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Protocols

WebGestalt specifications

Information


Unique identifier OMICS_02222
Name WebGestalt
Alternative name WEB-based GEne SeT AnaLysis Toolkit
Interface Web user interface
Restrictions to use None
Input data Some values for individual genes.
Output data The analysis summary, gene identifier (ID) mapping information, GO Slim summary and enrichment results.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Bing Zhang

Publications for WEB-based GEne SeT AnaLysis Toolkit

WebGestalt citations

 (358)
library_books

Expression of the Long Intergenic Non Protein Coding RNA 665 (LINC00665) Gene and the Cell Cycle in Hepatocellular Carcinoma Using The Cancer Genome Atlas, the Gene Expression Omnibus, and Quantitative Real Time Polymerase Chain Reaction

2018
PMCID: 5956974
PMID: 29728556
DOI: 10.12659/MSM.907389

[…] bsite. Additionally, 4,296 correlated genes were obtained from the Multi Experiment Matrix (MEM) database. Based on genes obtained from the above databases, 469 overlapped genes were obtained (). The WebGestalt (WEB-based GEne SeT AnaLysis Toolkit) analysis was used to confirm Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Protein Analysis Through Evolutionary Relationships (P […]

library_books

Exploring the mechanisms of resistance to Teladorsagia circumcincta infection in sheep through transcriptome analysis of abomasal mucosa and abomasal lymph nodes

2018
PMCID: 5922024
PMID: 29703268
DOI: 10.1186/s13567-018-0534-x

[…] ch group. These gene lists were subjected to three types of gene-set enrichment analysis [gene ontology (GO) analysis, KEGG pathway analysis and disease association analysis] using the web-based tool WebGestalt []. For these analyses, the human genome was considered as a reference and the parameters considered were the default statistical method Hypergeometric, multiple test adjustment with the BH […]

library_books

Environmental Enrichment Prevents Transcriptional Disturbances Induced by Alpha Synuclein Overexpression

2018
PMCID: 5932345
PMID: 29755323
DOI: 10.3389/fncel.2018.00112

[…] DAVID 6.7 and WebGestalt 2017 were employed to identify overrepresented Gene Ontology terms and associated cellular functions in sets of differentially expressed genes (Huang da et al., ; Wang et al., ). Terms with […]

call_split

Placental miR 340 mediates vulnerability to activity based anorexia in mice

2018
Nat Commun
PMCID: 5913294
PMID: 29686286
DOI: 10.1038/s41467-018-03836-2
call_split See protocol

[…] nd the Aquantile for between arrays normalization. A linear model was applied in order to find the differentially expressed genes (a simple Bayesian model). Gene ontology analysis was performed using WebGestalt 58. (http://bioinfo.vanderbilt.edu/webgestalt/) (Supplementary Data ). […]

call_split

Cholesterol metabolism promotes B‐cell positioning during immune pathogenesis of chronic obstructive pulmonary disease

2018
PMCID: 5938615
PMID: 29674392
DOI: 10.15252/emmm.201708349
call_split See protocol

[…] he log2 transformed expression values for each gene relative to filtered air or healthy controls. Gene Ontology pathway analysis was undertaken on GEO2R gene expression data with a P < 0.05 using the web‐based gene set analysis toolkit WebGestalt (Wang et al, ). A heat map of selected genes (log2 transformed expression values, with a P < 0.05, as calculated by GEO2R) taken from the Gene Ontology p […]

library_books

Integration of human adipocyte chromosomal interactions with adipose gene expression prioritizes obesity related genes from GWAS

2018
Nat Commun
PMCID: 5904163
PMID: 29666371
DOI: 10.1038/s41467-018-03554-9

[…] ry Table ). These 42 BMI-correlated genes are functionally enriched for four pathways with fatty acid metabolism as a top ranking pathway (Supplementary Table ) based on KEGG pathway enrichment using WebGestalt (Benjamini-Hochberg adjusted p < 0.05); however, the small number of genes in these pathway analyses warrant verification in future studies. Only these 42 replicated genes were further inve […]

Citations

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WebGestalt institution(s)
Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
WebGestalt funding source(s)
Supported by National Cancer Institute (NCI) [U24 CA210954]; Leidos Biomedical Research, Inc. [15X038]; Cancer Prevention & Research Institutes of Texas Scholarship (CPRIT) [RR160027] and McNair Medical Institute Scholarship.

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