Explore network modules for Rhodobacter sphaeroides 2.4.1

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


RSP_0014 RSP_0018 RSP_0032 fliA RSP_0068 rpoN2 RSP_0071 fleQ RSP_0087 RSP_0090 smoC RSP_0122 cerR RSP_0185 RSP_0186 RSP_0282 ppsR RSP_0316 RSP_0327 nnrR RSP_0386 RSP_0394 RSP_0395 rpoD RSP_0402 RSP_0415 RSP_0443 RSP_0457 glpR RSP_0489 RSP_0507 RSP_0511 RSP_0527 rpoN RSP_0547 nifA RSP_0591 RSP_0601 rpoH2 RSP_0607 RSP_0611 RSP_0616 RSP_0623 RSP_0641 RSP_0698 fnrL RSP_0722 RSP_0728 RSP_0755 nusB RSP_0760 mucS RSP_0768 RSP_0774 RSP_0794 catR RSP_0907 dctR RSP_0927 lyrS RSP_0958 RSP_0981 RSP_0999 RSP_1014 RSP_1032 RSP_1034 pdhR RSP_1040 RSP_1055 RSP_1077 RSP_1092 rpoE RSP_1139 RSP_1163 nusA RSP_1164 RSP_1191 RSP_1220 hrcA RSP_1225 spo0J RSP_1231 rho RSP_1243 RSP_1272 RSP_1274 RSP_1286 cbbR RSP_1297 RSP_1414 RSP_1435 RSP_1449 RSP_1486 RSP_1518 prrA RSP_1550 RSP_1577 putR RSP_1590 RSP_1606 RSP_1607 RSP_1612 RSP_1660 RSP_1663 RSP_1669 rpoZ RSP_1704 RSP_1712 rpoC RSP_1739 rpoA RSP_1741 RSP_1776 greA RSP_1785 RSP_1790 RSP_1866 RSP_1867 RSP_1871 RSP_1890 RSP_1892 RSP_1915 RSP_1922 RSP_1925 RSP_1936 RSP_1945 RSP_1952 RSP_1990 RSP_2011 RSP_2026 RSP_2027 RSP_2079 RSP_2130 RSP_2165 putR RSP_2171 metR RSP_2182 betI RSP_2200 RSP_2201 RSP_2236 RSP_2324 RSP_2346 RSP_2351 RSP_2362 RSP_2410 rpoH1 RSP_2425 RSP_2494 fur RSP_2533 RSP_2572 crpK RSP_2591 flhR RSP_2606 RSP_2610 RSP_2681 rpoE RSP_2719 RSP_2730 RSP_2780 oxyR RSP_2800 acoR RSP_2801 tetR RSP_2838 ntrC RSP_2840 ntrX RSP_2850 mfd RSP_2853 RSP_2867 rpoN4 RSP_2882 RSP_2888 RSP_2889 RSP_2922 RSP_2932 hutC RSP_2939 RSP_2950 RSP_2963 RSP_2965 RSP_3001 RSP_3022 RSP_3024 RSP_3026 RSP_3029 RSP_3042 dorX RSP_3052 RSP_3055 RSP_3064 RSP_3094 RSP_3095 RSP_3109 RSP_3124 RSP_3125 RSP_3165 RSP_3179 fur RSP_3202 RSP_3203 RSP_3226 RSP_3238 RSP_3298 RSP_3309 RSP_3317 RSP_3322 acoR RSP_3324 RSP_3339 RSP_3341 RSP_3385 RSP_3400 RSP_3405 gntR RSP_3418 RSP_3433 RSP_3436 RSP_3445 RSP_3448 RSP_3464 RSP_3505 RSP_3514 RSP_3528 RSP_3606 RSP_3609 RSP_3616 RSP_3620 RSP_3621 RSP_3664 RSP_3665 RSP_3667 RSP_3676 RSP_3680 RSP_3684 solR RSP_3686 RSP_3694 RSP_3700 RSP_3731 RSP_3748 ampR RSP_3862 RSP_3864 RSP_3865 RSP_3874 mopB RSP_3893 pdhR RSP_3939 RSP_3947 RSP_3971 RSP_3973 RSP_3977 RSP_3997 RSP_4017 RSP_4019 RSP_4022 repB1 RSP_4038 glpR RSP_4131 flcA RSP_4133 RSP_4178 RSP_4185 repB RSP_4201 RSP_4210 RSP_4245 RSP_4254 rnk RSP_4260 mexT RSP_4265 RSP_4275 RSP_4277 RSP_4278 yeaM RSP_6096 RSP_6137 RSP_6165 RSP_6209 RSP_7362 RSP_7368 RSP_7381 RSP_7395
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.