Functional Genomics Documentation

Functional genomics information is provided for C. elegans and yeast species.

Criteria and types of experiments

Functional genomics is defined as an approach directed towards uncovering properties for large numbers of genes/proteins within a single experiment. For this purpose, experimental design must allow large-scale, high-throughput, data gathering which frequently includes automation while preserving reliability and reproducibility of the results. Statistical and computational analyses of the data are used to assess the significance of findings. Functional genomics experiments currently included are:

  • DNA microarrays
  • 2-D protein gels
  • serial analysis of gene expression (SAGE)
  • global two-hybrid screens
  • systematic mutant construction and analysis
  • systematic Northern analysis

Sources of data

Only studies published in peer-reviewed journals are curated. This includes supplementary data made available on the Internet (journal or authors' websites), but only if they accompany a publication. It is possible to include unpublished results, but only if they are obtained within a broader project where experimental design, methods, and general conclusions are published.


Information retrieved from functional genomics studies is collected in the Annotations section of the Locus Report. Proteome curators do not perform analysis of the data, but report conclusions reached by the authors and presented in their publication. Conclusions pertinent to selected individual genes/proteins and explicitly discussed by the authors are often added to relevant Annotation topics (such as Function, Pathway, Regulation), with a wording that clearly indicates the type of experiments these conclusions are based upon. Conclusions pertinent to entire groups of genes/proteins, such as common regulatory responses identified by the cluster analysis in microarray experiments, are collected in annotations under the Functional Genomics heading. Conclusions derived from systematic Northern analyses are collected under the Regulation heading, and those from SAGE experiments are listed under the Abundance heading.

Such annotations contain a brief description of experimental conditions (treatment, environmental change, mutation), type of the effect (coinduction, corepression, coregulation) and common functional features of the group members, whenever this information is provided by the authors. In order to facilitate retrieval of the group members, the genes/protein names are included in square brackets at the end of the annotation line. Generally, gene names are not included in the annotations when the number of genes is larger than 200.


Data from global protein-protein interaction studies, such as large-scale two-hybrid screens, are displayed in the Protein-protein associations section of the Protein view of the Locus Report. Data from systematic Northern analysis are added as Regulatory factor properties in the Gene view of the Locus Report. Results of systematic mutant construction and analysis are added to the Mutant Phenotype property section of the General view of the Locus Report, without an additional indication that they have been obtained by high-throughput methods (the associated reference serves as a hint). Results from microarray, SAGE, and 2-D protein gels studies are not included in the protein properties.

Transcription profiles

Transcription profiling data are accessible from a Profile summary hyperlink in the Regulatory factors section of the Gene view of a Locus Report. Transcription profile data are collected from studies using various technologies:

  1. high-density oligonucleotide microarrays

  2. DNA microarrays (PCR-generated DNA fragments spotted on glass support)

  3. filter arrays (PCR-generated DNA fragments spotted on hybridization filters)

Regardless of the type of microarrays (single channel, or dual channel), the values are converted to fold change (induction or repression) relative to a control (for instance, wild-type cells, untreated cells, cells at time 0, etc, as provided by the authors). When multiple values for a single gene are present, the average value is used. Values for genes not encoding proteins, and for transposable or extrachromosomal elements are not included. Each Transcription Profile Report contains a short text description that summarizes the experimental protocol and main conclusions, a reference, and a link to the authors' website which provides access to the primary data and the authors' presentation or interpretation.

Raw transcription profiling data are downloaded from supplemental on-line materials on journal websites, from the authors' own websites, or as provided directly by the authors. Only publicly available data sets that accompany a publication are included. Please note that we are not a repository of raw transcription profiling data.

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