VLAD statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

VLAD specifications

Information


Unique identifier OMICS_21883
Name VLAD
Alternative name Visual annotation display
Interface Web user interface
Restrictions to use None
Input data A set of objects and optionally a customized data set of Gene Ontology, a personal ontology.
Input format GO,OBO
Output data A graphical and tabular representations of the ontology terms associated with the user-supplied gene list (i.e., the query set) and the calculated significance scores.
Output format HTML,XLS,TSV
Computer skills Basic
Version 1.6.0
Stability Stable
Maintained Yes

Versioning


No version available

Maintainers


  • person_outline Carol J. Bult
  • person_outline Joel Richardson

Publication for Visual annotation display

VLAD citations

 (7)
library_books

A retinoic acid dependent stroma leukemia crosstalk promotes chronic lymphocytic leukemia progression

2018
Nat Commun
PMCID: 5934403
PMID: 29725010
DOI: 10.1038/s41467-018-04150-7

[…] using the “weighted trimmed mean of M-values” described elsewhere. After normalization, differential gene expression was performed using the limi package in R. Annotation analysis was performed using VLAD – Visual Annotation Tool at MGI (Mouse Genome Informatics). No statistical method for sample size choice was used; however, a similar number of mice is generally used in the field for similar exp […]

call_split

Targeting of NAT10 enhances healthspan in a mouse model of human accelerated aging syndrome

2018
Nat Commun
PMCID: 5923383
PMID: 29703891
DOI: 10.1038/s41467-018-03770-3
call_split See protocol

[…] ower than 0.1. In edgeR differential expression analysis, we selected genes up or down regulated with a p-value less than 0.05. Gene ontology analysis was performed using the mouse genome informatics visual annotation display. For the analysis of the biological term fold enrichment, a ratio between the frequency of genes in our set to frequency of genes in the whole genome was calculated. […]

library_books

Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology

2018
Circ Cardiovasc Genet
PMCID: 5821137
PMID: 29440116
DOI: 10.1161/CIRCGEN.117.001813

[…] s freely available functional analysis tools, including Database for Annotation, Visualization and Integrated Discovery, g:profiler, Protein Analysis Through Evolutionary Relationships (PANTHER), and Visual Annotation Display (VLAD). Full methods are available in the Data Supplement. […]

library_books

Evolutionary adaptation revealed by comparative genome analysis of woolly mammoths and elephants

2017
PMCID: 5737375
PMID: 28369217
DOI: 10.1093/dnares/dsx007

[…] d amino acid substitutions was analysed using PANTHER (http://pantherdb.org/ (9 February 2017, date last accessed)), WebGestalt (http://www.webgestalt.org/ (9 February 2017, date last accessed)), and Vlad (http://proto.informatics.jax.org/prototypes/vlad/ (9 February 2017, date last accessed)), respectively. Using a set of SNVs (four variant-supporting reads, mapping quality ≥20, allele frequency  […]

library_books

Type IV collagen drives alveolar epithelial–endothelial association and the morphogenetic movements of septation

2016
BMC Biol
PMCID: 4942891
PMID: 27412481
DOI: 10.1186/s12915-016-0281-2

[…] homologous and named by Ensembl with BioMart (http://useast.ensembl.org/index.html). Once the murine homologous gene list was generated, functional classification of genes was performed using MGI and Vlad (http://proto.informatics.jax.org/prototypes/vlad/). […]

library_books

Precise genetic mapping and integrative bioinformatics in Diversity Outbred mice reveals Hydin as a novel pain gene

2014
Mamm Genome
PMCID: 4032469
PMID: 24700285
DOI: 10.1007/s00335-014-9508-0

[…] . The functional relationship networks generated by MouseMap and IPA were assessed for enrichment of Gene Ontology (GO) (Ashburner et al. ) and Mammalian Phenotype (MP) (Smith and Eppig ) terms using VLAD (http://proto.informatics.jax.org/prototypes/vlad-1.0.3/), a web-based tool for statistical term enrichment (annotation date: November 2, 2011).For each candidate gene, gene expression annotation […]

Citations

Looking to check out a full list of citations?

VLAD institution(s)
Mouse Genome Informatics (MGI) Database Consortium, The Jackson Laboratory, Bar Harbor, ME, USA
VLAD funding source(s)
Supported, in part, by NIH HG00330-P1

VLAD reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review VLAD