Explore network modules for Escherichia coli K12

Use residual and motif e-value sliders to filter modules

Residual: 0-0.3 Motif e-value 0-10
This is the section to display the module list


NP_414561.1 nhaR NP_414601.1 hepA NP_414606.1 araC NP_414618.4 leuO NP_414622.1 fruR NP_414643.1 yacG NP_414655.1 pdhR NP_414704.4 cdaR NP_414731.2 rof NP_414744.1 yafC NP_414788.1 perR NP_414806.1 yagI NP_414828.1 matA NP_414839.1 ykgD NP_414847.3 betI NP_414849.1 yahA NP_414850.1 yahB NP_414864.1 prpR NP_414872.3 cynR NP_414879.3 lacI NP_414880.2 mhpR NP_414928.2 mak NP_414933.1 phoB NP_414947.1 nrdR NP_414950.1 nusB NP_414981.4 ybaO NP_414997.1 acrR NP_415020.1 cueR NP_415037.1 allS NP_415039.1 allR NP_415068.1 fimZ NP_415078.1 ybcM NP_415096.1 appY NP_415098.1 envY NP_415103.1 cusR NP_415134.1 ybdM NP_415136.1 ybdO NP_415153.1 dpiA NP_415156.1 cspE NP_415162.4 ybeF NP_415202.1 nagC NP_415209.1 fur NP_415222.1 kdpE NP_415258.1 mngR NP_415282.1 modE NP_415289.4 ybhD NP_415317.4 ybiH NP_415320.1 dinG NP_415338.1 mntR NP_415361.1 deoR NP_415367.1 ybjK NP_415395.2 ybjE NP_415401.1 cspD NP_415409.1 lrp NP_415420.1 ycaN NP_415479.1 sxy NP_415509.1 cspH NP_415510.1 cspG NP_415515.1 torR NP_415533.1 rutR NP_415558.1 csgD NP_415589.1 flgM NP_415629.4 ycfQ NP_415632.1 mfd NP_415638.1 cobB NP_415648.1 phoP NP_415663.1 ymfK NP_415680.1 ycgE NP_415701.1 umuD NP_415705.1 fadR NP_415719.2 dhaR NP_415739.1 narL NP_415791.1 cysB NP_415800.1 yciT NP_415819.4 pspF NP_415820.1 pspA NP_415822.1 pspC NP_415836.1 ycjW NP_415839.1 tyrR NP_415844.1 ycjZ NP_415850.1 fnr NP_415855.1 abgR NP_415902.1 feaR NP_415917.1 paaX NP_415939.2 ydcI NP_415950.4 ydcO NP_415956.1 ydcR NP_415967.2 yncC NP_416016.1 ydeO NP_416025.1 hipB NP_416029.1 lsrR NP_416043.1 yneJ NP_416047.4 marR NP_416048.2 marA NP_416058.1 ydfH NP_416070.1 cspI NP_416075.1 cspB NP_416076.1 cspF NP_416111.1 dgsA NP_416112.1 ynfL NP_416125.2 rstA NP_416135.1 uidR NP_416137.1 malI NP_416159.2 slyA NP_416166.3 ydhM NP_416175.1 purR NP_416176.1 ydhB NP_416211.1 ydiP NP_416249.1 chbR NP_416284.1 ydjF NP_416304.1 yeaM NP_416313.4 yeaT NP_416322.1 yoaA NP_416337.1 cspC NP_416341.1 kdgR NP_416367.1 yebK NP_416378.1 yebC NP_416405.1 flhC NP_416406.4 flhD NP_416424.1 uvrY NP_416426.1 sdiA NP_416432.3 fliA NP_416461.1 rcsA NP_416478.2 yedW NP_416490.1 yeeN NP_416492.1 cbl NP_416493.1 nac NP_416519.4 yeeY NP_416583.1 baeR NP_416604.1 yegW NP_416629.4 yehT NP_416631.1 mlrA NP_416656.1 galS NP_416662.1 yeiE NP_416689.1 yejH NP_416697.1 narP NP_416717.1 ada NP_416721.1 rcsB NP_416724.1 atoC NP_416751.1 yfaX NP_416792.1 lrhA NP_416865.1 dsdC NP_416870.1 evgA NP_416882.1 ypdB NP_416883.1 ypdC NP_416900.1 xapR NP_416904.1 yfeR NP_416922.1 yfeT NP_416932.1 eutR NP_416966.1 yffB NP_416986.4 hyfR NP_417026.1 iscR NP_417030.2 csiE NP_417032.1 hcaR NP_417045.4 yphH NP_417049.1 yfhA NP_417056.2 yfhH NP_417068.1 rpoE NP_417072.4 yfiE NP_417109.1 yfjG NP_417113.1 alpA NP_417123.1 yfjR NP_417150.4 csiR NP_417153.1 ygaV NP_417169.1 mprA NP_417186.1 gutM NP_417187.1 srlR NP_417189.2 norR NP_417194.1 ascG NP_417207.1 hypB NP_417211.1 fhlA NP_417215.1 ygbI NP_417221.1 rpoS NP_417248.1 ygcP NP_417285.1 fucR NP_417288.1 gcvA NP_417314.1 galR NP_417316.1 lysR NP_417323.2 yqeH NP_417324.1 yqeI NP_417329.1 ygeH NP_417345.1 ygeV NP_417391.1 argP NP_417396.4 ygfI NP_417404.1 yggD NP_417423.4 yqgE NP_417454.1 glcC NP_417483.2 yqhC NP_417497.1 qseB NP_417532.1 ttdR NP_417539.1 rpoD NP_417542.1 yqjI NP_417546.1 ebgR NP_417553.1 ygjM NP_417565.2 exuR NP_417576.1 yhaJ NP_417588.1 tdcA NP_417598.1 sohA NP_417600.1 agaR NP_417638.1 nusA NP_417648.4 greA NP_417655.1 sfsB NP_417657.2 yrbA NP_417669.1 rpoN NP_417689.4 nanK NP_417693.3 nanR NP_417704.1 argR NP_417710.1 aaeR NP_417727.1 fis NP_417730.1 envR NP_417751.1 zntR NP_417754.1 rpoA NP_417763.1 rplR NP_417816.1 crp NP_417834.6 frlR NP_417835.1 yhfS NP_417864.1 ompR NP_417866.4 yhgF NP_417877.1 malT NP_417880.1 rtcR NP_417881.1 glpR NP_417918.1 rpoH NP_417938.1 nikR NP_417958.1 arsR NP_417964.1 dctR NP_417969.1 gadE NP_417972.1 gadW NP_417973.1 gadX NP_417977.1 yhjB NP_417978.2 yhjC NP_418011.1 yiaG NP_418012.1 cspA NP_418026.1 xylR NP_418031.1 yiaJ NP_418042.1 yiaU NP_418058.1 mtlR NP_418061.1 lldR NP_418098.4 slmA NP_418106.1 rpoZ NP_418107.1 spoT NP_418109.1 recG NP_418125.1 uhpA NP_418136.1 yidL NP_418139.1 yidP NP_418163.1 tnaC NP_418167.1 yidZ NP_418199.1 asnC NP_418209.1 rbsR NP_418221.1 ilvY NP_418230.1 rho NP_418272.1 metR NP_418284.1 rfaH NP_418304.1 glnG NP_418308.1 yihL NP_418320.2 yihW NP_418333.1 frvR NP_418341.1 rhaS NP_418342.1 rhaR NP_418348.1 cpxR NP_418369.1 cytR NP_418373.1 metJ NP_418389.1 yijO NP_418396.1 oxyR NP_418398.2 fabR NP_418404.1 birA NP_418409.1 nusG NP_418415.1 rpoC NP_418423.1 rsd NP_418432.1 zraR NP_418442.2 iclR NP_418467.1 lexA NP_418470.4 zur NP_418486.1 soxS NP_418487.1 soxR NP_418513.4 rpiR NP_418526.1 phnF NP_418537.1 basR NP_418540.1 adiY NP_418542.1 melR NP_418548.1 dcuR NP_418557.1 cadC NP_418558.2 yjdC NP_418599.1 nsrR NP_418600.4 rnr NP_418603.1 yjfJ NP_418612.1 ulaR NP_418632.1 ytfG NP_418633.4 ytfH NP_418662.1 treR NP_418672.4 yjgJ NP_418685.1 idnR NP_418713.1 fecI NP_418715.2 yjhU NP_418719.1 yjhI NP_418720.1 sgcR NP_418744.1 uxuR NP_418747.1 yjiE NP_418760.1 yjiR NP_418785.1 yjjQ NP_418786.3 bglJ NP_418810.1 trpR NP_418813.1 rob NP_418815.1 creB NP_418818.1 arcA YP_026216.2 greB YP_026222.1 gntR YP_026239.1 dgoR YP_026245.1 yieP YP_026246.1 hdfR YP_026290.1 yjjM
Network Exploration Help

