Frequently Asked Questions About CEBS

CEBS Development Forum

How do I share data with CEBS?

CEBS uses formatted text files to capture study design, assay endpoints such as histopathology findings, and microarray data. We load the data into the CEBS curation tool ARC, and then export to CEBS. We are in the process of writing a user-friendly interface to ARC; at the moment we collaborate with depositors to load data into CEBS.

What distinguishes CEBS from other microarray databases?

CEBS displays microarray data in the context of study design and assay measures such as clinical chemistry and histopathology. The CEBS user can use histopathology to select microarrays for comparison, for example.

What public data are in CEBS?

The CEBS home page lists all the public data in CEBS(http://cebs.niehs.nih.gov/).

What can CEBS tell me about the data?

Questions CEBS can answer: What gene expression signature is associated with centrilobular necrosis? Which subjects are biological replicates yet do not behave similarly?

CEBS permits you to combine microarray data from experiments done on the same array platform, select arrays for analysis, normalize the data, and carry out pairwise comparisons using a number of statistical methods / thresholds to identify differentially expressed genes.

CEBS supplies annotation for genes using caBIO, KEGG, BioCarta and GO. Users can upload a list of genes or identify a gene list by carrying out analysis within CEBS. CEBS can calculate the fold enrichment within particular categories of biological activity for genes identified by analysis within CEBS.

What exchange standards does CEBS use to capture data?

There are no widely-accepted exchange standards for study design and assay data, although the SEND Consortium(http://www.cdisc.org/standards/index.html) has developed a format that may be used for submission to the FDA. Additionally, OBI, the Ontology for Biomedical Investigations(http://fugo.sourceforge.net/) is under development and will be used once complete. CEBS supports MIAME standards(http://www.mged.org/Workgroups/MIAME/miame.html) for microarray data.

Why should I register?

An account is only needed to deposit data in CEBS. Public data in CEBS can be accessed without an account.

What plans are there for additional public data?

This depends on our depositors! Please contact us if you feel particular data are missing or if you have data to share via CEBS.

Who should we contact for more information?

Jennifer Fostel, fostel@niehs.nih.gov

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