Organism : Geobacter sulfurreducens | Module List:
Module 181 Profile

GeneModule member RegulatorRegulator MotifMotif
Network Help

A network view of the module is created using cytoscapeWeb and enables dynamic, interactive exploration of the module properties. In this view, module member genes, motifs, and regulatory influences are represented as peripheral nodes connected to core module node via edges.

Module members are green circles, regulators are red triangles and motifs are blue diamonds. Selection of a node gives access to detailed information in a pop-up window, which allows dragging and pinning to compare multiple selections. Selecting module members will show information about the selected gene such as name, species and fucntions. Motif selection will show motif logo image and e-values. Bicluster selction will show expression profile and summary statistics for the module.

GeneModule member RegulatorRegulator MotifMotif
Regulators for Module 181

There are 6 regulatory influences for Module 181

Regulator Table (6)
Regulator Name Type
GSU2177 tf
GSU1039 tf
GSU1495 tf
GSU2523 tf
GSU2520 tf
GSU0372 tf

Regulator Help

For each module, single or AND logic connected regulatory influences are listed under the regulators tab. These regulatory influences are identified by Inferelator. Table shows name of the regulator and its type.

tf: Transcription factor

ef: Environmental factor

combiner: Combinatorial influence of a tf or an ef through logic gate. Table is sortable by clicking on the arrows next to column headers.

Motif information (de novo identified motifs for modules)

There are 2 motifs predicted.

Motif Table (2)
Motif Id e-value Consensus Motif Logo
2522 5.90e-02 gcgTtctTaaAAg.agttta
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2523 2.70e+02 tTcTCTTTGacttAcataaaa
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

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.

Functional Enrichment

Regulon 181 is enriched for following functions.

Functions Help

Biological networks contain sets of regulatory units called functional modules that together play a role in regulation of specific functional processes. Connections between different modules in the network can help identify regulatory relationships such as hierarchy and epistasis. In addition, associating functions with modules enables putative assignment of functions to hypothetical genes. It is therefore essential to identify functional enrichment of modules within the regulatory network.

Functional annotations from single sources are often either not available or not complete. Therefore, we integrated KEGG pathway, Gene Ontology, TIGRFam and COG information as references for functional enrichment analysis.

We use hypergeometric p-values to identify significant overlaps between co-regulated module members and genes assigned to a particular functional annotation category. P-values are corrected for multiple comparisons by using Benjamini-Hochberg correction and filtered for p-values ≤ 0.05.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Members for Module 181

