Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 174 Profile

GeneModule member RegulatorRegulator MotifMotif
Cytoscape Web
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 174

There are 15 regulatory influences for Module 174

Regulator Table (15)
Regulator Name Type
RSP_2939 tf
RSP_2171 tf
RSP_0402 tf
RSP_1550 tf
RSP_2591 tf
RSP_2681 tf
RSP_0623 tf
RSP_1922 tf
RSP_2610 tf
RSP_2867 tf
RSP_3464 tf
RSP_1243 tf
RSP_1892 tf
RSP_0316 tf
RSP_1669 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
8068 7.00e+01 aAaGaAa.gccTGctac.aCATct
Loader icon
8069 2.90e+03 TTGACa
Loader icon
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 174 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Butanoate metabolism kegg pathway 3.13e-04 2.77e-03 3/31
Lipid Metabolism kegg subcategory 2.49e-04 2.37e-03 4/31
Xenobiotics Biodegradation and Metabolism kegg subcategory 1.57e-03 8.22e-03 3/31

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
GGDEF tigrfam 0.00e+00 1.00e-06 3/31
Signal transduction tigr mainrole 2.00e-06 6.00e-06 3/31
Other tigr sub1role 0.00e+00 1.00e-06 3/31

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Poorly characterized cog category 2.98e-02 4.53e-02 9/31
Signal transduction mechanisms cog subcategory 8.29e-03 1.35e-02 4/31
Lipid transport and metabolism cog subcategory 3.43e-03 5.79e-03 4/31
General function prediction only cog subcategory 2.33e-02 3.59e-02 6/31
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 174

There are 31 genes in Module 174

Gene Member Table (31)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0170 RSP_0170 CDS None chromosome 1 1887157 1887447 - hypothetical protein (NCBI) False
RSP_0329 RSP_0329 CDS None chromosome 1 2056160 2057170 + GAF sensor diguanylate cyclase (GGDEF) (NCBI) False
RSP_0803 DppF CDS None chromosome 1 2547213 2547968 - ABC dipeptide transporter, ATPase subunit DppF (NCBI) False
RSP_0959 RSP_0959 CDS None chromosome 1 2715617 2717317 - ATPase (NCBI) False
RSP_1361 RSP_1361 CDS None chromosome 1 3139640 3140170 + hypothetical protein (NCBI) False
RSP_1499 RSP_1499 CDS None chromosome 1 85545 87122 - Probable gamma-glutamyltranspeptidase (NCBI) False
RSP_1502 RSP_1502 CDS None chromosome 1 88207 88659 + GAF domain protein (NCBI) False
RSP_1523 RSP_1523 CDS None chromosome 1 109747 110772 + hypothetical protein (NCBI) False
RSP_1596 deoB CDS None chromosome 1 191024 192220 + probable phosphopentomutase protein (NCBI) False
RSP_1597 add CDS None chromosome 1 192217 193200 + adenosine deaminase (NCBI) False
RSP_1687 hbdA CDS None chromosome 1 278180 279055 - S(+)-beta-hydroxybutyryl CoA dehydrogenase (NCBI) False
RSP_1690 etfA CDS None chromosome 1 280096 281022 - Electron transfer flavoprotein, alpha subunit (NCBI) False
RSP_1691 etfB CDS None chromosome 1 281022 281783 - Electron transfer flavoprotein beta-subunit (NCBI) False
RSP_1777 RSP_1777 CDS None chromosome 1 360800 362455 + Putative electron transfer flavoprotein-ubiquinone oxidoreductase precursor (NCBI) False
RSP_2196 RSP_2196 CDS None chromosome 1 809387 811588 - enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase / 3-hydroxybutyryl-CoA epimerase (NCBI) False
RSP_2197 RSP_2197 CDS None chromosome 1 811603 812814 - Acetoacetyl-CoA thiolase (NCBI) False
RSP_2198 RSP_2198 CDS None chromosome 1 812885 813328 - hypothetical protein (NCBI) False
RSP_2208 RSP_2208 CDS None chromosome 1 821053 822021 - ABC sugar transporter, inner membrane subunit (NCBI) False
RSP_2209 RSP_2209 CDS None chromosome 1 822018 823112 - ABC sugar transporter, inner membrane subunit (NCBI) False
RSP_2210 RSP_2210 CDS None chromosome 1 823112 824689 - ABC sugar transporter, fused ATPase subunits (NCBI) False
RSP_2362 RSP_2362 CDS None chromosome 1 989506 990288 + transcriptional regulator, GntR family (NCBI) True
RSP_2398 RSP_2398 CDS None chromosome 1 1026077 1026877 - ABC putrescine transporter, inner membrane subunit (NCBI) False
RSP_2842 trkH1 CDS None chromosome 1 1465397 1466908 - potassium uptake transporter, transmembrane subunit, TrkH (NCBI) False
RSP_2939 RSP_2939 CDS None chromosome 1 1619069 1619704 - Predicted transcriptional regulator containing the HTH domain (NCBI) True
RSP_2940 RSP_2940 CDS None chromosome 1 1619701 1620489 - hypothetical protein (NCBI) False
RSP_3101 RSP_3101 CDS None chromosome 2 143700 146018 - periplasmic sensor diguanylate cyclase/phosphodiesterase (NCBI) False
RSP_3161 RSP_3161 CDS None chromosome 2 212647 215262 - hypothetical protein (NCBI) False
RSP_3344 RSP_3344 CDS None chromosome 2 408103 409575 - PAS sensor diguanylate cyclase (NCBI) False
RSP_3345 RSP_3345 CDS None chromosome 2 409838 411136 + hypothetical protein (NCBI) False
RSP_3826 RSP_3826 CDS None chromosome 2 22338 23123 + hypothetical protein (NCBI) False
RSP_3827 RSP_3827 CDS None chromosome 2 23204 23944 + Phospholipid/glycerol acyltransferase (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.

Comments for Module 174

Please add your comments for this module by using the form below. Your comments will be publicly available.

comments powered by Disqus
Social Help

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.

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.