README.rtf

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\f0\fs24 \cf2 \cb3 \expnd0\expndtw0\kerning0
\outl0\strokewidth0 \strokec2 The following data are in the attached matlab files:\
mtbpromdata - has data for tuberculosis\
ecoli_prom_growth_data - has data for ecoli\
the variable expression has the gene expression data; expressionid has the gene identifiers\cb1 \expnd0\expndtw0\kerning0
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\cb3 \expnd0\expndtw0\kerning0
\outl0\strokewidth0 the variable model has the corresponding metabolic model\cb1 \expnd0\expndtw0\kerning0
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\cb3 \expnd0\expndtw0\kerning0
\outl0\strokewidth0 variable 'regulator' is the name of transcription factors (tf) and 'regulated' are the target genes.\cb1 \expnd0\expndtw0\kerning0
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\cb3 \expnd0\expndtw0\kerning0
\outl0\strokewidth0 In ecoli file OUR, SUR are the uptake rates for oxygen and glucose \cb1 \expnd0\expndtw0\kerning0
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\cb3 \expnd0\expndtw0\kerning0
\outl0\strokewidth0 The ecoli regulatory interactions in the file were obtained from\'a0RegulonDB\'a0( use this data for the latest network)\cb1 \expnd0\expndtw0\kerning0
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\pard\pardeftab720
{\field{\*\fldinst{HYPERLINK "http://regulondb.ccg.unam.mx/"}}{\fldrslt \cf4 \cb3 \expnd0\expndtw0\kerning0
\ul \ulc4 \outl0\strokewidth0 \strokec4 http://regulondb.ccg.unam.mx/}}\
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\cf2 \cb3 \expnd0\expndtw0\kerning0
\outl0\strokewidth0 the expression data in the file is from m3d\'a0\cb1 \expnd0\expndtw0\kerning0
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{\field{\*\fldinst{HYPERLINK "http://m3d.bu.edu/norm/"}}{\fldrslt \cf4 \cb3 \expnd0\expndtw0\kerning0
\ul \ulc4 \outl0\strokewidth0 \strokec4 http://m3d.bu.edu/norm/}}\
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\cf2 \cb3 \expnd0\expndtw0\kerning0
\outl0\strokewidth0 the metabolic model is from the Palsson lab website \'a0-\'a0{\field{\*\fldinst{HYPERLINK "http://gcrg.ucsd.edu/InSilicoOrganisms/OtherOrganisms"}}{\fldrslt \cf4 \expnd0\expndtw0\kerning0
\ul \ulc4 \outl0\strokewidth0 \strokec4 http://gcrg.ucsd.edu/InSilicoOrganisms/OtherOrganisms}}\cb1 \expnd0\expndtw0\kerning0
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\cb3 \expnd0\expndtw0\kerning0
\outl0\strokewidth0 you can get the ecoli tf-environmental interactions from the covert et al nature paper\'a0\cb1 \expnd0\expndtw0\kerning0
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{\field{\*\fldinst{HYPERLINK "http://www.nature.com/nature/journal/v429/n6987/suppinfo/nature02456.html"}}{\fldrslt \cf4 \cb3 \expnd0\expndtw0\kerning0
\ul \ulc4 \outl0\strokewidth0 \strokec4 http://www.nature.com/nature/journal/v429/n6987/suppinfo/nature02456.html}}\
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You can download the latest version of the PROM code from \
http://sourceforge.net/projects/gemini-data/files/?source=navbar}