| Content | RUMCode |
|---|---|
| Species | XX |
| Gene | XX |
| ATAC-seq | XX |
| Chip-seq | XX |
| scRNA | XX |
※ Usage
In RUMCode database, we provide the browse option and search options.
1. Browse. You can browse the RUMCode database by species.
Browse by species: You can select one of these species to browse all genes with annotations.
2. Search. Five search options are provided, including gene search, advanced search, batch search and BLAST search.
(1) Gene Search could be used to input one or multiple keywords (separated by space character) to search the EPSD database. The search fields including EPSD ID, UniProt Accession, Protein Name, Protein Alias, Gene Name, Gene Alias and Species.
Example: Please click on the "Example" button to search "Serine/threonine-protein kinase PLK1" in Protein Name field. By clicking on the "Submit" button, the related proteins will be shown.
(3) Advanced Search could be used to input two or more terms to find the information more specifically. The querying fields can be empty if less terms are needed. The three terms could be connected by the following operators:
AND : the term following this operator has to be included in the specified field(s).
OR : either the preceding or the following term to this operator should occur in the specified field(s).
NOT : If selected, the term following this operator must be not contained in the specified field(s).
Example: You can click on the "Example" button to load an instance, which could search phosphoprotein "Serine/threonine-protein kinase PLK1" in Homo sapiens. The human Cellular tumor antigen p53 will be shown by clicking on the "Submit" button.
(4) Batch Search could be used to find a number of proteins such as a protein list. You can input keyword list, for example, a list of UniProt IDs to search the database. The list should be inputed as one keyword one line.
Example: You can click on the "Example" button to load three proteins UniProt accessions including P04637, P53350 and F8WH10. By clicking on the "Submit" button, you can find "Cellular tumor antigen p53", "Serine/threonine-protein kinase PLK1" and "Vascular endothelial growth factor A".
(5) BLAST Search could be used to find the specific protein and/or related homologues by sequence alignment. This search-option will help you to find the querying protein accurately and fast. Only one protein sequence in FASTA format is allowed per time. The E-value threshold could be user-defined. The default parameters of E-value is 0.01.
Example: You can click on the "Example" button to load the protein sequence of Homo sapiens Phosphoprotein PLK1. By clicking on the "Submit" button, you can find the related homologues.