all data available in compressed format for batch downloading. There are several common types of data: EXP, CEL (Probe-pair level information), DAT(images read by Affymetrix scanner), the normalized expression value files (using MAS 5.0 and RMA methods), and a table linking hybridization data files to each treatment and replication.

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4.1. How can I find an experiment? Can I view all experiments stored in PLEXdb?

You can query for experiments on the "Experiment Query" page. You will be able to see your own experiments, experiments you have been given permission to see by colleagues, and all of the public experiments.

4.2. I have sequence from other species, how can I find its homologous exemplar sequences and their expression in the supported GeneChips?

The best place to go is the "PLEXdb Blast" page. Input your sequence and click 'BLAST'. From the results page pick your sequence-of-interest for a detailed view.

4.3. My search returned a list of probe sets, can I get the probe-level data for them?

[Needs research]

4.4. I would like to analyze a data set obtained from my queries locally, what format is the data in?

You may now download them as tab-delimited text files, either as expression, or as annotation. This plain-text format can be easily imported to most microarray tools.

4.5. Where can I get all information for a given exemplar sequence or probe set?

Detailed information for probe sets or exemplars is available on the annotation page. For example, here is the annotation page for the Barley1 probes set, Contig1637_at. This page lists everything available within PLEXdb along with links to other databases on online resources for that probeset and microarray.

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