Lynx: a knowledge base and an analytical workbench for integrative medicine

Sulakhe, Dinanath; Xie, Bingqing; Taylor, Andrew; D’Souza, Mark; Balasubramanian, Sandhya; Hashemifar, Somaye; White, Steven R.; Dave, Utpal J.; Agam, Gady; Xu, Jinbo; Wang, Sheng; Gilliam, T. Conrad; Maltsev, Natalia

doi:10.1093/nar/gkv1257

Cited by 8 publications

(6 citation statements)

References 51 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…While most of these enrichment analysis tools are specific for mammalian organisms, some also support model organisms. The tools that support enrichment analyses in model organisms include, for example, AmiGO (5), DAVID (2), g-Profiler (12), KOBAS (13), LRpath (14), Lynx (15), modPhEA (16), STRING (17), ToppFun (18), WebGestalt (4) and WormBase (19). All these digital resources provide web-based organism-specific enrichment analyses, which offer users various interactive features, gene set libraries and visualizations of results (Table 1).…”

Section: Introductionmentioning

confidence: 99%

modEnrichr: a suite of gene set enrichment analysis tools for model organisms

Kuleshov

Diaz

Flamholz

et al. 2019

Nucleic Acids Research

View full text Add to dashboard Cite

High-throughput experiments produce increasingly large datasets that are difficult to analyze and integrate. While most data integration approaches focus on aligning metadata, data integration can be achieved by abstracting experimental results into gene sets. Such gene sets can be made available for reuse through gene set enrichment analysis tools such as Enrichr. Enrichr currently only supports gene sets compiled from human and mouse, limiting accessibility for investigators that study other model organisms. modEnrichr is an expansion of Enrichr for four model organisms: fish, fly, worm and yeast. The gene set libraries within FishEnrichr, FlyEnrichr, WormEnrichr and YeastEnrichr are created from the Gene Ontology, mRNA expression profiles, GeneRIF, pathway databases, protein domain databases and other organism-specific resources. Additionally, libraries were created by predicting gene function from RNA-seq co-expression data processed uniformly from the gene expression omnibus for each organism. The modEnrichr suite of tools provides the ability to convert gene lists across species using an ortholog conversion tool that automatically detects the species. For complex analyses, modEnrichr provides API access that enables submitting batch queries. In summary, modEnrichr leverages existing model organism databases and other resources to facilitate comprehensive hypothesis generation through data integration.

show abstract

Section: Introductionmentioning

confidence: 99%

modEnrichr: a suite of gene set enrichment analysis tools for model organisms

Kuleshov

Diaz

Flamholz

et al. 2019

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…We used R 70 for all statistics and data visualization. We obtained gene annotation information from the Ensembl 50 and Lynx 71 databases. The computational resources were provided by the University of Chicago Research Computing Center.…”

Section: Methodsmentioning

confidence: 99%

Predicting susceptibility to tuberculosis based on gene expression profiling in dendritic cells

Blischak

Tailleux

Myrthil

et al. 2017

Sci Rep

View full text Add to dashboard Cite

Tuberculosis (TB) is a deadly infectious disease, which kills millions of people every year. The causative pathogen, Mycobacterium tuberculosis (MTB), is estimated to have infected up to a third of the world’s population; however, only approximately 10% of infected healthy individuals progress to active TB. Despite evidence for heritability, it is not currently possible to predict who may develop TB. To explore approaches to classify susceptibility to TB, we infected with MTB dendritic cells (DCs) from putatively resistant individuals diagnosed with latent TB, and from susceptible individuals that had recovered from active TB. We measured gene expression levels in infected and non-infected cells and found hundreds of differentially expressed genes between susceptible and resistant individuals in the non-infected cells. We further found that genetic polymorphisms nearby the differentially expressed genes between susceptible and resistant individuals are more likely to be associated with TB susceptibility in published GWAS data. Lastly, we trained a classifier based on the gene expression levels in the non-infected cells, and demonstrated reasonable performance on our data and an independent data set. Overall, our promising results from this small study suggest that training a classifier on a larger cohort may enable us to accurately predict TB susceptibility.

show abstract

“…All genes containing somatic mutations were annotated using information from the Lynx Knowledge Base (LynxKB). 70 Enrichment analysis to discover over-represented functional categories and molecular pathways in the identified gene sets was done using Lynx enrichment analysis tools and ToppGene. 70,94 Reconstruction of molecular networks and pathways harboring somatic variations of strong clinical and diagnostic significance was also performed using the Lynx suite of tools.…”

Section: Enrichment and Analysismentioning

confidence: 99%

“…70 Enrichment analysis to discover over-represented functional categories and molecular pathways in the identified gene sets was done using Lynx enrichment analysis tools and ToppGene. 70,94 Reconstruction of molecular networks and pathways harboring somatic variations of strong clinical and diagnostic significance was also performed using the Lynx suite of tools. 70 STRING 10 was used as an underlying global network for network-based gene prioritization.…”

Section: Enrichment and Analysismentioning

confidence: 99%

Unique somatic variants in DNA from urine exosomes of individuals with bladder cancer

Xunian

Kurywchak

Wolf-Dennen

et al. 2021

Molecular Therapy - Methods & Clinical Development

Self Cite

View full text Add to dashboard Cite

Bladder cancer (BC), a heterogeneous disease characterized by high recurrence rates, is diagnosed and monitored by cystoscopy. Accurate clinical staging based on biopsy remains a challenge, and additional, objective diagnostic tools are needed urgently. We used exosomal DNA (exoDNA) as an analyte to examine cancer-associated mutations and compared the diagnostic utility of exoDNA from urine and serum of individuals with BC. In contrast to urine exosomes from healthy individuals, urine exosomes from individuals with BC contained significant amounts of DNA. Whole-exome sequencing of DNA from matched urine and serum exosomes, bladder tumors, and normal tissue (peripheral blood mononuclear cells) identified exonic and 3 0 UTR variants in frequently mutated genes in BC, detectable in urine exoDNA and matched tumor samples. Further analyses identified somatic variants in driver genes, unique to urine exoDNA, possibly because of the inherent intra-tumoral heterogeneity of BC, which is not fully represented in random small biopsies. Multiple variants were also found in untranslated portions of the genome, such as micro-RNA (miRNA)-binding regions of the KRAS gene. Gene network analyses revealed that exoDNA is associated with cancer, inflammation, and immunity in BC exosomes. Our findings show utility of exoDNA as an objective, non-invasive strategy to identify novel biomarkers and targets for BC.

show abstract

Lynx: a knowledge base and an analytical workbench for integrative medicine

Cited by 8 publications

References 51 publications

modEnrichr: a suite of gene set enrichment analysis tools for model organisms

modEnrichr: a suite of gene set enrichment analysis tools for model organisms

Predicting susceptibility to tuberculosis based on gene expression profiling in dendritic cells

Unique somatic variants in DNA from urine exosomes of individuals with bladder cancer

Contact Info

Product

Resources

About