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PCOSBase Database

PCOSBase Schema

PCOSBase currently consists of 29 tables. Figure 1 shows all the 29 tables with the connections between table to table.

Figure 1: PCOSBase schema

Table Information

  1. pcosproteins. This is the main table of PCOSBase. This table has basic information including Entrez Gene ID, UniProt ID, gene symbol, gene description and the chromosomal location of all 8,185 PCOS-related proteins.
  2. geneontologies. This table contains the information of 13,237 gene ontologies that are associated with all PCOS-related proteins. GO ID, GO term, the definition/description of the GO term and ontology (BP, MF, CC) are provided.
  3. pcosproteins_geneontologies. This is the pivot table between pcosproteins and geneontologies The evidence is the source of GO annotation for particular PCOS-related proteins.
  4. pathways. This table lists 1,004 pathways obtained from three pathway databases, KEGG, BioCarta and WikiPathways.
  5. pcosproteins_pathways. This table links pcosproteins and pathways tables.
  6. domains. A total of 7,936 domains/families from InterPro database are listed in this table.
  7. crossrefs_domains. This table records all the signatures that contribute to domain entry. One domain id could have more than one signature. All of these data were retrieved from InterPro database.
  8. pcosproteins_domains. It links pcosproteins with domains tables.
  9. tissues. This table contains information of all the tissues and the cell types on where the PCOS-related proteins were expressed.
  10. pcosproteins_tissues. This table is the connective for pcosproteins and tissues tables.
  11. diseases. This table lists 1,928 diseases in Unified Medical Language System (UMLS) ID. Medical Subject Headings (MeSH) IDs are also provided in this table.
  12. classes. There are 39 classes of disease listed in this table.
  13. diseases_classes. This table classifies all the diseases in ‘diseases’ table into classes in ‘classes’ table. The diseases were classified based on MeSH database.
  14. pcosproteins_diseases. This table connects pcosproteins and diseases tables.
  15. partners. This table lists 16,847 proteins that interact with PCOS-related proteins.
  16. interactions. This table records all the interactions between PCOS-related proteins with the proteins in ‘partners’ table.
  17. imethods. This table lists 122 methods that have been used to detect the protein-protein interactions (PPI).
  18. interactions_imethods. This table links imethods with interactions table. It records which interactions have been detected using which methods.
  19. ipmids. This table contains 36,110 references from PubMed database for every interaction.
  20. interactions_ipmids. This table links interactions and ipmids.
  21. isources. This table has 24 sources (PPI databases and PPI publications), where all the interactions have been retrieved.
  22. interactions_isources. This table links which interactions were retrieved from.
  23. rdatabases.  This table lists nine databases, where PCOS-related proteins have been retrieved.
  24. pcosproteins_rdatabases. This table links pcosproteins and rdatabases tables.
  25. source_types. This table contains only two source types which are transcriptomics and proteomics.
  26. sources. This table lists all the sources of PCOS-related proteins have been retrieved. All the sources are either gene expression studies (transcriptomics) or protein expression studies (proteomics).
  27. expressions. This table contains 28 expression patterns for the proteins in the sources tables.
  28. pcosproteins_sources_expressions. This table is a connective table between pcosproteins, sources and expressions tables.
  29. publications. This table is not connected to other tables. It listed all the publications that are related to PCOS.

 

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