Dataset Information

Plant Reactome: a knowledgebase and resource for comparative pathway analysis.

ABSTRACT: Plant Reactome (https://plantreactome.gramene.org) is an open-source, comparative plant pathway knowledgebase of the Gramene project. It uses Oryza sativa (rice) as a reference species for manual curation of pathways and extends pathway knowledge to another 82 plant species via gene-orthology projection using the Reactome data model and framework. It currently hosts 298 reference pathways, including metabolic and transport pathways, transcriptional networks, hormone signaling pathways, and plant developmental processes. In addition to browsing plant pathways, users can upload and analyze their omics data, such as the gene-expression data, and overlay curated or experimental gene-gene interaction data to extend pathway knowledge. The curation team actively engages researchers and students on gene and pathway curation by offering workshops and online tutorials. The Plant Reactome supports, implements and collaborates with the wider community to make data and tools related to genes, genomes, and pathways Findable, Accessible, Interoperable and Re-usable (FAIR).

SUBMITTER: Naithani S

PROVIDER: S-EPMC7145600 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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Plant Reactome: a knowledgebase and resource for comparative pathway analysis.

Naithani Sushma S Gupta Parul P Preece Justin J D'Eustachio Peter P Elser Justin L JL Garg Priyanka P Dikeman Daemon A DA Kiff Jason J Cook Justin J Olson Andrew A Wei Sharon S Tello-Ruiz Marcela K MK Mundo Antonio Fabregat AF Munoz-Pomer Alfonso A Mohammed Suhaib S Cheng Tiejun T Bolton Evan E Papatheodorou Irene I Stein Lincoln L Ware Doreen D Jaiswal Pankaj P

Nucleic acids research 20200101 D1

Plant Reactome (https://plantreactome.gramene.org) is an open-source, comparative plant pathway knowledgebase of the Gramene project. It uses Oryza sativa (rice) as a reference species for manual curation of pathways and extends pathway knowledge to another 82 plant species via gene-orthology projection using the Reactome data model and framework. It currently hosts 298 reference pathways, including metabolic and transport pathways, transcriptional networks, hormone signaling pathways, and plant ...[more]

PMID: 31680153

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Project description:Endometriosis is a complex, benign, estrogen-dependent gynecological disorder with an incidence of ~10% women in reproductive age. The implantation and growth of endometrial cells outside the uterus leads to the development of endometriosis. Endometriosis is also associated with comorbid conditions like cardiovascular and autoimmune diseases. The absence of non-invasive diagnostic markers, delayed diagnosis, high risk of recurrence of the disease on surgical removal of the tissue and absence of a definitive cure for endometriosis makes it imperative to gain insights into the complex etiology of endometriosis. A plethora of genes identified from blood and endometrial biopsies, involved in different pathways like steroid metabolism, angiogenesis, inflammation, etc. have been associated with endometriosis. However, the exact mechanism and genetic etiology of endometriosis still remain unclear. The polygenic nature of the disease, incongruent phenotypic manifestations in different ethnic populations and information scattered in literature makes it difficult to delineate the sub-network of genes that will aid in disease diagnosis and effective treatment. Endometriosis Knowledgebase is a manually curated database with information on genes associated with endometriosis. It holds information on 831 genes, their associated polymorphisms, gene ontologys, pathways and diseases. Genes in the database are enriched in pathways important for cell signaling, immune regulation and reproduction. A genetic overlap is seen between endometriosis and cancers, endocrine/reproductive, nervous system, immune and metabolic diseases. Network analysis of genes in the Endometriosis Knowledgebase helped predict 13 new candidate genes for endometriosis. These genes were found to be enriched in biological processes associated with endometriosis. The Endometriosis Knowledgebase and incorporated tools for gene and sequence-based analysis will benefit both researchers and clinicians working in the realm of reproductive biology.

Dataset Information

Plant Reactome: a knowledgebase and resource for comparative pathway analysis.

Publications

Plant Reactome: a knowledgebase and resource for comparative pathway analysis.

Similar Datasets

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