The Gene Sorter provides dozens of columns containing information on genes computed at UCSC or provided by outside collaborators. In addition to these standard columns, users may also upload their own columns for temporary display in the browser. Custom columns are viewable only on the machine from which they were uploaded and are kept only for 8 hours after the last time they were accessed. Optionally, users can make custom columns viewable by others as well.
Gene Sorter custom columns are based on files in line-oriented format. Each column is described by an initial column line followed by one or more data lines. The column line describes the name, hyperlinks, and other overall characteristics of the column. Each data line contains specific information about a gene annotated by the column. Lines starting with # are ignored. Only one column file may be loaded at a time; however, multiple column descriptions may be included in the same custom file, separated by blank lines.
Each column description must begin with a column line containing the keyword column followed by an optional set of one or more attribute pairs:
column [attribute1]=[value1] [attribute2]=[value2]...
Attribute values must be enclosed in quotes if they contain spaces or tabs. Attribute names and data values are case-sensitive. The following attributes may be defined:
Data lines are of the format:
[key] [value]
Data line keys and values are case-sensitive.
Example #1
This example defines a custom column for the Jul. 2003 Gene Sorter. The column's key values are linked to data in the refSeq column. Column rows can be filtered by numerical range by setting the max/min values for the column on the filter page.
#Custom column file for MyLab Trial 3
#
#Column line:
#
column name="MyLab Data" shortLabel="MyLab" longLabel="MyLab Trial 3"
visibility=on priority=2.05 idLookup=refSeq isNumber=on
#
#Data lines (key links to refSeq column):
#
NM_005523 1.2
NM_005522 4.5
NM_018951 5.1
NM_000522 5.7
NM_030661 9.4
NM_002141 5.2
NM_024014 4.3
NM_006896 6.0
Example #2
This example defines a custom column for the Oct. 2003 mouse Gene Sorter. The column's key values are linked by default to the acc (GenBank) column. Clicking on the column's title (UCSCLab) displays the web page http://genome.ucsc.edu/. Clicking on a specific data value displays the web page http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm4 (the UCSC Genome Browser) at the position specified by the data value. A search on the word MOUSE will display a list of all UCSC BioLab data that contains the string "MOUSE".
#Custom column file for UCSC BioLab Test Data
#
#Column line:
#
column name="UCSCLab Data" shortLabel="UCSCLab" longLabel="UCSC BioLab Test Data 4/4/04"
visibility=on priority=2.05
itemUrl=http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm4&position=%s
labelUrl=http://genome.ucsc.edu search=fuzzy
#
#Data lines (key links to refSeq column):
#
U20370 HXAB_MOUSE
L08757 HXAA_MOUSE
NM_008264 HXAD_MOUSE
# The following 2 lines demonstrate multiple data values for 1 key:
AK083575 NM_010449
AK083575 Q8BNI8
M95599 NM_010451
M28021 HXA5_MOUSE
NM_010454 HXA6_MOUSE