A preliminary computational outputs versus experimental results: Application of sTRAP, a biophysical tool for the analysis of SNPs of transcription factor-binding sites.

Molecular Genetics & Genomic Medicine
Shirin MoradifardMina Ebrahimi-Rad

Abstract

In the human genome, the transcription factors (TFs) and transcription factor-binding sites (TFBSs) network has a great regulatory function in the biological pathways. Such crosstalk might be affected by the single-nucleotide polymorphisms (SNPs), which could create or disrupt a TFBS, leading to either a disease or a phenotypic defect. Many computational resources have been introduced to predict the TFs binding variations due to SNPs inside TFBSs, sTRAP being one of them. A literature review was performed and the experimental data for 18 TFBSs located in 12 genes was provided. The sequences of TFBS motifs were extracted using two different strategies; in the size similar with synthetic target sites used in the experimental techniques, and with 60 bp upstream and downstream of the SNPs. The sTRAP (http://trap.molgen.mpg.de/cgi-bin/trap_two_seq_form.cgi) was applied to compute the binding affinity scores of their cognate TFs in the context of reference and mutant sequences of TFBSs. The alternative bioinformatics model used in this study was regulatory analysis of variation in enhancers (RAVEN; http://www.cisreg.ca/cgi-bin/RAVEN/a). The bioinformatics outputs of our study were compared with experimental data, electrophoretic mobi...Continue Reading

References

Jan 23, 2008·PLoS Computational Biology·Malin C AndersenJacob Odeberg
Dec 10, 2009·PLoS Computational Biology·Yue ZhaoGary D Stormo
Feb 4, 2010·Human Mutation·Thomas MankeMartin Vingron
Sep 9, 2010·Bioinformatics·Geoff MacintyreAdam Kowalczyk
Mar 3, 2012·American Journal of Respiratory Cell and Molecular Biology·Rajesh ChowdharyVladimir B Bajic
Mar 23, 2012·PloS One·Jittima PiriyapongsaSissades Tongsima
Mar 30, 2012·PLoS Genetics·Matthew T MauranoJohn A Stamatoyannopoulos
Sep 8, 2012·Nature·UNKNOWN ENCODE Project Consortium
Sep 8, 2012·Genome Research·Alan P BoyleMichael Snyder
Apr 10, 2013·Human Mutation·Birgit Sikkema-RaddatzRichard J Sinke
Sep 17, 2013·PLoS Computational Biology·Anthony Mathelier, Wyeth W Wasserman
Dec 25, 2013·Proceedings of the National Academy of Sciences of the United States of America·David H SkuseLarry J Young
Jan 11, 2014·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Samuel P StromJoshua L Deignan
Dec 4, 2014·Trends in Pharmacological Sciences·Sharadha Dayalan NaiduAlbena T Dinkova-Kostova
Aug 13, 2015·ELife·Vikram AgarwalDavid P Bartel
Jul 30, 2016·Cell·Bart DeplanckeVincent Gardeux
Dec 3, 2016·Nucleic Acids Research·Jacqueline MacArthurHelen Parkinson
Feb 16, 2017·Cell Biology International·Manjul RanaRakesh K Tyagi
Sep 1, 2015·Biophysics Reviews·Amir Hossein KamaliJoshua W K Ho
Nov 21, 2017·Nucleic Acids Research·Dimitra KaragkouniArtemis G Hatzigeorgiou
Feb 10, 2018·Cell·Samuel A LambertMatthew T Weirauch
Sep 27, 2018·BMC Bioinformatics·Christopher I CooperPaul C Boutros
Jan 12, 2019·Genome Biology·Jens KeilwagenJan Grau
Mar 22, 2019·International Journal of Molecular Sciences·René HuberRaimund W Kinne
Jul 18, 2019·Frontiers in Immunology·Adewunmi Adelaja, Alexander Hoffmann

❮ Previous
Next ❯

Methods Mentioned

BETA
electrophoretic mobility shift assay

Software Mentioned

sTRAP
RAVEN
EMSA

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.