PAGED: a pathway and gene-set enrichment database to enable molecular phenotype discoveries.

BMC Bioinformatics
Hui HuangJake Y Chen

Abstract

Over the past decade, pathway and gene-set enrichment analysis has evolved into the study of high-throughput functional genomics. Owing to poorly annotated and incomplete pathway data, researchers have begun to combine pathway and gene-set enrichment analysis as well as network module-based approaches to identify crucial relationships between different molecular mechanisms. To meet the new challenge of molecular phenotype discovery, in this work, we have developed an integrated online database, the Pathway And Gene Enrichment Database (PAGED), to enable comprehensive searches for disease-specific pathways, gene signatures, microRNA targets, and network modules by integrating gene-set-based prior knowledge as molecular patterns from multiple levels: the genome, transcriptome, post-transcriptome, and proteome. The online database we developed, PAGED http://bio.informatics.iupui.edu/PAGED is by far the most comprehensive public compilation of gene sets. In its current release, PAGED contains a total of 25,242 gene sets, 61,413 genes, 20 organisms, and 1,275,560 records from five major categories. Beyond its size, the advantage of PAGED lies in the explorations of relationships between gene sets as gene-set association networks (GS...Continue Reading

References

Dec 26, 2001·Nucleic Acids Research·Ron EdgarAlex E Lash
May 1, 2004·Nature Genetics·Kevin G BeckerS Alex Wang
Dec 21, 2004·Nucleic Acids Research·Ada HamoshVictor A McKusick
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Dec 5, 2006·Oncogene·S Segditsas, I Tomlinson
Oct 30, 2007·American Journal of Human Genetics·Kai WangMaja Bucan
Nov 11, 2008·Nucleic Acids Research·Feifei XiaoTongbin Li
Sep 4, 2009·BMC Bioinformatics·Luca AbatangeloNicola Ancona
Oct 14, 2009·BMC Bioinformatics·Sudhir R ChowbinaJake Y Chen
Mar 30, 2010·American Journal of Human Genetics·Hua ZhongEric E Schadt
Dec 15, 2010·Bioinformatics·Michael E SmootTrey Ideker
May 7, 2011·Bioinformatics·Arthur LiberzonJill P Mesirov
Nov 24, 2011·Nucleic Acids Research·Aedín C CulhaneJohn Quackenbush
Mar 3, 2012·PLoS Computational Biology·Purvesh KhatriAtul J Butte
Apr 7, 2012·Trends in Genetics : TIG·Vijay K RamananAndrew J Saykin
May 26, 2012·Frontiers in Genetics·Madhankumar SonachalamXiaogang Wu

❮ Previous
Next ❯

Citations

Jun 10, 2014·Journal of Theoretical Biology·Xiaogang WuJake Yue Chen
Jun 15, 2015·Bioinformatics·Zongliang YueJake Y Chen
Nov 8, 2014·Computational and Structural Biotechnology Journal·Bjoern TitzManuel C Peitsch
Aug 12, 2016·Human Molecular Genetics·Tune H Pers
Aug 10, 2013·Expert Review of Clinical Pharmacology·Debraj GuhathakurtaJames B Trager
Oct 30, 2015·Human Genomics·Anis Karimpour-FardLawrence E Hunter
Sep 18, 2021·Nucleic Acids Research·Xuelian MaZhen Su

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE8671

Methods Mentioned

BETA
FCS

Software Mentioned

MicroArray Suite ( MAS5 )
Perl
Apache
Java
OMIM
Oracle
PAGED
Cytoscape
Pathway And Gene Enrichment Database ( PAGED )
BioConductor

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.