What is the gene symbol and chromosome of a specific gene id?
This is a simple query on one table.
-
SELECT
gene_id,
symbol,
chromosome
FROM gene_info
WHERE gene_id = "352937";
Sample Output.
+---------+--------------+------------+
| gene_id | symbol | chromosome |
+---------+--------------+------------+
| 352937 | dio2 | 20 |
+---------+--------------+------------+
Given a specific RefSeq Gene id, select general information
This will provide an across-the-board information based on a RefSeq Gene Id.
-
SELECT
RNA_nuc_access_version,
protein_access_version,
gene_id
FROM gene2refseq
WHERE RNA_nuc_access_version LIKE "NM_126167%";
Sample Output.
+------------------------+------------------------+---------+
| RNA_nuc_access_version | protein_access_version | gene_id |
+------------------------+------------------------+---------+
| NM_126167.1 | NP_178215.1 | 814629 |
+------------------------+------------------------+---------+
Given a specific Gene id, select GO terms
This will provide GO informatin for a specific Gene Id.
-
SELECT
gene_id,
go_id,
go_term
FROM gene2go
WHERE gene_id = "101";
Sample Output.
+---------+------------+-------------------------------+
| gene_id | go_id | go_term |
+---------+------------+-------------------------------+
| 101 | GO:0004222 | metalloendopeptidase activity |
| 101 | GO:0005887 | integral to plasma membrane |
| 101 | GO:0006508 | proteolysis |
| 101 | GO:0008270 | zinc ion binding |
| 101 | GO:0016020 | membrane |
| 101 | GO:0046872 | metal ion binding |
+---------+------------+-------------------------------+
Given a species and Gene Symbol, select general information
This will provide an across-the-board information based on a gene symbol for a
speicific organism.
-
SELECT
distinct(gene_info.symbol),
gene_info.gene_id,
tax2name.organism, gene_info.full_name_nomen AS Name, gene2refseq.RNA_nuc_access_version AS "RefSeq Nuc", gene2refseq.protein_access_version AS "RefSeq Prot"
FROM gene_info LEFT JOIN tax2name ON gene_info.tax_id = tax2name.tax_id
LEFT JOIN gene2refseq ON gene_info.gene_id = gene2refseq.gene_id
WHERE gene_info.tax_id = "9606" AND gene_info.symbol = "CCNJ";
Sample Output.
+--------+---------+--------------+----------+-------------+-------------+
| symbol | gene_id | organism | Name | RefSeq Nuc | RefSeq Prot |
+--------+---------+--------------+----------+-------------+-------------+
| CCNJ | 54619 | Homo sapiens | cyclin J | NM_019084.2 | NP_061957.2 |
+--------+---------+--------------+----------+-------------+-------------+