Question: Where Do I Find Genomic Coordinates For Human Cytogenetic Bands According To Entrez Gene/Hgcn?
3
gravatar for Jarretinha
5.3 years ago by
Jarretinha3.3k
São Paulo, Brazil
Jarretinha3.3k wrote:

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 • 3.5k views
ADD COMMENTlink modified 5.3 years ago by Neilfws48k • written 5.3 years ago by Jarretinha3.3k
2
gravatar for Neilfws
5.3 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

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
ADD COMMENTlink written 5.3 years ago by Neilfws48k

Oh yeah!!! They're exactly what I need! Thank you very much!!!

ADD REPLYlink written 5.3 years ago by Jarretinha3.3k

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

ADD REPLYlink written 5.3 years ago by Jarretinha3.3k

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

ADD REPLYlink written 5.3 years ago by Jarretinha3.3k
1
gravatar for pstew
5.3 years ago by
pstew50
United States
pstew50 wrote:

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.

ADD COMMENTlink modified 5.3 years ago • written 5.3 years ago by pstew50

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.

ADD REPLYlink written 5.3 years ago by Jarretinha3.3k

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

ADD REPLYlink written 5.3 years ago by Jarretinha3.3k
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