Summary: Differential Expression Gene Explorer (DrEdGE) is a web-based tool that guides genomicists through easily creating interactive online data visualizations, which colleagues can query according to their own conditions to discover genes, samples or patterns of interest. We demonstrate DrEdGE's features with three example websites generated from publicly available datasets-human neuronal tissue, mouse embryonic tissue and Caenorhabditis elegans whole embryos. DrEdGE increases the utility of large genomics datasets by removing technical obstacles to independent exploration.
Availability And Implementation: Freely available at http://dredge.bio.unc.edu.
Supplementary Information: Supplementary data are available at Bioinformatics online.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7178403 | PMC |
| http://dx.doi.org/10.1093/bioinformatics/btz972 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
The MADS-box protein SHATTERPROOF 2 regulates TAA1 expression in the gynoecium valve margins.
Plant Reprod
January 2025
Hormonal Crosstalk in Plant Development, Mendel Center for Plant Genomics and Proteomics, CEITEC MU-Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic.
SHATTERPROOF 2 regulates TAA1 expression for the establishment of the gynoecium valve margins. Gynoecium development and patterning play a crucial role in determining the ultimate structure of the fruit and, thus, seed production. The MADS-box transcription factor SHATTERPROOF 2 (SHP2) contributes to valve margin differentiation and plays a major role in fruit dehiscence and seed dispersal.
View Article and Find Full Text PDFAmyotrophic Lateral Sclerosis and Parkinson's Disease: Brain Tissue Transcriptome Analysis Reveals Interactions.
Mol Neurobiol
January 2025
Hebei Medical University-Galway University Stem Cell Research Center, Hebei Medical University, Shijiazhuang, 050017, Hebei Province, China.
This study utilises amyotrophic lateral sclerosis (ALS) and Parkinson's disease (PD) human brain samples from the GEO database and employs differential expression gene (DEG) analysis to identify genes that are pivotal in both neurodegenerative diseases. Through in depth GO and KEGG enrichment analyses, we elucidated the biological functions and potential pathways associated with these DEGs. Furthermore, by constructing protein‒protein interaction networks, we highlight the significance of shared DEGs in both cellular physiology and disease contexts.
View Article and Find Full Text PDFGalectin-1 and galectin-3 in male reproduction - impact in health and disease.
Semin Immunopathol
January 2025
Institute of Anatomy and Cell Biology, Hessian Centre of Reproductive Medicine, Justus-Liebig University Giessen, Aulweg 123, 35392, Giessen, Germany.
The formation and differentiation of mature, motile male germ cells, which can fertilize the egg and ensure successful implantation and development of a healthy embryo, are essential functions of the testis and epididymis. Spermatogenesis is a complex, multistep process that results in the formation of motile haploid gametes, requiring an immunoregulatory environment to maintain tolerance to developing neo-antigens. Different cell types (Sertoli cells, macrophages), immunoregulatory factors and tolerance mechanisms are involved.
View Article and Find Full Text PDFJoint analysis of genome-wide cross-trait and multi-omics reveals molecular mechanisms of inflammatory bowel disease and nominates its novel therapeutic genes.
FASEB J
January 2025
College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.
Inflammatory bowel disease (IBD) with the two predominant endophenotypes-Crohn's disease (CD) and ulcerative colitis (UC)-represents a group of chronic gastrointestinal inflammatory conditions. Since most genetic associations with IBD are often limited to independent subtypes, we reported a genome-wide association study (GWAS) cross-trait analysis combined with CD and UC to enhance statistical power. Initially, we detected 256 association signals at 54 genomic susceptibility loci and further characterized the functionality of variants within these regions.
View Article and Find Full Text PDFSox10 is required for systemic initiation of bone mineralization.
Development
January 2025
Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
Heterozygous variants in SOX10 cause congenital syndromes affecting pigmentation, digestion, hearing, and neural development, primarily attributable to failed differentiation or loss of non-skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest- nor mesoderm-derived bones initiate mineralization on time in zebrafish sox10 mutants, despite normal osteoblast differentiation and matrix production.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!