Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 100 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 100

There are 16 regulatory influences for Module 100

Regulator Table (16)
Regulator Name Type
RSP_3238 tf
RSP_3322 tf
RSP_0282 tf
RSP_0601 tf
RSP_2572 tf
RSP_2606 tf
RSP_0087 tf
RSP_0489 tf
RSP_2171 tf
RSP_2410 tf
RSP_2838 tf
RSP_2888 tf
RSP_2963 tf
RSP_1590 tf
RSP_2800 tf
RSP_2939 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
7920 1.40e-01 GccTCGCcCAAggAacGgGCa
Loader icon
7921 3.60e-02 GccGgctttccCgatgCGCacAgG
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 100 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism of Terpenoids and Polyketides kegg subcategory 5.00e-06 1.01e-04 4/23
Terpenoid backbone biosynthesis kegg pathway 0.00e+00 1.00e-06 4/23
Biosynthesis of secondary metabolites kegg pathway 1.86e-02 3.98e-02 4/23

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 2.71e-03 4.03e-03 3/23

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 7.41e-03 1.22e-02 13/23
Coenzyme transport and metabolism cog subcategory 1.08e-02 1.74e-02 3/23
Lipid transport and metabolism cog subcategory 8.45e-04 1.56e-03 4/23
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 100

There are 23 genes in Module 100

Gene Member Table (23)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0162 RSP_0162 CDS None chromosome 1 1878943 1879134 + hypothetical protein (NCBI) False
RSP_0308 ureB CDS None chromosome 1 2038238 2038543 - Urease, beta subunit (NCBI) False
RSP_0309 ureA CDS None chromosome 1 2038594 2038896 - Urease, gamma subunit (NCBI) False
RSP_0310 ureD CDS None chromosome 1 2038908 2039735 - Urease accessory protein UreD (NCBI) False
RSP_0311 RSP_0311 CDS None chromosome 1 2039862 2040977 + Putative aminotransferase protein (NCBI) False
RSP_0312 RSP_0312 CDS None chromosome 1 2041012 2042322 + Aminotransferase class-III (NCBI) False
RSP_0880 dadA CDS None chromosome 1 2628970 2630031 + putative oxidoreductase, possibly D-amino acid oxidase protein (NCBI) False
RSP_1134 Dxs CDS None chromosome 1 2896821 2898734 - 1 deoxyxylulose-5-phosphate synthase (NCBI) False
RSP_1135 ispA CDS None chromosome 1 2898744 2899613 - geranylgeranyl pyrophosphate synthetase (NCBI) False
RSP_1136 xseB CDS None chromosome 1 2899610 2899849 - exonuclease VII small subunit (NCBI) False
RSP_2045 RSP_2045 CDS None chromosome 1 639541 641055 + hypothetical protein (NCBI) False
RSP_2047 RSP_2047 CDS None chromosome 1 642382 644187 + ThiF family protein (NCBI) False
RSP_2048 RSP_2048 CDS None chromosome 1 644180 644698 + hypothetical protein (NCBI) False
RSP_2249 RSP_2249 CDS None chromosome 1 865112 866332 - multidrug (Tetracycline) efflux pump, Major facilitator superfamily (MFS) (NCBI) False
RSP_2551 exoO CDS None chromosome 1 1194718 1196148 + Glycosyl transferase, family 2 (NCBI) False
RSP_2709 dxr CDS None chromosome 1 1357368 1358552 + probable 1-deoxy-D-xylulose 5-phosphate reductoisomerase protein (NCBI) False
RSP_2833 cinA CDS None chromosome 1 1477549 1478034 + Putative competence-damaged inducible protein (NCBI) False
RSP_2834 pgpA CDS None chromosome 1 1477055 1477552 + Putative Phosphatidylglycerophosphatase A (NCBI) False
RSP_2835 ispD CDS None chromosome 1 1475793 1476470 + Probable 4-diphosphocytidyl-2C-methyl-D-erythritol synthase (YgbP) (NCBI) False
RSP_3207 RSP_3207 CDS None chromosome 2 262583 263200 + putative cobalamin biosynthesis protein CbiM (NCBI) False
RSP_3208 RSP_3208 CDS None chromosome 2 263202 263795 + putative CbiL protein (NCBI) False
RSP_3209 cbiQ CDS None chromosome 2 263792 264502 + ABC cobalt transporter, inner membrane subunit, CbiQ (NCBI) False
RSP_3754 RSP_3754 CDS None chromosome 2 878814 879776 + hypothetical 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.

Comments for Module 100

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.