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mapping_data_on_genome_projector [2008/05/14 09:39]
gaou
mapping_data_on_genome_projector [2009/04/19 15:41] (current)
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  * gene name   * gene name
  * locus tag   * locus tag
-  * position+  * position (eg. 190..255)
Gene name is the common gene name as specified in the GenBank flatfile. For example, the first gene in //Escherichia coli// K12 MG1655 genome is **thrL**. Locus tag is the canonical gene name, such as **b0001**. Position is the locations of starting and ending base number joined with ".." in between, such as **190..255**. An entry is considered to be located in the direct strand of the DNA duplex when the first position is smaller than the second, and thus considered to be in the complementary strand when reversed, as **255..190**. Gene name is the common gene name as specified in the GenBank flatfile. For example, the first gene in //Escherichia coli// K12 MG1655 genome is **thrL**. Locus tag is the canonical gene name, such as **b0001**. Position is the locations of starting and ending base number joined with ".." in between, such as **190..255**. An entry is considered to be located in the direct strand of the DNA duplex when the first position is smaller than the second, and thus considered to be in the complementary strand when reversed, as **255..190**.
 +
 +==== 2nd column ====
 +2nd column can be one of the following:
 +  * color value in RGB, such as rgb(192 150 20)
 +  * intensity value ranging from 0 to 100
 +  * transparent
 +
 +Color can be specified using RGB (Red Green Blue) code as **rgb(192 150 20)**. Note that the numbers are separated by single space (and not commas), and that they are embraced within **rgb()**. Color values range from 0 to 255. Following are examples for common colors:
 +  * white: rgb(255 255 255)
 +  * black: rgb(0 0 0)
 +  * red: rgb(255 0 0)
 +  * green: rgb(0 255 0)
 +  * blue: rgb(0 0 255)
 +  * yellow: rgb(255 255 0)
 +
 +Alternatively, color can be specified using values ranging from 0 to 100, which represent a color spectrum from red to yellow to green. This is useful for example when visualizing microarray intensity data.
 +
 +Lastly, color can be specified as **transparent**. This can be used with **black** background color to produce an overlay similar to that of organism specific PathwayMap.
 +
 +==== 3rd column ====
 +
 +3rd column is optional, which can be used to specify the **height** of displayed box. If this column is omitted, a value of 50 is used. A value in the range from 0 to 100 can be used here.
 +
 +===== Data format for PathwayMap =====
 +
 +==== 1st column ====
 +1st column is an EC number such as **3.1.2.5**. In PathwayMap, EC number is the only available ID for mapping.
 +
 +==== 2nd column ====
 +2nd column can be one of the following:
 +  * color value in RGB, such as rgb(192 150 20)
 +  * intensity value ranging from 0 to 100
 +  * transparent
 +
 +Color can be specified using RGB (Red Green Blue) code as **rgb(192 150 20)**. Note that the numbers are separated by single space (and not commas), and that they are embraced within **rgb()**. Color values range from 0 to 255. Following are examples for common colors:
 +  * white: rgb(255 255 255)
 +  * black: rgb(0 0 0)
 +  * red: rgb(255 0 0)
 +  * green: rgb(0 255 0)
 +  * blue: rgb(0 0 255)
 +  * yellow: rgb(255 255 0)
 +
 +Alternatively, color can be specified using values ranging from 0 to 100, which represent a color spectrum from red to yellow to green. This is useful for example when visualizing microarray intensity data.
 +
 +Lastly, color can be specified as **transparent**. This can be used with **black** background color to produce an overlay similar to that of organism specific PathwayMap.
 +
 +==== 3rd column ====
 +
 +3rd column is optional, which can be used to specify the **diameter** of displayed circle. If this column is omitted, a value of 300 is used. There is no defined limit or range for this value,
 +