Inferring Higher Functional Information for RIKEN Mouse Full-Lenth cDNA Clones with FACTS
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Nagashima, Takeshi; Silva, Diego; Petrovsky, Nikolai; Socha, L; Suzuki, Harukazu; Saito, Rintaro; Kasukawa, Takeya; Kurochkin, Igor; Konagaya, Akihiko; Schonbach, Christian
Description
FACTS (Functional Association /Annotation of cDNA Clones from Text/Sequence Sources) is a semiautomated knowledge discovery and annotation system that integrates molecular function information derived from sequence analysis results (sequence inferred) with functional information extracted from text. Text-inferred information was extracted from keyword-based retrievals of MEDLINE abstracts and by matching of gene or protein names to OMIM, BIND, and DIP database entries. Using FACTS, we found...[Show more]
dc.contributor.author | Nagashima, Takeshi | |
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dc.contributor.author | Silva, Diego | |
dc.contributor.author | Petrovsky, Nikolai | |
dc.contributor.author | Socha, L | |
dc.contributor.author | Suzuki, Harukazu | |
dc.contributor.author | Saito, Rintaro | |
dc.contributor.author | Kasukawa, Takeya | |
dc.contributor.author | Kurochkin, Igor | |
dc.contributor.author | Konagaya, Akihiko | |
dc.contributor.author | Schonbach, Christian | |
dc.date.accessioned | 2015-12-13T22:37:01Z | |
dc.identifier.issn | 1088-9051 | |
dc.identifier.uri | http://hdl.handle.net/1885/77055 | |
dc.description.abstract | FACTS (Functional Association /Annotation of cDNA Clones from Text/Sequence Sources) is a semiautomated knowledge discovery and annotation system that integrates molecular function information derived from sequence analysis results (sequence inferred) with functional information extracted from text. Text-inferred information was extracted from keyword-based retrievals of MEDLINE abstracts and by matching of gene or protein names to OMIM, BIND, and DIP database entries. Using FACTS, we found that 47.5% of the 60,770 RIKEN mouse cDNA FANTOM2 clone annotations were informative for text searches. MEDLINE queries yielded molecular interaction-containing sentences for 23.1% of the clones. When disease MeSH and GO terms were matched with retrieved abstracts, 22.7% of clones were associated with potential diseases, and 32.5% with GO identifiers. A significant number (23.5%) of disease MeSH-associated clones were also found to have a hereditary disease association (OMIM Morbidmap). Inferred neoplastic and nervous system disease represented 49.6% and 36.0% of disease MeSH-associated clones, respectively. A comparison of sequence-based GO assignments with informative text-based GO assignments revealed that for 78.2% of clones, identical GO assignments were provided for that clone by either method, whereas for 21.8% of clones, the assignments differed. In contrast, for OMIM assignments, only 28.5% of clones had identical sequence-based and text-based OMIM assignments. Sequence, sentence, and term-based functional associations are included in the FACTS database (http://facts.gsc.riken.go.jp/), which permits results to be annotated and explored through web-accessible keyword and sequence search interfaces. The FACTS database will be a critical tool for investigating the functional complexity of the mouse transcriptome, cDNA-inferred interactome (molecular interactions), and pathome (pathologies). | |
dc.publisher | Cold Spring Harbor Laboratory Press | |
dc.source | Genome Research | |
dc.subject | Keywords: complementary DNA; article; automation; computer interface; computer program; gene function; gene sequence; genetic disorder; information retrieval; Internet; medical information; MEDLINE; molecular cloning; molecular interaction; mouse; neoplasm; neurolo | |
dc.title | Inferring Higher Functional Information for RIKEN Mouse Full-Lenth cDNA Clones with FACTS | |
dc.type | Journal article | |
local.description.notes | Imported from ARIES | |
local.description.refereed | Yes | |
local.identifier.citationvolume | 13 | |
dc.date.issued | 2003 | |
local.identifier.absfor | 080614 - Pacific Peoples Information and Knowledge Systems | |
local.identifier.ariespublication | MigratedxPub5911 | |
local.type.status | Published Version | |
local.contributor.affiliation | Nagashima, Takeshi, RIKEN | |
local.contributor.affiliation | Silva, Diego, College of Medicine, Biology and Environment, ANU | |
local.contributor.affiliation | Petrovsky, Nikolai, College of Medicine, Biology and Environment, ANU | |
local.contributor.affiliation | Socha, L, College of Medicine, Biology and Environment, ANU | |
local.contributor.affiliation | Suzuki, Harukazu, RIKEN | |
local.contributor.affiliation | Saito, Rintaro, RIKEN | |
local.contributor.affiliation | Kasukawa, Takeya, RIKEN | |
local.contributor.affiliation | Kurochkin, Igor, RIKEN | |
local.contributor.affiliation | Konagaya, Akihiko, Japan Advanced Institute of Science and Technology (JAIST) | |
local.contributor.affiliation | Schonbach, Christian, RIKEN | |
local.description.embargo | 2037-12-31 | |
local.bibliographicCitation.issue | 6b | |
local.bibliographicCitation.startpage | 1520 | |
local.bibliographicCitation.lastpage | 1533 | |
local.identifier.doi | 10.1101/gr.1019903 | |
dc.date.updated | 2015-12-11T09:34:37Z | |
local.identifier.scopusID | 2-s2.0-0037673436 | |
Collections | ANU Research Publications |
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