This page gives you overview of the network modules for a particular organism. You can explore these modules by using various filters.

Currently we support two filters, Residual and Motif e-values. Network modules are loaded with default residual and motif e-value filters. In order to change filters, simply move the slider to select the desired range. Results table will automatically update to reflect your filter selections. If you would like to remove filters, click on "Reset Filters" button.

Network Table

Network table will show the following columns for each module.

Module: Number of the module for the given version of the network.

Residual: is a measure of bicluster quality. Mean bicluster residual is smaller when the expression profile of the genes in the module is "tighter". So smaller residuals are usually indicative of better bicluster quality.

Expression Profile: is a preview of the expression profiles of all the genes under subset of conditions included in the module. Tighter expression profiles are usually indicative of better bicluster quality.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Genes: Number of genes included in the module.

Functions: We identify functional enrichment of each module by camparing to different functional categories such as KEGG, COG, GO etc. by using hypergeometric function. If the module is significantly enriched for any of the functions, this column will list few of the these functions as an overview. Full list of functions is available upon visiting the module page under the Functions tab.


Inferelator algorithm identifies most probable regulatory influences for each module. These influences can be transcription factors or environmental factors. Influences section lists all the regulators that have influences on modules. Click on the regulator name If you would like to access which modules are regulated by these regulators.