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According to different entry points to search, three parts were deposited in PTGBase which contained searching by identifiers or names of tandem duplicated genes, searching by identifiers of functional annotations and searching by keywords of functional annotations.
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In the section to search by identifiers of a functional annotation, users can supply a GO ID or InterPro accession number to obtain tandem duplicated genes with those annotations among species that can be used to understand certain functional types of clustered genes on assembled pseudomolecules.
Tandem duplicated genes in PTGBase can be explored through browsing or searching by identifiers or keywords of functional annotation and sequence similarity.
Therefore, the human orthologs of transcripts with significant differential expression were used as input identifiers for functional annotation clustering in DAVID.
MIPS FunCat is a hierarchical database that links Arabidopsis locus identifiers to functional categories.
Depending on the respective focus of data mining, a precise query for identifiers and a fuzzy query for keywords of functional annotations were designed for automated data retrieval of tandem duplicated gene clusters and flexible functional annotations.
Searching the function module of identifiers related to tandem duplicated genes or keywords of functional annotation was developed by Perl and JavaScript scripts which supplied a visual and powerful searching platform.
The use of gene categories (inner ear tissue; deafness; ion channels; ion transporters; transcription factors) facilitated the assignment of functional significance to probe set identifiers.
ClinicalTrials.gov Identifier: NCT00426881 Gait speed is a global indicator of functional mobility and status.
User can search and analyze TS containing a list of identifiers (gene symbols or AffyIDs) or associated with a set of functional terms.
Additionally, the Affymetrix probe identifiers were tested by Gene Set Enrichment Analysis (GSEA, [ 45]) for enrichment of functional ontologies using Gene Ontology terms [ 46] within Mayday.
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