Gene Ontology and Pathway Hierarchy EncodeR (“GOPHER”) - v1.2

Introduction

More than 5,200 biological networks and pathways are currently available through online resources such as Kegg, Biocarta, Genmapp, and the Gene Ontology Consortium. GOPHER v1.1 provides a rank-prioritization of these networks and pathways for any one comparison of interest. Such that, the rankings themselves can be used as a network-level signature to cross-compare any number of comparisons. However, to do so, requires manual manipulation of data and organization of output. To circumvent, GOPHER v1.2 was designed to facilitate the cross-comparison of any one network-level signature with a reference database of network-level signatures automatically.

My Contribution

I used Perl CGI, Javascript, R, and NCBI GEO to develop, test, and make ready for web deployment GOPHER v1.2. Specifically, I used Perl CGI and Javascript to modify GOPHER v1.1 to satisfy GOPHER v1.2 design. Moreover, I used R in conjunction NCBI GEO to generate network-level signatures for a variety of NINDS-related conditions. Including: acute quadriplegic myopathy, amyotophic lateral sclerosis, Becker muscular dystrophy, Duchenne muscular dystrophy, dysferlin mutation, Emery-Dreifuss muscular dystrophy, fascioscapulohumeral muscular dystrophy, juvenile dermatomyositis, spastic paraplegia, Ishemic Stroke, Glioblastoma, primary hyperaldosteronism, Parkinson's disease, Alzheimer's Disease, HIV encephalitis, spinal bifida, Sjogren's syndrome, Atherosclerosis, Hypercholesterolemia, Vulvar Intraepithelial Neoplasia (VIN).

Result of My Contribution

NINDS research community now has a deployable web resource capable of generating and comparing network-level signatures within, between, and across biological conditions of interest. Such that, network and pathway relationships between or across biological conditions can be readily identified and classified as shared, conserved, or specific.