PeptideAtlas:Chromosomal coverage
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| When using the Browse Proteins function in PeptideAtlas, one can generate a graphical depiction of the chromosomal coverage for an atlas build. | When using the Browse Proteins function in PeptideAtlas, one can generate a graphical depiction of the chromosomal coverage for an atlas build. | ||
| ==Listing proteins== | ==Listing proteins== | ||
| - | In order to get such a depiction, one must restrict the listing to proteins from only a single chromosome. | + | In order to get such a depiction, one must restrict the listing to proteins from a single chromosome on a human build. Any location values must be inputted through the "Start in Chromosome"/"End in Chromosome" boxes - not via genetic locus. |
| ==Interpreting the graphical depiction== | ==Interpreting the graphical depiction== | ||
| The graphical depiction has a title bar and five tracks of information. The title bar shows which chromosome is being viewed, and what portion of the chromosome is shown. The five informational tracks are from top to bottom "Protein Location", "Chromosome Length", "Karyotypic Banding", "Genes covered by PeptideAtlas", and "Gene Location". | The graphical depiction has a title bar and five tracks of information. The title bar shows which chromosome is being viewed, and what portion of the chromosome is shown. The five informational tracks are from top to bottom "Protein Location", "Chromosome Length", "Karyotypic Banding", "Genes covered by PeptideAtlas", and "Gene Location". | ||
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| "Karyotypic Banding" is another form of ruler, except that it uses chromosomal banding instead base pairs. It is useful when comparing with outside information that gives location in genetic locus format, or when looking at a subsection of a chromosome. Unlike the base pair ruler, this one does not change when you zoom into a section of a chromosome. | "Karyotypic Banding" is another form of ruler, except that it uses chromosomal banding instead base pairs. It is useful when comparing with outside information that gives location in genetic locus format, or when looking at a subsection of a chromosome. Unlike the base pair ruler, this one does not change when you zoom into a section of a chromosome. | ||
| - | The other three tracks depict the location of proteins, genes, and those genes that contain at least one PeptideAtlas protein. The proteins and genes are drawn as bars with length based on the length of the protein/gene in base pairs. The longer the protein/gene, the longer the bar. | + | The other three tracks depict the location of proteins, genes, and those genes that contain at least one PeptideAtlas protein. The proteins and genes are drawn as bars with length based on the length of the protein/gene in base pairs. The longer the protein/gene, the longer the bar. Staggering of the bars happens when they are so close to one another that if shown in a single row it would be nearly impossible to distinguish all individual bars. |
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| + | The "Protein Location" track shows the positions of all the proteins in the requested PeptideAtlas build. The "Genes covered by PeptideAtlas" track shows which genes contain at least one protein of the requested build. Contain is defined as the start and end coordinates of the protein are between the start and end coordinates of the gene. This track should show completeness of a build in a given region, because if PeptideAtlas contains all proteins, then all genes should be represented, and thus both gene tracks would look the same. The "Gene Location" track shows all genes in the requested portion of the chromosome drawn by location. | ||
Revision as of 20:03, 10 August 2010
When using the Browse Proteins function in PeptideAtlas, one can generate a graphical depiction of the chromosomal coverage for an atlas build.
Listing proteins
In order to get such a depiction, one must restrict the listing to proteins from a single chromosome on a human build. Any location values must be inputted through the "Start in Chromosome"/"End in Chromosome" boxes - not via genetic locus.
Interpreting the graphical depiction
The graphical depiction has a title bar and five tracks of information. The title bar shows which chromosome is being viewed, and what portion of the chromosome is shown. The five informational tracks are from top to bottom "Protein Location", "Chromosome Length", "Karyotypic Banding", "Genes covered by PeptideAtlas", and "Gene Location".
"Chromosome Length" is a ruler so that you can know at which base pair a protein or gene is located. Be warned that the numbers on its tick marks are relative to the portion of the chromosome being viewed - it will start at zero no matter what you're viewing. In order to find the true base pair location of a point on the ruler, add the number of base pairs that the viewed portion begins with. For example, if you're viewing a portion between 30 and 50 million, the spot on the ruler that says 4 million is in reality 34 million base pairs from the beginning of the chromosome.
"Karyotypic Banding" is another form of ruler, except that it uses chromosomal banding instead base pairs. It is useful when comparing with outside information that gives location in genetic locus format, or when looking at a subsection of a chromosome. Unlike the base pair ruler, this one does not change when you zoom into a section of a chromosome.
The other three tracks depict the location of proteins, genes, and those genes that contain at least one PeptideAtlas protein. The proteins and genes are drawn as bars with length based on the length of the protein/gene in base pairs. The longer the protein/gene, the longer the bar. Staggering of the bars happens when they are so close to one another that if shown in a single row it would be nearly impossible to distinguish all individual bars.
The "Protein Location" track shows the positions of all the proteins in the requested PeptideAtlas build. The "Genes covered by PeptideAtlas" track shows which genes contain at least one protein of the requested build. Contain is defined as the start and end coordinates of the protein are between the start and end coordinates of the gene. This track should show completeness of a build in a given region, because if PeptideAtlas contains all proteins, then all genes should be represented, and thus both gene tracks would look the same. The "Gene Location" track shows all genes in the requested portion of the chromosome drawn by location.
