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GiSAO.db: a database for ageing research.

Hofer E, Laschober GT, Hackl M, Thallinger GG, Lepperdinger G, Grillari J, Jansen-Dürr P, Trajanoski Z - BMC Genomics (2011)

Bottom Line: KEGG pathways were incorporated and links to external databases augment the information in GiSAO.db.Search functions facilitate retrieval of data which can also be exported for further processing.We have developed a centralized database that is very well suited for the management of data for ageing research.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division for Bioinformatics, Biocenter, Innsbruck Medical University, Schöpfstrasse, Austria.

ABSTRACT

Background: Age-related gene expression patterns of Homo sapiens as well as of model organisms such as Mus musculus, Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster are a basis for understanding the genetic mechanisms of ageing. For an effective analysis and interpretation of expression profiles it is necessary to store and manage huge amounts of data in an organized way, so that these data can be accessed and processed easily.

Description: GiSAO.db (Genes involved in senescence, apoptosis and oxidative stress database) is a web-based database system for storing and retrieving ageing-related experimental data. Expression data of genes and miRNAs, annotation data like gene identifiers and GO terms, orthologs data and data of follow-up experiments are stored in the database. A user-friendly web application provides access to the stored data. KEGG pathways were incorporated and links to external databases augment the information in GiSAO.db. Search functions facilitate retrieval of data which can also be exported for further processing.

Conclusions: We have developed a centralized database that is very well suited for the management of data for ageing research. The database can be accessed at https://gisao.genome.tugraz.at and all the stored data can be viewed with a guest account.

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Related in: MedlinePlus

Display of expression values obtained from Affymetrix one-colour arrays. The values are colour coded to facilitate the identification of prominent expression values and comparison between values of a gene of different arrays. Additionally, tags are displayed for a quick overview of experimental data. In this case, for the gene THBS a follow-up experiment was performed with the organism Homo sapiens (HS), experiment classification oxidative stress (OS) and experiment type qPCR (QP).
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Figure 2: Display of expression values obtained from Affymetrix one-colour arrays. The values are colour coded to facilitate the identification of prominent expression values and comparison between values of a gene of different arrays. Additionally, tags are displayed for a quick overview of experimental data. In this case, for the gene THBS a follow-up experiment was performed with the organism Homo sapiens (HS), experiment classification oxidative stress (OS) and experiment type qPCR (QP).

Mentions: The database system offers a user-friendly web interface which facilitates data input and retrieval. Results of microarray experiments can be viewed in detail as both the expression value of each spot for one-colour microarray chips, and the expression ratio between the colour channels for two-colour microarrays are displayed. Expression values and ratios are represented by colour-coded boxes which facilitate the determination of highly expressed genes, up- or down-regulated miRNAs and the comparison of expression values and ratios of different microarrays (Figure 2). The values and ratios can be displayed in a logarithmic or decimal scale, and a threshold can be defined to show only those genes or miRNAs whose expression values or ratios exceed the defined cut-off.


GiSAO.db: a database for ageing research.

Hofer E, Laschober GT, Hackl M, Thallinger GG, Lepperdinger G, Grillari J, Jansen-Dürr P, Trajanoski Z - BMC Genomics (2011)

Display of expression values obtained from Affymetrix one-colour arrays. The values are colour coded to facilitate the identification of prominent expression values and comparison between values of a gene of different arrays. Additionally, tags are displayed for a quick overview of experimental data. In this case, for the gene THBS a follow-up experiment was performed with the organism Homo sapiens (HS), experiment classification oxidative stress (OS) and experiment type qPCR (QP).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3113790&req=5

Figure 2: Display of expression values obtained from Affymetrix one-colour arrays. The values are colour coded to facilitate the identification of prominent expression values and comparison between values of a gene of different arrays. Additionally, tags are displayed for a quick overview of experimental data. In this case, for the gene THBS a follow-up experiment was performed with the organism Homo sapiens (HS), experiment classification oxidative stress (OS) and experiment type qPCR (QP).
Mentions: The database system offers a user-friendly web interface which facilitates data input and retrieval. Results of microarray experiments can be viewed in detail as both the expression value of each spot for one-colour microarray chips, and the expression ratio between the colour channels for two-colour microarrays are displayed. Expression values and ratios are represented by colour-coded boxes which facilitate the determination of highly expressed genes, up- or down-regulated miRNAs and the comparison of expression values and ratios of different microarrays (Figure 2). The values and ratios can be displayed in a logarithmic or decimal scale, and a threshold can be defined to show only those genes or miRNAs whose expression values or ratios exceed the defined cut-off.

Bottom Line: KEGG pathways were incorporated and links to external databases augment the information in GiSAO.db.Search functions facilitate retrieval of data which can also be exported for further processing.We have developed a centralized database that is very well suited for the management of data for ageing research.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division for Bioinformatics, Biocenter, Innsbruck Medical University, Schöpfstrasse, Austria.

ABSTRACT

Background: Age-related gene expression patterns of Homo sapiens as well as of model organisms such as Mus musculus, Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster are a basis for understanding the genetic mechanisms of ageing. For an effective analysis and interpretation of expression profiles it is necessary to store and manage huge amounts of data in an organized way, so that these data can be accessed and processed easily.

Description: GiSAO.db (Genes involved in senescence, apoptosis and oxidative stress database) is a web-based database system for storing and retrieving ageing-related experimental data. Expression data of genes and miRNAs, annotation data like gene identifiers and GO terms, orthologs data and data of follow-up experiments are stored in the database. A user-friendly web application provides access to the stored data. KEGG pathways were incorporated and links to external databases augment the information in GiSAO.db. Search functions facilitate retrieval of data which can also be exported for further processing.

Conclusions: We have developed a centralized database that is very well suited for the management of data for ageing research. The database can be accessed at https://gisao.genome.tugraz.at and all the stored data can be viewed with a guest account.

Show MeSH
Related in: MedlinePlus