Finding nearby genes

Let's say you had a position, and you wanted to find a sample of nearby genes upstream and downstream from this position.

This can be done with a MySQL query to the public MySQL server

Alternatives:

• Galaxy has a "Fetch closest non-overlapping feature" tool
• the BedTools include a tool "closestBed"

#!/bin/sh

# given position chr1:710000-720000
# find a sample of genes near this upstream and downstream
C=chr1
S=710000
E=720000

echo "three upstream genes from ${C}:${S}-${E}"
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -N -e \
'select e.chrom,e.txStart,e.txEnd,e.alignID,j.geneSymbol FROM
   knownGene e,
   kgXref j
WHERE e.alignID = j.kgID AND e.chrom="'${C}'" AND e.txEnd < '${S}'
ORDER BY e.txEnd DESC limit 3;' hg18

echo "three downstream genes from ${C}:${S}-${E}"
mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -N -e \
'select e.chrom,e.txStart,e.txEnd,e.alignID,j.geneSymbol FROM
   knownGene e,
   kgXref j
WHERE e.alignID = j.kgID AND e.chrom="'${C}'" AND e.txStart > '${E}'
ORDER BY e.txStart ASC limit 3;' hg18

This produces the output:

three upstream genes from chr1:710000-720000
+------+--------+--------+------------+----------+
| chr1 | 690107 | 703869 | uc001abo.1 | BC006361 |
| chr1 | 665195 | 665226 | uc001abn.1 | DQ599872 |
| chr1 | 665086 | 665147 | uc001abm.1 | DQ600587 |
+------+--------+--------+------------+----------+
three downstream genes from chr1:710000-720000
+------+--------+--------+------------+----------+
| chr1 | 752926 | 778860 | uc001abp.1 | BC102012 |
| chr1 | 752926 | 778860 | uc001abq.1 | BC042880 |
| chr1 | 752926 | 779603 | uc001abr.1 | CR601056 |
+------+--------+--------+------------+----------+