FlyTF: a systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster.

Bioinformatics
Boris Adryan, Sarah A Teichmann

Abstract

We present a manually annotated catalogue of site-specific transcription factors (TFs) in the fruit fly Drosophila melanogaster. These were identified from a list of candidate proteins with transcription-related Gene Ontology (Go) annotation as well as structural DNA-binding domain assignments. For all 1052 candidate proteins, a defined set of rules was applied to classify information from the literature and computational data sources with respect to both DNA-binding and transcriptional regulatory properties. We propose a set of 753 TFs in the fruit fly, of which 23 are confident novel predictions of this function for previously uncharacterized proteins.

References

Dec 11, 1999·Nucleic Acids Research·A V SpirovJ Reinitz
Mar 25, 2000·Science·M D AdamsJ C Venter
Jan 23, 2003·Genome Biology·Sima MisraSuzanna E Lewis
Sep 6, 2003·Trends in Genetics : TIG·Erik van Nimwegen
Sep 2, 2004·PLoS Biology·Mark D SchroederUlrike Gaul
Nov 24, 2005·Bioinformatics·Steven M GalloMarc S Halfon
Dec 13, 2005·Genome Research·Michael Ashburner, Casey M Bergman

❮ Previous
Next ❯

Citations

Oct 12, 2010·Cellular and Molecular Life Sciences : CMLS·Johannes Jaeger
Nov 1, 2011·Nature Methods·Korneel HensBart Deplancke
Oct 1, 2011·Proceedings of the National Academy of Sciences of the United States of America·Sriram ChandrasekaranGene E Robinson
Mar 28, 2009·Briefings in Functional Genomics & Proteomics·Bart Deplancke
Nov 4, 2009·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Keiichi MochidaLam-Son Phan Tran
Dec 13, 2007·Nucleic Acids Research·Derek WilsonSarah A Teichmann
Nov 15, 2011·Nucleic Acids Research·Sergio ContrinoGos Micklem
Nov 15, 2011·Nucleic Acids Research·Hong-Mei ZhangAn-Yuan Guo
Nov 9, 2007·Genome Research·Pouya KheradpourManolis Kellis
Feb 18, 2009·Genes, Brain, and Behavior·C AlauxG E Robinson
Feb 15, 2008·Genome Biology·Stein AertsUNKNOWN Open Regulatory Annotation Consortium
Mar 17, 2009·Genome Biology·Debra L FultonRob Sladek
Apr 14, 2010·Genome Biology·Boris Adryan, Sarah A Teichmann
Jan 24, 2007·PLoS Computational Biology·Thomas A DownTim J P Hubbard
Aug 5, 2011·PLoS Computational Biology·Iulian Pruteanu-MaliniciUwe Ohler
Dec 24, 2013·Genome Biology·Ann S HammondsSusan E Celniker
Dec 25, 2013·Nucleic Acids Research·Peng Jiang, Mona Singh
Sep 23, 2014·Cell Reports·David Y RheeSpyros Artavanis-Tsakonas
Mar 11, 2009·Nature Reviews. Genetics·Juan M VaquerizasNicholas M Luscombe
Feb 21, 2016·Database : the Journal of Biological Databases and Curation·Lei ShengBeijiu Cheng
Nov 26, 2013·Nucleic Acids Research·Shula ShazmanBarry Honig
Oct 30, 2012·Trends in Genetics : TIG·J Omar Yáñez-CunaAlexander Stark
Jun 3, 2015·Scientific Reports·Bao-Fa SunDa-Wei Huang
Apr 27, 2013·Evolution; International Journal of Organic Evolution·Arnaud Martin, Virginie Orgogozo
Jan 5, 2010·Developmental Biology·Julia Zeitlinger, Alexander Stark
Nov 26, 2013·Developmental Biology·William A RogersThomas M Williams
May 9, 2014·Neuron·Jay Z ParrishGraeme W Davis
May 10, 2011·Cell Stem Cell·Ralph A NeumüllerJuergen A Knoblich
Oct 21, 2006·Developmental Cell·François Spitz, Eileen E M Furlong
Apr 15, 2009·Journal of Biomedical Informatics·Hui YangGoran Nenadic

❮ 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.