A literature network of human genes for high-throughput analysis of gene expression

Nature Genetics
T K JenssenE Hovig

Abstract

We have carried out automated extraction of explicit and implicit biomedical knowledge from publicly available gene and text databases to create a gene-to-gene co-citation network for 13,712 named human genes by automated analysis of titles and abstracts in over 10 million MEDLINE records. The associations between genes have been annotated by linking genes to terms from the medical subject heading (MeSH) index and terms from the gene ontology (GO) database. The extracted database and accompanying web tools for gene-expression analysis have collectively been named 'PubGene'. We validated the extracted networks by three large-scale experiments showing that co-occurrence reflects biologically meaningful relationships, thus providing an approach to extract and structure known biology. We validated the applicability of the tools by analyzing two publicly available microarray data sets.

References

Oct 25, 1996·Science·A GoffeauS G Oliver
Dec 9, 1998·Proceedings of the National Academy of Sciences of the United States of America·M B EisenD Botstein
Dec 16, 1998·Science·UNKNOWN C. elegans Sequencing Consortium
Mar 25, 2000·Science·M D AdamsJ C Venter
May 16, 2000·Arteriosclerosis, Thrombosis, and Vascular Biology·P Parsons-WingerterA G Farr
May 29, 2000·Immunology Today·K StamatopoulosT Papadaki
Jul 6, 2000·FEBS Letters·M A Andrade, P Bork
Aug 24, 2000·Proceedings of the National Academy of Sciences of the United States of America·I S LossosR Levy
Jan 1, 1990·IEEE Transactions on Neural Networks·R Eberhart, E Micheli-Tzanakou

❮ Previous
Next ❯

Citations

Jul 17, 2008·Comparative and Functional Genomics·C BlaschkeA Valencia
Jul 17, 2008·Comparative and Functional Genomics·Christian Blaschke, Alfonso Valencia
Jul 17, 2008·Comparative and Functional Genomics·Sergio Nasi
Jul 17, 2008·Comparative and Functional Genomics·David MilwardJulie Barnes
Jan 11, 2005·The Journal of Pathology·Jayne L Dennis, Karin A Oien
Feb 1, 2008·Journal of Structural and Functional Genomics·Xiaokang PanCraig A Bingman
Nov 5, 2003·Methods : a Companion to Methods in Enzymology·Robnet T KernsMichael F Miles
Aug 11, 2006·Nature Biotechnology·Dietrich Rebholz-SchuhmannPeter Stoehr
Jul 1, 2004·Nature Genetics·Robert Hoffmann, Alfonso Valencia
Feb 3, 2005·Nature Reviews. Drug Discovery·David B Searls
Jul 22, 2004·Nature Reviews. Genetics·Orjan Carlborg, Chris S Haley
Feb 24, 2006·European Journal of Human Genetics : EJHG·Marc A van DrielJack A M Leunissen
May 29, 2002·International Journal of Andrology·S ClaussenJ Gromoll
Nov 16, 2011·Proceedings of the National Academy of Sciences of the United States of America·Ka Yee YeungAdrian E Raftery
Jun 25, 2010·Journal of Toxicology and Environmental Health. Part B, Critical Reviews·Richard Judson
Feb 26, 2004·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Hagit Shatkay, Ronen Feldman
Aug 24, 2010·Cellular Reprogramming·Joonghoon ParkXiuchun Cindy Tian
Apr 2, 2011·Cellular Reprogramming·Joonghoon ParkX Cindy Tian
Apr 29, 2005·Diabetes Technology & Therapeutics·Jack PollardJacques Pappo
Jan 24, 2006·Journal of Interferon & Cytokine Research : the Official Journal of the International Society for Interferon and Cytokine Research·Lin TangMichael A Tainsky
Aug 22, 2008·Journal of Interferon & Cytokine Research : the Official Journal of the International Society for Interferon and Cytokine Research·Lai WeiLawrence M Pfeffer
Oct 15, 2013·Omics : a Journal of Integrative Biology·Anna Louise SwanJaume Bacardit
Jul 29, 2008·Briefings in Bioinformatics·Jung-Jae Kim, Dietrich Rebholz-Schuhmann
Sep 30, 2008·Briefings in Bioinformatics·Pankaj Agarwal, David B Searls
Dec 25, 2010·Briefings in Bioinformatics·Rob JelierPeter A C 't Hoen
Jun 30, 2011·Briefings in Bioinformatics·Christos AndronisAris Persidis
Aug 17, 2004·Bioinformatics·Ramin HomayouniMichael W Berry
Aug 31, 2004·Bioinformatics·Lifeng ChenCarol Friedman
Jan 22, 2005·Bioinformatics·Oliver Hofmann, Dietmar Schomburg
May 5, 2005·Bioinformatics·Mark DelongHolly Dressman
May 12, 2005·Bioinformatics·Tsutomu Matsunaga, Masa-Aki Muramatsu
Jul 5, 2005·Bioinformatics·Ungsik YuSangsoo Kim
Jan 24, 2007·Bioinformatics·Dietrich Rebholz-SchuhmannPeter Stoehr
Sep 27, 2006·Bioinformatics·Jeffrey T Chang, Joseph R Nevins
Dec 5, 2006·Bioinformatics·Katrin FundelRalf Zimmer
Apr 28, 2007·Bioinformatics·Vetle I Torvik, Neil R Smalheiser
Jul 25, 2007·Bioinformatics·Jeroen de RidderMarcel Reinders
Feb 12, 2008·Bioinformatics·Norio Kobayashi, Tetsuro Toyoda
Apr 17, 2009·Bioinformatics·Rajesh ChowdharyJun S Liu

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.