There are 34 genes in Module 181

Gene Member Table (34)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
GSU0105 GSU0105 CDS None chromosome 121302 121613 - cytochrome c family protein, putative (NCBI) False
GSU0107 spo0J CDS None chromosome 122567 123376 + parB-like domain protein (NCBI) True
GSU0422 fliN CDS None chromosome 452645 452950 + flagellar motor switch protein FliN (NCBI) False
GSU0515 GSU0515 CDS None chromosome 549161 549616 + universal stress protein family (VIMSS) False
GSU0758 GSU0758 CDS None chromosome 808948 809634 + membrane protein, putative (VIMSS) False
GSU1039 GSU1039 CDS None chromosome 1125639 1127339 + sigma-54 dependent DNA-binding response regulator (VIMSS) True
GSU1047 GSU1047 CDS None chromosome 1134505 1135587 + conserved hypothetical protein (VIMSS) False
GSU1114 GSU1114 CDS None chromosome 1199618 1200517 + TPR domain protein (VIMSS) False
GSU1181 GSU1181 CDS None chromosome 1288446 1288763 - hypothetical protein (VIMSS) False
GSU1216 cydC CDS None chromosome 1319807 1321453 + transport ATP-binding protein CydC (NCBI) False
GSU1222 GSU1222 CDS None chromosome 1326135 1327292 + histone deacetylase/AcuC/AphA family protein (VIMSS) False
GSU1240 GSU1240 CDS None chromosome 1342846 1343844 - hypothetical protein (VIMSS) False
GSU1281 nikO CDS None chromosome 1396577 1397326 + component of nickel ABC transport system (Dmitry Rodionov) False
GSU1310 GSU1310 CDS None chromosome 1435797 1436897 - pyridine nucleotide-disulfide oxidoreductase (Regina ONeil) False
GSU1319 GSU1319 CDS None chromosome 1444965 1446068 + sensor histidine kinase (VIMSS) False
GSU1446 GSU1446 CDS None chromosome 1585073 1586404 + radical SAM domain protein (NCBI) False
GSU1545 GSU1545 CDS None chromosome 1697747 1698361 + transporter, LysE family (VIMSS) False
GSU1573 GSU1573 CDS None chromosome 1725783 1726538 + CAAX amino terminal protease family protein (NCBI) False
GSU1715 GSU1715 CDS None chromosome 1879203 1879451 - hypothetical protein (VIMSS) False
GSU1740 GSU1740 CDS None chromosome 1905670 1905993 + cytochrome c family protein, putative (VIMSS) False
GSU2116 GSU2116 CDS None chromosome 2334447 2335415 + hypothetical protein (VIMSS) False
GSU2117 GSU2117 CDS None chromosome 2335443 2335727 + hypothetical protein (VIMSS) False
GSU2163 GSU2163 CDS None chromosome 2376777 2377046 + hypothetical protein (VIMSS) False
GSU2177 GSU2177 CDS None chromosome 2387321 2387878 + hypothetical protein (VIMSS) True
GSU2293 GSU2293 CDS None chromosome 2511728 2512108 + hypothetical protein (VIMSS) False
GSU2297 GSU2297 CDS None chromosome 2514738 2517026 - sensory box histidine kinase (VIMSS) False
GSU2312 GSU2312 CDS None chromosome 2529292 2531064 + sulfate transporter family protein (VIMSS) False
GSU2472 vapC CDS None chromosome 2710996 2711397 - virulence associated protein C (NCBI) False
GSU2474 GSU2474 CDS None chromosome 2711639 2711737 - hypothetical protein (VIMSS) False
GSU2540 GSU2540 CDS None chromosome 2804108 2804653 - transcriptional regulator, Cro/CI family (VIMSS) True
GSU2664 GSU2664 CDS None chromosome 2934692 2939182 - outer membrane efflux protein (VIMSS) False
GSU2927 GSU2927 CDS None chromosome 3226255 3226539 + cytochrome c, putative (NCBI) False
GSU3184 GSU3184 CDS None chromosome 3491320 3493002 + hypothetical protein (VIMSS) False
GSU3361 GSU3361 CDS None chromosome 3692660 3694207 - transglutaminase domain protein (NCBI) False

Genes Help

Gene member table shows all the genes included in the module. Listed attributes are;

  1. Name: Gene name or Locus tag
  2. Common Name: Gene short name
  3. Type: Type of the feature, usually CDS.
  4. Gene ID: Link to NCBI Gene ID
  5. Chromosome: Chromosome name from annotation file
  6. Start/End:Feature start and end coordinates
  7. Strand: strand of the gene
  8. Description: Description of the gene from annotation file
  9. TF: If the gene is a Transcription Factor or not.

If you are browsing the Network Portal by using Gaggle/Firegoose, firegoose plugin will capture the NameList of the gene members. Captured names can be saved into your Workspace by clicking on "Capture" in the firegoose toolbar or can be directly sent other desktop and web resources by using "Broadcast" option.

Help

What is a module?

Regulatory units (modules) in the Network Portal are based on the network inference algorithm used. For the current version, modules are based on cMonkey modules and Inferelator regulatory influences on these modules. More specifically, module refers to set of genes that are conditionally co-regulated under subset of the conditions. Identification of modules integrates co-expression, de-novo motif identification, and other functional associations such as operon information and protein-protein interactions.

