NFPscanner: a webtool for knowledge-based deciphering of biomedical networks

BMC Bioinformatics
Wenjian XuFei Li

Abstract

Many biological pathways have been created to represent different types of knowledge, such as genetic interactions, metabolic reactions, and gene-regulating and physical-binding relationships. Biologists are using a wide range of omics data to elaborately construct various context-specific differential molecular networks. However, they cannot easily gain insight into unfamiliar gene networks with the tools that are currently available for pathways resource and network analysis. They would benefit from the development of a standardized tool to compare functions of multiple biological networks quantitatively and promptly. To address this challenge, we developed NFPscanner, a web server for deciphering gene networks with pathway associations. Adapted from a recently reported knowledge-based framework called network fingerprint, NFPscanner integrates the annotated pathways of 7 databases, 4 algorithms, and 2 graphical visualization modules into a webtool. It implements 3 types of network analysis: Fingerprint: Deciphering gene networks and highlighting inherent pathway modules Alignment: Discovering functional associations by finding optimized node mapping between 2 gene networks Enrichment: Calculating and visualizing gene ontolog...Continue Reading

References

Aug 10, 2002·Bioinformatics·Trey IdekerAndrew F Siegel
Jun 25, 2004·Nucleic Acids Research·Brian P KelleyTrey Ideker
Aug 13, 2005·Bioinformatics·Tobias SingThomas Lengauer
Sep 27, 2006·Bioinformatics·Jeffrey T Chang, Joseph R Nevins
Oct 4, 2008·Nucleic Acids Research·Carl F SchaeferKenneth H Buetow
Mar 25, 2009·Bioinformatics·Jitao David Zhang, Stefan Wiemann
May 30, 2009·Bioinformatics·Chung-Shou LiaoBonnie Berger
Jun 10, 2010·Nucleic Acids Research·Sabine DietmannAlexey V Antonov
Jul 27, 2010·Bioinformatics·Christian T LopesGary D Bader
Dec 15, 2010·Bioinformatics·Michael E SmootTrey Ideker
May 26, 2011·Nucleic Acids Research·Alexey V Antonov
Jul 9, 2011·Bioinformatics·Ulrich BodenhoferSepp Hochreiter
Nov 24, 2011·Nucleic Acids Research·Aedín C CulhaneJohn Quackenbush
Jan 12, 2012·Integrative Biology : Quantitative Biosciences From Nano to Macro·Vesna Memišević, Nataša Pržulj
Feb 2, 2012·BMC Bioinformatics·Gabriele SalesChiara Romualdi
Mar 30, 2012·Omics : a Journal of Integrative Biology·Guangchuang YuQing-Yu He
May 24, 2012·Nucleic Acids Research·Roland A PachePatrick Aloy
Oct 11, 2012·Bioinformatics·Rob Patro, Carl Kingsford
Feb 16, 2013·Bioinformatics·Ahmet E Aladag, Cesim Erten
May 23, 2013·Bioinformatics·Behnam NeyshaburSeyed Shahriar Arab
Jun 26, 2013·Nucleic Acids Research·Khalid ZuberiQuaid Morris
Apr 3, 2014·BMC Systems Biology·Mohammed El-KebirGunnar W Klau
May 6, 2014·Bioinformatics·Connor Clark, Jugal Kalita
Oct 30, 2014·Nucleic Acids Research·Damian SzklarczykChristian von Mering
Mar 1, 2015·Bioinformatics·Noël Malod-Dognin, Nataša Pržulj
Aug 27, 2015·Scientific Reports·Xiuliang CuiXiaochen Bo
Oct 18, 2015·Nucleic Acids Research·Minoru KanehisaMao Tanabe
Nov 19, 2015·Nucleic Acids Research·Huaiyu MiPaul D Thomas
Dec 15, 2015·Nucleic Acids Research·Antonio FabregatPeter D'Eustachio
Dec 17, 2015·Bioinformatics·Maximilian MalekJan Baumbach
Feb 18, 2016·PloS One·Jaisri JagannadhamKamal Rawal
May 7, 2016·Bioinformatics·Ivan H GoenawanDavid J Lynn

❮ Previous
Next ❯

Software Mentioned

Biocarta
Internet Explorer
Chrome
R
HumanCyc
KEGGgraph
Opera
NFPscanner
js
jsPDF

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.