cnv

[Schema]

+----------+------------------+------+-----+---------+-------+
| Field    | Type             | Null | Key | Default | Extra |
+----------+------------------+------+-----+---------+-------+
| sample   | char(100)        | NO   | PRI |         |       | 
| source   | char(100)        | NO   | PRI |         |       | 
| chr      | int(10) unsigned | NO   | PRI | 0       |       | 
| start    | int(10) unsigned | NO   | PRI | 0       |       | 
| end      | int(10) unsigned | NO   |     | 0       |       | 
| mean     | float(4,2)       | NO   |     | 0.00    |       | 
| snpnum   | int(10) unsigned | NO   |     | 0       |       | 
| assembly | int(10) unsigned | NO   |     | 0       |       | 
+----------+------------------+------+-----+---------+-------+

sample is the name of the sample. Unfortunately, this was the first table built when CELLX was a CNV database. The sample is largely the same for cell lines in the cells table and contains no spaces for cell line names. However, subsequent GSE and TCGA datasets have appended meta information to the sample name and thus searching for particular samples that are not cell lines is problematic. Needs to be refactored to use the cells table and cellid primary key.

source is the dataset source. Similar to sample, the source needs to be refactored to use the source table primary key. Parts of the codebase use the suffix 'HG19' appended to the source as the indication to map the CNV segments to the hg19 assembly whereas mapping to the hg18 assembly is the default.

chr is the chromosome number. 23 = X. chrY is not called.
start = start position of the CNV segment
end = end position of the CNV segment
mean = mean log2R of the CNV segment
snpnum = number of probes which comprise the CNV segment
assembly = 18 or 19 ( ie. hg18 or hg19) Most of the data is in hg18, but some data derived from non-SNP6 chips were called in hg19. This affects how segments are mapped to genes. 18 segments are mapped using the hg18 table. 19 segments are mapped using the hg19 table.