• Pathway Projector overview
• Search
• Annotation
• Data
• Installation
Annotation
• Data mapping
Users can reflect experimental data, such as transcriptomics, proteomics or metabolomics. Specify the color or scale of the lines or circles freely, a customized map overlays on the pathway map. Furthermore, users can put original pictures on map.
1st step : Open a Data Mapping tab window in the Tools and input own data. Or else, users can upload data file following data format.
2nd step : Click a "Generate Overlay Map" button.
Finish : A browser backs to main page and shows the mapped pathway. Users can switch to reference pathway map from the top-right buttons.
• Mapping format
» Organism
To set organism, users should use KEGG organism IDs (e.g. E. coli is eco, Human is hsa). Default is reference pathway map.
Organism:eco
» Genes
When the "organism" is set, users can change this gene parameters. 1st column is "gene name", 2nd column is color (e.g. #FF0000, red), 3rd column is stroke width (default: 8).
// when the organism is eco
pgk,#FF0000,12
tpiA,blue
eco:b2926,red
» Proteins
1st column is EC number (e.g. 1.1.1.1) or reaction ID (e.g. R00010), 2nd column is color, 3rd column is stroke width (default: 8).
Set ALL reactions to black with 10px stroke width
reaction,black,10
Enzyme: EC Number, stroke-width=10px
1.1.1.-,black,10
Reaction: KEGG ID
R01512,blue
» Metabolites
1st column is compound ID, 2nd column is color, 3rd column is circle size, 4th colum is label, 5th column is label size.
Set all compounds/glycans to gray with r = 13px.
compound,#cccccc,13
KEGG ID, color, size, label="Coenzyme A", label size.
C00010,red,13,Coenzyme A,20
» Time series data
1st line is target components' ID with chart type (line or bar). 2nd line or later, plese input own data by CSV format. At the end, it should be remembered that "//".
>C00158,line
1,10
2,20
3,30
4,40
5,60
6,90
7,109
8,200
9,80
10,9
//
Or alternatively, please upload the 【Tab-delimited data】 file. The format is following:
the first rows are components name, and the first column is time point. And the columns are experimental data.
For example;
C00111 C00118 C00236 C00197 1 45 53 53 23 2 98 79 79 69 3 45 53 53 23 4 79 34 69 43 5 32 79 67 0 6 11 20 44 20 7 20 30 55 30 8 31 40 64 40 9 71 10 74 70 10 87 45 10 52
» Pathway
1st column is pathway name e.g. glycolysis (or pathway id e.g. rn00010), 2nd column is color
glycolysis,red
rn00020,blue
» Organism comparison
• SOAP service
Pathway Projector provides web-service as SOAP service. Users can get the data mapped pathway maps URLs
by service.
This service is Perl, Ruby and Phthon compliant.
The sample codes for each language are as follows;
» SOAP
This SOAP service is SOAP1.1 (Latest version is SOAP1.2).
» Perl
require SOAP::Lite ver0.60.
#!/usr/bin/perl
use SOAP::Lite;
use warnings;
use strict;
# WSDL file
my $WSDL = "http://www.g-language.org/PathwayProjector/PathwayProjector.wsdl";
# create SOAP driver
my $soap = SOAP::Lite->service($WSDL)->proxy('http://localhost/', timeout=>600);
# input data
my $input = SOAP::Data->type(array => ['Organism:eco', 'pgk,red']);
# run your job
my ($pngFile, $pathway) = $soap->mapping( $input );
print "PNG file : " . $pngFile . "\n";
print "Pathway URL : " . $pathway . "\n";
» Python
require SOAPpy and related library.
#!/usr/bin/python
from SOAPpy import WSDL
# create WSDL driver
wsdl = 'http://www.g-language.org/PathwayProjector/PathwayProjector.wsdl'
serv = WSDL.Proxy(wsdl)
# input data
input = ['Organism:eco', 'pgk,red']
# run your job
(pngFile, pathway) = serv.mapping(input)
# polling your job
print "PNG file : " + pngFile + "\n"
print "Pathway URL : " + pathway + "\n"
» Ruby
require Ruby1.8.1 or later, or install SOAP library for Ruby.
#!/usr/bin/ruby
require 'soap/wsdlDriver'
# create WSDL driver
wsdl = "http://www.g-language.org/PathwayProjector/PathwayProjector.wsdl"
serv = SOAP::WSDLDriverFactory.new(wsdl).create_rpc_driver
serv.generate_explicit_type = true
# input data
input = ['Organism:eco', 'pgk,red']
# run your job
(pngFile, pathway) = serv.mapping(input)
# polling your job
print "PNG file : " + pngFile + "\n"
print "Pathway URL : " + pathway + "\n"
• Manual editing
Users can easily annotate and edit the maps by placing custom markers, scribing lines. Moreover, users can share these added custom comments or annotations among researchers as XML.
» XML export
Output XML format file by "GetXML" button.
After clicking the "GetXML" button, a new window will open with XML data.
» XML import
If you input the XML data in this text area and click "Import" button, your previous edited picture is reproduced.
