ArticleBMC genomics2010
PathLocdb: a comprehensive database for the subcellular localization of metabolic pathways and its application to multiple localization analysis.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- dbMisLoc: A Manually Curated Database of Conditional Protein Mis-localization Events.Interdisciplinary sciences, computational life sciences · 2023Article
- Quantitative Imaging of BiochemistryACS central science · 2020Review
- Integrative analysis to identify oncogenic gene expression changes associated with copy number variations of enhancer in ovarian cancer.Oncotarget · 2017Article
- A gene browser of colorectal cancer with literature evidence and pre-computed regulatory information to identify key tumor suppressors and oncogenes.Scientific reports · 2016Article
- GCGene: a gene resource for gastric cancer with literature evidence.Oncotarget · 2016Article
- ECGene: A Literature-Based Knowledgebase of Endometrial Cancer Genes.Human mutation · 2016Article
- REGene: a literature-based knowledgebase of animal regeneration that bridge tissue regeneration and cancer.Scientific reports · 2016Article
- Multi-tissue transcriptomics for construction of a comprehensive gene resource for the terrestrial snail Theba pisana.Scientific reports · 2016Article
- CSGene: a literature-based database for cell senescence genes and its application to identify critical cell aging pathways and associated diseases.Cell death & disease · 2016Article
- An evidence-based knowledgebase of metastasis suppressors to identify key pathways relevant to cancer metastasis.Scientific reports · 2015Article
- dbEMT: an epithelial-mesenchymal transition associated gene resource.Scientific reports · 2015Article
- Pedican: an online gene resource for pediatric cancers with literature evidence.Scientific reports · 2015Article
- METSP: a maximum-entropy classifier based text mining tool for transporter-substrate identification with semistructured text.BioMed research international · 2015Article
- Human transporter database: comprehensive knowledge and discovery tools in the human transporter genes.PloS one · 2014Article
- IQdb: an intelligence quotient score-associated gene resource for human intelligence.Database : the journal of biological databases and curation · 2013Article
- Challenges of the next decade for the Asia Pacific region: 2010 International Conference in Bioinformatics (InCoB 2010).BMC genomics · 2010Article
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Abstract
backgroundIn eukaryotes, the cell is divided into several compartments enclosed by unitary membranes. Such compartmentalization is critical for cells to restrict different pathways to be carried out in different subcellular regions. The summary and classification of subcellular localizations of metabolic pathways are the first steps towards understanding their roles in spatial differentiation and the specialization of metabolic pathways in different organisms.
resultsIntegrating the subcellular localization of enzymes and their pathways from UniProt Knowledgebase and KEGG pathway databases, we present the first database for subcellular localization of 43014 pathways from 80676 UniProt entries and their pathway annotations from UniProt and KEGG pathway databases. To extract pathway localization across organisms, we defined 889 superpathways as clusters of basic pathways with the same pathway annotations from different organisms. Over eighty-eight percent of superpathways in the Swiss-Prot dataset occur in cytoplasm and mitochondria. And over seventy percent of UniProt superpathways have multiple localization annotations. We summarized four common reasons for the multiple localization of superpathways. Based on this database, we also discovered 88 potential transport systems between different steps of multiply localized pathways and 45 duplicated genes from 17 pathways, occurring in parallel in several locations in humans.
conclusionsPathLocdb is a free web-accessible database that enables biochemical researchers to quickly access summarized subcellular localization of pathways from UniProt and KEGG pathway databases. As the first effort to systematically integrate pathway localization, this database is very useful in discovering the variation of localization of pathways between organisms and also cross-talk between different organelles within a pathway. The Pathlocdb database is available at http://pathloc.cbi.pku.edu.cn.
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