Trends Genet. 2008 Dec;24(12):587-90. Epub 2008 Oct 24.

Inferring molecular function: contributions from functional linkages.

Source

Howard Hughes Medical Institute (HHMI), 675C. E. Young Drive South, Los Angeles, CA 90095, USA.

Abstract

In the current era of high-throughput sequencing and structure determination, functional annotation has become a bottleneck in biomedical science. Here, we show that automated inference of molecular function using functional linkages among genes increases the accuracy of functional assignments by > or =8% and enriches functional descriptions in > or =34% of top assignments. Furthermore, biochemical literature supports >80% of automated inferences for previously unannotated proteins. These results emphasize the benefit of incorporating functional linkages in protein annotation.

PMID:: 18951645; [PubMed - indexed for MEDLINE]

Publication Types, MeSH Terms, Substances, Grant Support

Publication Types

MeSH Terms

Substances

Proteins

Grant Support

Howard Hughes Medical Institute/United States

LinkOut - more resources

Full Text Sources

Other Literature Sources

COS Scholar Universe

Supplemental Content

Save items

Related citations in PubMed

Annotating proteins with generalized functional linkages. [Proc Natl Acad Sci U S A. 2008]
Annotating proteins with generalized functional linkages.
Llewellyn R, Eisenberg DS. Proc Natl Acad Sci U S A. 2008 Nov 18; 105(46):17700-5. Epub 2008 Nov 12.
Review Piecing together the structure-function puzzle: experiences in structure-based functional annotation of hypothetical proteins. [Proteomics. 2007]
Review Piecing together the structure-function puzzle: experiences in structure-based functional annotation of hypothetical proteins.
Adams MA, Suits MD, Zheng J, Jia Z. Proteomics. 2007 Aug; 7(16):2920-32.
Functional linkages can reveal protein complexes for structure determination. [Structure. 2007]
Functional linkages can reveal protein complexes for structure determination.
Kim SM, Bowers PM, Pal D, Strong M, Terwilliger TC, Kaufmann M, Eisenberg D. Structure. 2007 Sep; 15(9):1079-89.
Review New in protein structure and function annotation: hotspots, single nucleotide polymorphisms and the 'Deep Web'. [Curr Opin Drug Discov Devel. 2...]
Review New in protein structure and function annotation: hotspots, single nucleotide polymorphisms and the 'Deep Web'.
Bromberg Y, Yachdav G, Ofran Y, Schneider R, Rost B. Curr Opin Drug Discov Devel. 2009 May; 12(3):408-19.
Reverse engineering module networks by PSO-RNN hybrid modeling. [BMC Genomics. 2009]
Reverse engineering module networks by PSO-RNN hybrid modeling.
Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW. BMC Genomics. 2009 Jul 7; 10 Suppl 1:S15. Epub 2009 Jul 7.

See reviews... See all...

Cited by 2 PubMed Central articles

Functional analysis beyond enrichment: non-redundant reciprocal linkage of genes and biological terms. [PLoS One. 2011]
Functional analysis beyond enrichment: non-redundant reciprocal linkage of genes and biological terms.
Fontanillo C, Nogales-Cadenas R, Pascual-Montano A, De las Rivas J. PLoS One. 2011; 6(9):e24289. Epub 2011 Sep 16.
A new approach to assess and predict the functional roles of proteins across all known structures. [J Struct Funct Genomics. 2011]
A new approach to assess and predict the functional roles of proteins across all known structures.
Julfayev ES, McLaughlin RJ, Tao YP, McLaughlin WA. J Struct Funct Genomics. 2011 Mar; 12(1):9-20. Epub 2011 Mar 29.

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

Inferring molecular function: contributions from functional linkages.
Inferring molecular function: contributions from functional linkages.
Trends Genet. 2008 Dec ;24(12):587-90. Epub 2008 Oct 24 .

PubMed
A randomized, double-blind, placebo-controlled study of milk oral immunotherapy ...
A randomized, double-blind, placebo-controlled study of milk oral immunotherapy for cow's milk allergy.
J Allergy Clin Immunol. 2008 Dec ;122(6):1154-60. Epub 2008 Oct 25 .

PubMed
Use of circulating cathodic antigen strips for the diagnosis of urinary schistos...
Use of circulating cathodic antigen strips for the diagnosis of urinary schistosomiasis.
Trans R Soc Trop Med Hyg. 2009 Jan ;103(1):45-51. Epub 2008 Oct 31 .

PubMed
Backward walking in Parkinson's disease.
Backward walking in Parkinson's disease.
Mov Disord. 2009 Jan 30 ;24(2):218-23.

PubMed
Mechanisms of pathogenicity in human MSH2 missense mutants.
Mechanisms of pathogenicity in human MSH2 missense mutants.
Hum Mutat. 2008 Nov ;29(11):1355-63.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: