About the Experimental Technology and Study Type Definitions

The large-scale data sets in YFGdb are organized by "study type" such as "genomic expression study" or "large-scale protein interaction". The "experimental technology" information gives the technology used to generate the data set. Brief definitions of the different study types and experimental technologies are given below.

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Study Type Definitions

The data sets in YFGdb are organized by "Study Type". The different study types are as follows:

Comparative genomic hybridization:
Involves DNA-DNA hybridization to assay for chromosomal rearrangements (e.g. PMID:12446845) or SNP detection (e.g. PMID:11923494) using comparative genomic hybridization techniques, for example array CGH (e.g. PMID:15833139).
Genomic co-immunoprecipitation study:
Involves large-scale co-immunoprecipitation of proteins cross-linked to DNA or RNA in order to characterize protein-DNA or protein-RNA interactions using genomic techniques (for example ChIP-on-Chip experiments) (e.g. PMID:11455386).
Genomic expression study:
Includes microarray/chip/SAGE or other genome-wide techniques to assay gene expression on a genomic scale (e.g. PMID: 9381177).
Large-scale genetic interaction:
Includes large-scale screens for genetic interactions including Synthetic Genetic Analysis (SGA, e.g. PMID:14661025), Diploid-based Synthetic Lethality Analysis on Microarrays (dSLAM, e.g. PMID:15525520), and other types of genetic interaction screens that use genomic techniques. Would not include traditional synthetic lethal or high copy suppressor screens.
Large-scale phenotype analysis:
Involves any large-scale phenotype analysis that utilizes genomic techniques (e.g. PMID:12134085) or a systematic analysis of a collection of genes, e.g. genes on a single chromosome (e.g. PMID:10590466) or preferentially expressed genes in meiotic cells (e.g. PMID:11470404). Applies if a genomic technique was used (e.g. many mutants grown in 96 well plates, growth of all mutants assayed via competition, bar codes utilized, etc).
Large-scale protein detection:
Includes 2-D PAGE, mass spectrometry, immunodetection schemes and other studies that measure or examine protein levels on a large-scale. Includes identification, detection, and expression (e.g. PMID:14562106).
Large-scale protein interaction:
Includes large-scale two hybrid, phage display and other large-scale protein-protein interaction experiments (e.g. PMID:14690591).
Large-scale protein localization:
Involves methods for determining the subcellular distribution of a large number of proteins (e.g. PMID:11914276).
Large-scale protein modification:
Includes large-scale identification of various types of protein modifications, such as phosphorylation (e.g. PMID:14574415), ubiquitination (e.g. PMID:12872131), etc.
Other genomic analysis:
Includes other large-scale analyses not described by the types above, for example, statistical methods for predicting functional gene linkages (e.g. PMID:16103904), small molecule protein-binding assays (e.g. PMID:11948353), using microarray technology to identify replication origins (e.g. PMID:12167157) or ribosome abundance (e.g. PMID:12660367), etc.
Other large-scale proteomic analysis:
Includes other large-scale analyses not described by the other large-scale proteomics topics (e.g. PMID:17078969).
Not yet curated:
Refers to large-scale studies that have not yet been curated by YFGdb curators.

Experimental Technology Definitions

The "Experimental Technology" indicates the technology type used to generate the data set. The different technology types are as follows:
Affymetrix:
Microarray experiment that specifically uses stock arrays manufactured by Affymetrix.
Agilent:
Microarray experiment that specifically uses stock arrays manufactured by Agilent.
Genetic footprinting:
Experiment where a large population of cells are mutagenized by transposition of a marked transposable element. The population is grown and individual mutants can be assayed for presence and abundance utilizing the Ty insertions (e.g. PMID: 8953036).
Mass spec:
Experiment that uses any form of mass spectrometry. This type is only listed if the data set clearly includes mass spec data. If mass spectrometry was used to identify proteins in a data set, but the data set does not have any actual mass spec data, then 'other' was selected for the experimental technology type.
Nimblegen:
Microarray experiment that specifically uses stock arrays manufactured by Nimblegen.
Oligos:
Microarray experiment that uses chips that contain oligonucleotides synthesized or spotted on the chips, but not any of the stock arrays produced by Affymetrix, Agilent, or Nimblegen.
SAGE:
Serial Analysis of Gene Expression, an alternative, sequence-based technique to microarrays that allows analysis of genome-wide RNA expression (e.g. PMID: 7570003).
SGA:
Synthetic Genetic Analysis, a particular technique used to identify genetic interactions on a large scale in yeast (e.g. PMID: 16118434).
Spotted:
Microarray experiment that uses chips that contain spotted elements, usually PCR products.
Two-hybrid:
Any experiment that utilizes the yeast two-hybrid system.
Other:
Any experimental technology that does not fit in any of the above categories.
Unknown:
Any experimental technology that cannot be determined.
Not yet curated:
Any experimental technology that has not yet been curated in YFGdb.