Where Do I Find Genomic Coordinates For Human Cytogenetic Bands According To Entrez Gene/Hgcn?
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7.7 years ago

I have to plot some MLPA data using circos and the idea is to focus on cytobands. Circos uses the cytobands as described by UCSC/Ensembl. Looking at some genes in GeneCards I found different cytoband locations for the same gene (e. g. SCN5A). Now, I want to compare Ensembl and Entrez Gene cytoband systems and see how the plots behave. I was unable to find a file/page/table similar to UCSC goldenPath cytoBand at NCBI. Could someone point the direction, please?

coordinates genomic human • 4.5k views
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7.7 years ago
Neilfws 49k

Do these files from the NCBI MapView FTP site help?

wget ftp://ftp.ncbi.nih.gov/genomes/MapView/Homo_sapiens/objects/BUILD.37.3/initial_release/ideogram_9606_GCF_000001305.13_400_V1
wget ftp://ftp.ncbi.nih.gov/genomes/MapView/Homo_sapiens/objects/BUILD.37.3/initial_release/ideogram_9606_GCF_000001305.13_550_V1
wget ftp://ftp.ncbi.nih.gov/genomes/MapView/Homo_sapiens/objects/BUILD.37.3/initial_release/ideogram_9606_GCF_000001305.13_850_V1

# examine contents
# head -5 ideogram_9606_GCF_000001305.13_400_V1

1    p    36.3    0    451    1    7200000    gneg    
1    p    36.2    451    682    7200000    16200000    gpos    100
1    p    36.1    682    1259    16200000    28000000    gneg    
1    p    35    1259    1583    28000000    34600000    gpos    100
1    p    34.3    1583    1779    34600000    40100000    gneg
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Oh yeah!!! They're exactly what I need! Thank you very much!!!

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Oh my! They're just the same as those found at UCSC.

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And not all BUILDs have this sort of file. BUILDs 36 and 35 don't have. . .

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7.7 years ago
pstew ▴ 50

It sounds like the R Bioconductor package org.Hs.eg.db might have what you're looking for. It allows you to map between Entrez gene identifiers and cytoband locations.

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Unfortunately, the mappings don't provide coordinates for the cytobands. I can compare its names but not its locations. Without start and end locations I can't plot them with circos.

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Ah! I've found other utilities for this package.

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