Module Overview

The landing module page shows quick summary info including co-expression profiles, de-novo identified motifs, and transcription factors and/or environmental factors as regulatory influences. It also includes module residual, motif e-values, conditions and links to other resources such as NCBI and Microbesonline. . If a transcription factor is included in the manually curated RegPrecise database, further information from RegPrecise is shown, allowing users to perform comparative analysis.

Expression Profiles

Expression profiles is a plot of the expression ratios (log10) of the module's genes, over all subset of the conditions included in the module. The X-axis represent conditions and the Y-axis represents log10 expression ratios. Each gene is plotted as line plot with different colors. Colored legend for the lines are presented under the plot. This plot is dynamic. Clicking on the gene names in the legend will show/hide the plot for that particular gene. A tooltip will show expression ratio information if you mouseover the lines in the plot.

Motif Locations

Location of the Identified motifs for the module in the upstream regions of the member genes are shown under the expression profiles plot. This plot shows the diagram of the upstream positions of the motifs, colored red and green for motifs #1, and 2, respectively. Intensity of the color is proportional to the significance of the occurence of that motif at a given location. Motifs on the forward and reverse strand are represented over and under the line respectively.

Network

A network view of the module is created using cytoscapeWeb and enables dynamic, interactive exploration of the module properties. In this view, module member genes, motifs, and regulatory influences are represented as peripheral nodes connected to core module node via edges. Module members are green circles, regulators are red triangles and motifs are blue diamonds. Selection of a node gives access to detailed information in a pop-up window, which allows dragging and pinning to compare multiple selections. Selecting module members will show information about the selected gene such as name, species and fucntions. Motif selection will show motif logo image and e-values. Bicluster selction will show expression profile and summary statistics for the module.

GeneModule member RegulatorRegulator MotifMotif

Regulators

For each module, single or AND logic connected regulatory influences are listed under the regulators tab. These regulatory influences are identified by Inferelator. Table shows name of the regulator and its type. tf: Transcription factor, ef: Environmental factor and combiner:Combinatorial influence of a tf or an ef through logic gate. Tabel is sortable by clicking on the arrows next to column headers.

Motifs

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Functions

Biological networks contain sets of regulatory units called functional modules that together play a role in regulation of specific functional processes. Connections between different modules in the network can help identify regulatory relationships such as hierarchy and epistasis. In addition, associating functions with modules enables putative assignment of functions to hypothetical genes. It is therefore essential to identify functional enrichment of modules within the regulatory network.

Functional annotations from single sources are often either not available or not complete. Therefore, we integrated KEGG pathway, Gene Ontology, TIGRFam and COG information as references for functional enrichment analysis.

We use hypergeometric p-values to identify significant overlaps between co-regulated module members and genes assigned to a particular functional annotation category. P-values are corrected for multiple comparisons by using Benjamini-Hochberg correction and filtered for p-values ≤ 0.05.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Genes

Gene member table shows all the genes included in the module. Listed attributes are;

  1. Name: Gene name or Locus tag
  2. Common Name: Gene short name
  3. Type: Type of the feature, usually CDS.
  4. Gene ID: Link to NCBI Gene ID
  5. Chromosome: Chromosome name from annotation file
  6. Start/End:Feature start and end coordinates
  7. Strand: strand of the gene
  8. Description: Description of the gene from annotation file
  9. TF: If the gene is a Transcription Factor or not.

If you are browsing the Network Portal by using Gaggle/Firegoose, firegoose plugin will capture the NameList of the gene members. Captured names can be saved into your Workspace by clicking on "Capture" in the firegoose toolbar or can be directly sent other desktop and web resources by using "Broadcast" option.

Social

You can start a conversation about this module or join the existing discussion by adding your comments. In order to be able to add your comments you need to sign in by using any of the following services;Disqus, Google, Facebook or Twitter. For full compatibility with other network portal features, we recommend using your Google ID.

Definitions

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.