Biointelligence

September 22, 2009

Minimum Information about a Microarray Experiment

Filed under: Bioinformatics,Microarray — Biointelligence: Education,Training & Consultancy Services @ 11:20 am
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After genome sequencing, DNA microarray analysis has become the most widely used source of genome scale data in the life sciences. Microarray expression studies are producing massive qunatities of gene expression and other functional genomics data, which priomise to provide an insight into gene function and inetractions within and across metabolic pathways. Unlike genome sequence data, however, which have standard formats for presentation and widely used tools and databases, much of the microarray daa generated so far remain inaccessible.

To make this information accesible in a proper format MIAME (Minimum Information About a Microarray Experiment) was introduced. MIAME format was introduced to address the ned for comprehensive annotation necessary to interpret the results of microarray data. It is platform independent but includes essential evidence about how the gene expression level measurements have been obtained.

Although the goal of MIAME is to specify only the content of the information and not the technical format, MIAME includes recommendations for which parts of the information should be provided as controlled vocabularies. MIAME includes a description of the six sections which need to be included:

1. Experimental Design
2. Array Design
3. Samples
4. Hybridizations
5. Measurements
6. Normalization controls

This specific format would really make it easy to interpret microarray data obtained from various experiments.
To read more on MIAME click here-  http://www.mged.org/Workgroups/MIAME/miame.html

 

 
After genome sequencing, DNA microarray analysis has become the most widely used source of genome scale data in the life sciences. Microarray expression studies are producing massive qunatities of gene expression and other functional genomics data, which priomise to provide an insight into gene function and inetractions within and across metabolic pathways. Unlike genome sequence data, however, which have standard formats for presentation and widely used tools and databases, much of the microarray daa generated so far remain inaccessible.

To make this information accesible in a proper format MIAME (Minimum Information About a Microarray Experiment) was introduced. MIAME format was introduced to address the ned for comprehensive annotation necessary to interpret the results of microarray data. It is platform independent but includes essential evidence about how the gene expression level measurements have been obtained.

Although the goal of MIAME is to specify only the content of the information and not the technical format, MIAME includes recommendations for which parts of the information should be provided as controlled vocabularies. MIAME includes a description of the six sections which need to be included:

1. Experimental Design
2. Array Design
3. Samples
4. Hybridizations
5. Measurements
6. Normalization controls

This specific format would really make it easy to interpret microarray data obtained from various experiments.
To read more on MIAME click here-  http://www.mged.org/Workgroups/MIAME/miame.html

 

 
After genome sequencing, DNA microarray analysis has become the most widely used source of genome scale data in the life sciences. Microarray expression studies are producing massive qunatities of gene expression and other functional genomics data, which priomise to provide an insight into gene function and inetractions within and across metabolic pathways. Unlike genome sequence data, however, which have standard formats for presentation and widely used tools and databases, much of the microarray daa generated so far remain inaccessible.

To make this information accesible in a proper format MIAME (Minimum Information About a Microarray Experiment) was introduced. MIAME format was introduced to address the ned for comprehensive annotation necessary to interpret the results of microarray data. It is platform independent but includes essential evidence about how the gene expression level measurements have been obtained.

Although the goal of MIAME is to specify only the content of the information and not the technical format, MIAME includes recommendations for which parts of the information should be provided as controlled vocabularies. MIAME includes a description of the six sections which need to be included:

1. Experimental Design
2. Array Design
3. Samples
4. Hybridizations
5. Measurements
6. Normalization controls

This specific format would really make it easy to interpret microarray data obtained from various experiments.
To read more on MIAME click here-  http://www.mged.org/Workgroups/MIAME/miame.html

September 3, 2009

WebArrayDB: A Platform for Microarray Data Analysis

Filed under: Bioinformatics,Microarray — Biointelligence: Education,Training & Consultancy Services @ 3:02 pm
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 Microarray Data Analysis

Cross-platform microarray analysis is an increasingly important research tool, but researchers still lack open source tools for storing, integrating, and analyzing large amounts of microarray data obtained from different array platforms.

An open source integrated microarray database and analysis suite, WebArrayDB (http://www.webarraydb.org), has been developed that features convenient uploading of data for storage in a MIAME (Minimal Information about a Microarray Experiment) compliant fashion, and allows data to be mined with a large variety of R-based tools, including data analysis across multiple platforms. Different methods for probe alignment, normalization and statistical analysis are included to account for systematic bias. Student’s t-test, moderated t-tests, non-parametric tests, and analysis of variance or covariance (ANOVA/ANCOVA) are among the choices of algorithms for differential analysis of data. Users also have the flexibility to define new factors and create new analysis models to fit complex experimental designs. All data can be queried or browsed through a web browser. The computations can be performed in parallel on symmetric multiprocessing (SMP) systems or Linux clusters.
The software package is available for use on a public web server (http://www.webarraydb.org) or can be downloaded.

Check out WebArray at: http://www.webarraydb.org