README.md

In bingqing-Xie/LynxEnrichR: Enrichment Analysis using Lynx Web Service

LynxEnrichR

R based Lynx enrichment tool (based on Lynx: an Integrated Systems Biology Platform)

Install requested libraries:

install.packages(c("httr","jsonlite"))

Usage:

enrichResults = get_lynx_enrichment(categories=c("go_bp"), genelist=c("AKT1","CASK","PXN"), tax_id="9606")

enrichResults (output)

featureId | featureName| pValue| Bonferroni.adjusted.pValue | FDR.adjusted.pValue | bayesFactor| inQuery| inSearch | gene| category| ------------ | -------------| -------------| ------| ----| -----| -----| ------| -------| -------| GO:0034614 | cellular response to reactive oxygen species| 1.436206e-05 | 0.002269205 | 0.002269205| 9.542656726756832 | 2 | 33| AKT1,PXN | go_bp GO:0100002| negative regulation of protein kinase activity by protein phosphorylation |1.905955e-04 | 0.030114090| 0.015057045| 6.956106872996315 | 1 | 1 | AKT1 | go_bp GO:0060709| glycogen cell differentiation involved in embryonic placenta development| 1.905955e-04 | 0.030114090 | 0.015057045| 6.956106872996315 | 1 | 1 | AKT1 | go_bp| GO:0090288 | negative regulation of cellular response to growth factor stimulus| 3.813566e-04 | 0.060254346| 0.020084782| 6.262596785731148 | 1 | 2 | CASK | go_bp|

Available databases:

|Databases| code| tax_id| ----------|--------------|----| GO biological process |go_bp|9606| GO cellular component |go_cc|9606| GO molecular function |go_mf|9606| Collection of pathways from KEGG, REACTOME, NCI, WIKI pathway | pathway|9606| GO with general Hierarchy - Molecular Function | go_hie_mf|9606| GO with general Hierarchy - Biological Process | go_hie_bp|9606| GO with general Hierarchy - Cellular Component | go_hie_cc|9606| Pubmed (Uniprot & NCBI Generif) | pubmed|9606| Diseases (OMIM, AutDB, DISEASE DB (Univ of Copenhagen), Cancer Gene Index [CGI], Schizophrenia Gene Resource [SZGR]) | disease|9606| Tissues (NCBI Unigene) | tissue|9606| Phenotype (Human Phenotype Ontology) | phenotype|9606| Uniprot Keywords | uniprot_kw|9606| Interpro Domain | domain|9606| Customized Brain Connectivity Ontology (Lynx Brain Connectivity Ontology) | custom_brain_connectivity|9606| VISTA TFBS Clusters | vista_tbfs|9606| VISTA Tissue Enhancers |vista_enhancers|9606| GO biological process (MGI) | mmu_go_bp|10040| GO cellular component (MGI) |mmu_go_cc|10040| GO molecular function (MGI) |mmu_go_mf|10040| KEGG (mouse) |mouse_pathway|10040|

Cite us

Dinanath Sulakhe, Sandhya Balasubramanian, Bingqing Xie, Bo Feng, Andrew Taylor, Sheng Wang, Eduardo Berrocal, Utpal Dave, Jinbo Xu, Daniela Börnigen, T. Conrad Gilliam, Natalia Maltsev, Lynx: a database and knowledge extraction engine for integrative medicine, Nucleic Acids Research, Volume 42, Issue D1, 1 January 2014, Pages D1007–D1012, https://doi.org/10.1093/nar/gkt1166

bingqing-Xie/LynxEnrichR documentation built on April 4, 2022, 1:57 p.m.