[Arabidopsis] genomic and proteomic data not matching

Stacey, Gary via arab-gen%40net.bio.net (by staceyg from missouri.edu)
Tue Sep 22 17:32:34 EST 2009

This is what one would expect. Transcriptomic and proteomic data have very low correlation. Check the literature and you will find numerous examples of this.

Gary Stacey, Ph.D.
Director, Center for Sustainable Energy
Assoc. Director, National Center for Soybean Biotechnology
Divisions of Plant Sciences and Biochemistry
Department of Molecular Microbiology and Immunology
271E Christopher S. Bond Life Sciences Center
University of Missouri
Columbia, MO  65211
Office phone: 573-884-4752
Lab Phone: 573-884-4799
FAX: 573-884-9676
email: staceyg from missouri.edu
NEW LAB WEBSITE: http://www.staceylab.missouri.edu/
MU CSE site: http://www.energy.missouri.edu/
NCSB site: http://www.soybiotechcenter.org
NSF Project site: http://www.soybeangenome.org

-----Original Message-----
From: arab-gen-bounces from oat.bio.indiana.edu [mailto:arab-gen-bounces from oat.bio.indiana.edu] On Behalf Of Prakash M G
Sent: Monday, September 21, 2009 10:49 PM
To: arab-gen from oat.bio.indiana.edu
Subject: [Arabidopsis] genomic and proteomic data not matching

Dear all,

I have a problem on matching or correlating the gene expression data with
proteomic data.  The micro array data for the treatments are not matching
with the proteomic data for the same treatments.  Charecterisation of
differentially expressed proteins are not matching with the differentially
expressed genes.  May I know why this problem and how to overcome this

Thanking you all

with regards

On Mon, Sep 21, 2009 at 2:20 AM, <arab-gen-request from oat.bio.indiana.edu>wrote:

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> Today's Topics:
>   1. Microarray Workshop in Tucson, Arizona (David Galbraith)
>   2. seeking TAIR9 bpmap file for Arabidopsis tiling array     1.0R
>      (Ann Loraine)
> ----------------------------------------------------------------------
> Message: 1
> Date: Thu, 17 Sep 2009 10:25:04 -0700
> From: David Galbraith <galbraith from arizona.edu>
> Subject: [Arabidopsis] Microarray Workshop in Tucson, Arizona
> To: arab-gen from magpie.bio.indiana.edu
> Message-ID: < from ag.arizona.edu>
> Content-Type: text/plain; charset="us-ascii"; format=flowed
> January 3-8, 2010
> The University of Arizona
> Tucson, Arizona
> This workshop will comprise a combination of lectures and hand-on
> laboratory sessions. The participants will primarily employ
> Arabidopsis and maize (plant side) and human, bovine and
> porcine (animal side)  whole genome 70-mer oligonucleotide
> microarrays in their laboratory work (for details of the plant arrays see
> http://www.ag.arizona.edu/microarray and
> http://www.maizearray.org/.
> The workshop will be divided into two parts: Part I (Sunday 4PM to
> Wednesday 5PM) will cover wet-lab aspects of microarray target
> production and amplification, microarray hybridization, and scanning.
> Part II (all day, Thursday and Friday) will concentrate on data extraction,
> statistical analysis, and experimental design. Together these topics
> are aimed at the goal of the participants obtaining optimal results using
> oligonucleotide-based microarrays. Part II may be taken separately.
> Specific topics to be covered include:
> * Experimental design.
> * Probe preparation and microarray printing.
> * Microarray rehydration and probe immobilization.
> * Target preparation, including RNA extraction, direct and indirect
> labeling, and amplification techniques.
> * Microarray hybridization.
> * Array scanning and data extraction.
> * Data analysis and archiving.
> Registration (Part I plus Part II) is $700, which includes costs of
> the microarrays and other supplies that you will use.
> Part II registration only is $300. Part I participants will be
> limited to 40 on a first-come, first-serve basis. Overall
> participation will be limited to 60 individuals.
> Note:  There are a number of airline connections from
> Tucson to San Diego on Friday evening, allowing
> workshop participants convenient access to the Plant
> and Animal Genome XVIII Meeting (January 9-13).
> For further details and to register, please contact
> David Galbraith (galbraith from arizona.edu) or Georgina Lambert
> (georgina from cals.arizona.edu)
> David W. Galbraith
> Professor of Plant Sciences
> & Professor, Bio5 Institute
> University of Arizona
> Office: 341 Keating Building
> Mailing address:
> BIO5 Institute
> The University of Arizona
> 1657 E. Helen St.
> Tucson, AZ 85721-0240
> Tel: (520) 621-9153
> Fax: (520) 626-4824
> Email: galbraith from arizona.edu
> http://cals.arizona.edu/galbraith
> ------------------------------
> Message: 2
> Date: Thu, 17 Sep 2009 18:30:32 -0400
> From: Ann Loraine <aloraine from gmail.com>
> Subject: [Arabidopsis] seeking TAIR9 bpmap file for Arabidopsis tiling
>        array   1.0R
> To: arab-gen from magpie.bio.indiana.edu
> Message-ID:
>        <83722dde0909171530w6bd02b7do197669db757274cd from mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> Dear Colleagues,
> I'm looking for a "bpmap" file that maps Affymetrix Arabidopsis tiling
> array
> 1.0R probes onto the TAIR9 or TAIR8 genome sequence.
> (This is for setting up a demonstration server that will show labs how they
> can easily visualize and share tiling array and RNA-Seq data via the
> Integrated Genome Browser (igb.bioviz.org) and DAS, one of the
> deliverables
> for an NSF 2010 award, which started a year ago.)
> The array corresponds to GEO platform accession GPL1980. (If this is wrong,
> please let me know...the Web page for it is here:
> http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL1980)
> The Web page for GPL1980 at GEO links to a bpmap file, but we are not yet
> sure which genome it references. Probably it is the TAIR7 genome, but we
> haven't tested it as yet. The bpmap file that Affymetrix distributes
> references TAIR7 (what they call Jan 2004) and the company has no immediate
> plans to update it because their tiling array support relies on a genome
> being supported by the UCSC Genome Bioinformatics group, which only
> supports
> animal and some fungal genomes.
> If you know of anyone who has a bpmap file for the Arabidopsis Tiling 1.0R
> Array for TAIR9, or even TAIR8, I would be very grateful if you would give
> me their contact information or send me a link to the file.
> Also, if you are looking for such a file, please let me know, and I'll get
> in touch as soon as I find one...or as soon as we create it, if one cannot
> be found.
> Thank you very much for your time,
> Ann Loraine
> Associate Professor
> Dept. of Bioinformatics and  Genomics
> UNC Charlotte
> ------------------------------
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