SaVanT: a web-based tool for the sample-level visualization of molecular signatures in gene expression profiles

BMC Genomics
David LopezMatteo Pellegrini

Abstract

Molecular signatures are collections of genes characteristic of a particular cell type, tissue, disease, or perturbation. Signatures can also be used to interpret expression profiles generated from heterogeneous samples. Large collections of gene signatures have been previously developed and catalogued in the MSigDB database. In addition, several consortia and large-scale projects have systematically profiled broad collections of purified primary cells, molecular perturbations of cell types, and tissues from specific diseases, and the specificity and breadth of these datasets can be leveraged to create additional molecular signatures. However, to date there are few tools that allow the visualization of individual signatures across large numbers of expression profiles. Signature visualization of individual samples allows, for example, the identification of patient subcategories a priori on the basis of well-defined molecular signatures. Here, we generate and compile 10,985 signatures (636 newly-generated and 10,349 previously available from MSigDB) and provide a web-based Signature Visualization Tool (SaVanT; http://newpathways.mcdb.ucla.edu/savant ), to visualize these signatures in user-generated expression data. We show that ...Continue Reading

References

Apr 13, 2004·Proceedings of the National Academy of Sciences of the United States of America·Andrew I SuJohn B Hogenesch
Sep 15, 2005·BMC Bioinformatics·John TomfohrThomas B Kepler
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Dec 20, 2007·The Journal of General Virology·Richard E Randall, Stephen Goodbourn
Apr 30, 2008·Immunome Research·Jane E LattinMatthew J Sweet
Sep 19, 2008·Nature Immunology·Tracy S P HengUNKNOWN Immunological Genome Project Consortium
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
Jan 26, 2010·Biostatistics·Matthew N McCallRafael A Irizarry
Jan 18, 2013·BMC Bioinformatics·Sonja HänzelmannJustin Guinney
May 2, 2013·Trends in Immunology·Tal Shay, Joonsoo Kang
Oct 31, 2013·Current Opinion in Immunology·Charles C Kim, Lewis L Lanier
Nov 12, 2013·Nucleic Acids Research·Minoru KanehisaMao Tanabe
Dec 18, 2013·Bioinformatics·Andreas KrämerStuart Tugendreich
Aug 12, 2014·The Journal of Investigative Dermatology·Megan S InkelesMatteo Pellegrini
Aug 22, 2014·Science Translational Medicine·Dennis MontoyaRobert L Modlin
Dec 15, 2015·Nucleic Acids Research·Antonio FabregatPeter D'Eustachio

❮ Previous
Next ❯

Citations

Mar 19, 2019·Frontiers in Medicine·Tim HulsenEoin F McKinney
Jun 21, 2020·Nature Communications·Igor MandricSerghei Mangul
Feb 25, 2020·The Journal of Investigative Dermatology·Hongsheng WangRobert L Modlin
Sep 24, 2021·Journal of Cellular Physiology·Min WangYongping Shao

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE29883
GSE32962

Methods Mentioned

BETA
RNA-seq
biopsies

Software Mentioned

frmavecs
R
Signature Visualization Tool ( SaVanT )
Java
GSVA
SaVanT
Python scripts
gplots
S ign a ture V isu a lizatio n T ool ( SaVanT )
GSEA

Related Concepts

Related Feeds

Bacterial Pneumonia (ASM)

Bacterial pneumonia is a prevalent and costly infection that is a significant cause of morbidity and mortality in patients of all ages. Here is the latest research.

Bacterial Pneumonia

Bacterial pneumonia is a prevalent and costly infection that is a significant cause of morbidity and mortality in patients of all ages. Here is the latest research.

AML: Role of LSD1 by CRISPR (Keystone)

Find the latest rersearrch on the ability of CRISPR-Cas9 mutagenesis to profile the interactions between lysine-specific histone demethylase 1 (LSD1) and chemical inhibitors in the context of acute myeloid leukemia (AML) here.

Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is a clinically and genetically heterogeneous disease with approximately 20,000 cases per year in the United States. AML also accounts for 15-20% of all childhood acute leukemias, while it is responsible for more than half of the leukemic deaths in these patients. Here is the latest research on this disease.

Blood And Marrow Transplantation

The use of hematopoietic stem cell transplantation or blood and marrow transplantation (bmt) is on the increase worldwide. BMT is used to replace damaged or destroyed bone marrow with healthy bone marrow stem cells. Here is the latest research on bone and marrow transplantation.