zebrafishMAP {zebrafish}R Documentation

Mappings between probe identifiers and cytogenetic maps/bands


When viewed using a microscope and special stains a chromosome is divided into regions, or cytogenetic bands, of transverse alternating light and dark or fluorescent and nonfluorescent bands. zebrafishMAP maps probe identifiers to the labels of cytogenetic bands within chromosomes where genes represented by the probe ids are located


Cytogenetic bands for most higher organisms are labeled p1, p2, p3, q1, q2, q3 (p and q are the p and q arms), etc., counting from the centromere out toward the telomeres. At higher resolutions, sub-bands can be seen within the bands. The sub-bands are also numbered from the centromere out toward the telomere. Thus, a label of 7q31.2 indicates that the band is on chromosome 7, q arm, band 3, sub-band 1, and sub-sub-band 2.

A given probe id may be mapped to one or more cytogenetic bands depending on whether genes represented by probe ids have only one or more chromosomal locations. Different genes may also be mapped to the same cytogenetic bands.

The physical location of each band on a chromosome can be obtained from another environment named "organism"CYTOLOC in a separate data package for human(humanCHRLOC), mouse(mouseCHRLOC), and rat(ratCHRLOC).

Mappings were based on data provided by:

LocusLink:ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz. Built: September 16, 2004

Package built Fri Sep 17 09:37:03 2004




    # Convert the environment to a list
    xx <- as.list(zebrafishMAP)
    # Remove probe ids that do not map to any cytoband
    xx <- xx[!is.na(xx)]
    if(length(xx) > 0){
        # The cytobands for the first two elements of XX
        # Get the first one

[Package zebrafish version 1.6.5 Index]