More than 60000 records with unique ENSG tag in ensGene.txt.gz downloaded from UCSC

Question

[Emma]

Hi all,

I downloaded ensGene.txt.gz from UCSC, and found that there were 60234 records with unique ENSG...ID. Does this mean there are more than 60000 genes? However, there were only ~20000 unique gene names in the refGene.txt.gz which also downloaded from UCSC. How such discrepancy came along?

Thank you!

Emma

[Nicolas Rosewick]

in UCSC I found 54,210 refseq genes for hg19. Where do you download your refGene.txt.gz file ?

[Emma]

Here is the link:

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ensGene.txt.gz

Answer 1

[Pierre Lindenbaum]

Those are Ensembl Genes that are not par of RefGene. Let's looks at some records (ensembl with no overlap to refGene)

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu hg19  -A

mysql> select distinct G.name2,R.name,R.name2 from ensGene as G left join refGene as R on R.chrom=G.chrom and NOT(R.txStart>=G.txEnd OR R.txEnd<G.txStart) where R.name is NULL limit 10;
+-----------------+------+-------+
| name2           | name | name2 |
+-----------------+------+-------+
| ENSG00000268020 | NULL | NULL  |
| ENSG00000240361 | NULL | NULL  |
| ENSG00000238009 | NULL | NULL  |
| ENSG00000239945 | NULL | NULL  |
| ENSG00000241860 | NULL | NULL  |
| ENSG00000222623 | NULL | NULL  |
| ENSG00000241599 | NULL | NULL  |
| ENSG00000228463 | NULL | NULL  |
| ENSG00000241670 | NULL | NULL  |
| ENSG00000237094 | NULL | NULL  |
+-----------------+------+-------+
10 rows in set (0.80 sec)

ENSG00000268020 : Havana Gene
ENSG00000240361 : Havana Gene
ENSG00000238009 : Havana Gene
....

Answer 2

[Emily]

There's a breakdown of gene types here. >20,000 coding genes, >25,000 non-coding, >14,000 pseudogenes. That comes out at <60,000 but that's the current release - not sure which release you downloaded.

[Emma]

I am sorry but I do not know where to find out the release version. But here is the link:

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ensGene.txt.gz

There is a date "06-Apr-2014" with it.

I grep the unique ENSG ID with the following commend line:

less ensGene.txt.gz | awk '{print $13}' | sort | uniq |wc -l

Hope this information helps.

Thank you!