Local network-based measures to assess the inferability of different regulatory networks

IET Systems Biology
Frank Emmert-Streib, Gökmen Altay

Abstract

The purpose of this study is to compare the inferability of various synthetic as well as real biological regulatory networks. In order to assess differences we apply local network-based measures. That means, instead of applying global measures, we investigate and assess an inference algorithm locally, on the level of individual edges and subnetworks. We demonstrate the behaviour of our local network-based measures with respect to different regulatory networks by conducting large-scale simulations. As inference algorithm we use exemplarily ARACNE. The results from our exploratory analysis allow us not only to gain new insights into the strength and weakness of an inference algorithm with respect to characteristics of different regulatory networks, but also to obtain information that could be used to design novel problem-specific statistical estimators.

References

Aug 8, 1970·Nature·F Crick
Aug 1, 1997·Computer Applications in the Biosciences : CABIOS·J H Hofmeyr, A Cornish-Bowden
Dec 9, 1998·Proceedings of the National Academy of Sciences of the United States of America·M B EisenD Botstein
Oct 16, 1999·Science·A L Barabasi, R Albert
Oct 12, 2000·Proceedings of the National Academy of Sciences of the United States of America·A J ButteI S Kohane
Apr 23, 2002·Nature Genetics·Shai S Shen-OrrUri Alon
Nov 9, 2002·Bioinformatics·Olga G TroyanskayaRuss B Altman
Oct 10, 2003·Bioinformatics·Pedro MendesKeying Ye
Mar 17, 2004·Genetics·Momiao XiongXiangzhong Fang
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Nov 23, 2005·Proceedings of the National Academy of Sciences of the United States of America·Daehee HwangHamid Bolouri
Dec 2, 2006·Proceedings of the National Academy of Sciences of the United States of America·Timothy R LezonNina V Fedoroff
Sep 7, 2007·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Frank Emmert-Streib
Oct 3, 2007·IET Systems Biology·M Bansal, D di Bernardo
Oct 11, 2007·Annals of the New York Academy of Sciences·Gustavo StolovitzkyAndrea Califano
Oct 11, 2007·Annals of the New York Academy of Sciences·Diogo CamachoReinhard Laubenbacher
Jan 17, 2009·EURASIP Journal on Bioinformatics & Systems Biology·Catharina OlsenGianluca Bontempi
Mar 3, 2009·Bioinformatics·Hendrik HacheRalf Herwig
Jun 25, 2009·EURASIP Journal on Bioinformatics & Systems Biology·Hendrik HacheRalf Herwig
Feb 17, 2010·Database : the Journal of Biological Databases and Curation·L WisslerG Procaccini
Mar 24, 2010·Proceedings of the National Academy of Sciences of the United States of America·Daniel MarbachGustavo Stolovitzky
May 4, 2010·Food and Chemical Toxicology : an International Journal Published for the British Industrial Biological Research Association·A PetrócziD P Naughton
Jan 1, 2009·Language Learning and Development : the Official Journal of the Society for Language Development·Daniel J WeissAaron D Mitchel

❮ Previous
Next ❯

Citations

Jul 23, 2011·BMC Bioinformatics·Gökmen AltayDavid E Neal
May 15, 2013·BMC Genomics·Ricardo de Matos SimoesFrank Emmert-Streib
Jun 24, 2011·Biology Direct·Gökmen Altay, Frank Emmert-Streib
Oct 6, 2010·BMC Systems Biology·Gökmen Altay, Frank Emmert-Streib
May 16, 2012·BMC Systems Biology·Ricardo de Matos SimoesFrank Emmert-Streib
May 30, 2012·BMC Systems Biology·Paola LeccaCorrado Priami
Apr 6, 2012·PloS One·Ricardo de Matos Simoes, Frank Emmert-Streib
Aug 1, 2014·Frontiers in Genetics·Benjamin Haibe-Kains, Frank Emmert-Streib
Nov 5, 2014·Frontiers in Cell and Developmental Biology·Frank Emmert-StreibBenjamin Haibe-Kains
Feb 15, 2014·Evolutionary Bioinformatics Online·Gökmen AltayFrank Emmert-Streib
Jan 20, 2011·PloS One·Matthias DehmerFrank Emmert-Streib

❮ 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.