CanGEM
 
Tuesday, January 16, 2018
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Genes
CG-PLM-26

Ensembl
from Ensembl Database
Homo sapiens
This "platform" contains the genes imported from the Ensembl database.
The files were generated with the following commands:

echo "SELECT stable_id gene, seq_region.name chromosome, gene.seq_region_start start, gene.seq_region_end end, display_label symbol, biotype type, CONCAT(seq_region.name, band) cytoband, gene.seq_region_strand strand FROM gene_stable_id JOIN gene USING (gene_id) JOIN seq_region USING (seq_region_id) JOIN xref ON display_xref_id = xref_id LEFT JOIN karyotype ON gene.seq_region_id = karyotype.seq_region_id AND gene.seq_region_start+(gene.seq_region_end-gene.seq_region_start)/2 BETWEEN karyotype.seq_region_start AND karyotype.seq_region_end WHERE name IN ('1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','X','Y','MT') ORDER BY CAST((CASE Chr WHEN 'X' THEN 23 WHEN 'Y' THEN 24 WHEN 'MT' THEN 25 ELSE Chr END) AS UNSIGNED), Start" | mysql -h ensembldb.ensembl.org -P 5306 -u anonymous -p homo_sapiens_core_63_37 > GRCh37.txt

echo "SELECT stable_id Gene, seq_region.name Chr, gene.seq_region_start Start, gene.seq_region_end End, display_label Symbol, biotype Type, CONCAT(seq_region.name, band) Band, gene.seq_region_strand Strand FROM gene_stable_id JOIN gene USING (gene_id) JOIN seq_region USING (seq_region_id) JOIN xref ON display_xref_id = xref_id LEFT JOIN karyotype ON gene.seq_region_id = karyotype.seq_region_id AND gene.seq_region_start+(gene.seq_region_end-gene.seq_region_start)/2 BETWEEN karyotype.seq_region_start AND karyotype.seq_region_end WHERE name IN ('1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','X','Y','MT') ORDER BY CAST((CASE Chr WHEN 'X' THEN 23 WHEN 'Y' THEN 24 WHEN 'MT' THEN 25 ELSE Chr END) AS UNSIGNED), Start" | mysql -h ensembldb.ensembl.org -P 5306 -u anonymous -p homo_sapiens_core_54_36p > NCBI36.txt

echo "SELECT stable_id Gene, seq_region.name Chr, gene.seq_region_start Start, gene.seq_region_end End, display_label Symbol, biotype Type, CONCAT(seq_region.name, band) Band, gene.seq_region_strand Strand FROM gene_stable_id JOIN gene USING (gene_id) JOIN seq_region USING (seq_region_id) JOIN xref ON display_xref_id = xref_id LEFT JOIN karyotype ON gene.seq_region_id = karyotype.seq_region_id AND gene.seq_region_start+(gene.seq_region_end-gene.seq_region_start)/2 BETWEEN karyotype.seq_region_start AND karyotype.seq_region_end WHERE name IN ('1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','X','Y','MT') ORDER BY CAST((CASE Chr WHEN 'X' THEN 23 WHEN 'Y' THEN 24 WHEN 'MT' THEN 25 ELSE Chr END) AS UNSIGNED), Start" | mysql -h ensembldb.ensembl.org -P 3306 -u anonymous -p homo_sapiens_core_37_35j > NCBI35.txt

echo "SELECT stable_id Gene, seq_region.name Chr, gene.seq_region_start Start, gene.seq_region_end End, display_label Symbol, type Type, CONCAT(seq_region.name, band) Band, gene.seq_region_strand Strand FROM gene_stable_id JOIN gene USING (gene_id) JOIN seq_region USING (seq_region_id) JOIN xref ON display_xref_id = xref_id LEFT JOIN karyotype ON gene.seq_region_id = karyotype.seq_region_id AND gene.seq_region_start+(gene.seq_region_end-gene.seq_region_start)/2 BETWEEN karyotype.seq_region_start AND karyotype.seq_region_end WHERE name IN ('1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','X','Y','MT') ORDER BY CAST((CASE Chr WHEN 'X' THEN 23 WHEN 'Y' THEN 24 WHEN 'MT' THEN 25 ELSE Chr END) AS UNSIGNED), Start" | mysql -h ensembldb.ensembl.org -P 3306 -u anonymous -p homo_sapiens_core_25_34e > NCBI34.txt
Data Files
GRCh37.txt (3.62 MB)
NCBI36.txt (2.44 MB)
NCBI35.txt (1.56 MB)
NCBI34.txt (1.16 MB)

2007-07-30 18:02:04 by Ilari Scheinin
2011-07-01 12:13:03 by Ilari Scheinin

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