Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 16 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 16

There are 17 regulatory influences for Module 16

Regulator Table (17)
Regulator Name Type
RSP_3238 tf
RSP_1866 tf
RSP_1741 tf
RSP_0601 tf
RSP_2922 tf
RSP_1243 tf
RSP_3324 tf
RSP_2681 tf
RSP_2171 tf
RSP_3684 tf
RSP_1550 tf
RSP_2939 tf
RSP_0032 tf
RSP_2730 tf
RSP_0722 tf
RSP_3436 tf
RSP_0327 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
7752 5.70e-06 tttgcTgCGgcggcGGcgGaatcc
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7753 5.30e-03 aA.ctTTccccccgcCcGAtcCTt
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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 16 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Amino Acid Metabolism kegg subcategory 2.33e-02 4.74e-02 4/28
Arginine and proline metabolism kegg pathway 1.40e-05 2.39e-04 4/28
Xenobiotics Biodegradation and Metabolism kegg subcategory 8.00e-05 9.99e-04 4/28
Global kegg category 1.93e-02 4.12e-02 9/28
Metabolism kegg subcategory 1.93e-02 4.12e-02 9/28
Microbial metabolism in diverse environments kegg pathway 9.60e-05 1.16e-03 7/28

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 2.53e-04 5.35e-04 18/28
Amino acid transport and metabolism cog subcategory 2.91e-03 4.94e-03 7/28
Secondary metabolites biosynthesis, transport and catabolism cog subcategory 4.20e-05 1.21e-04 5/28
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 16

There are 28 genes in Module 16

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
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_0379 RSP_0379 CDS None chromosome 1 2110203 2111570 + putative aminotransferase protein (NCBI) False
RSP_0810 RSP_0810 CDS None chromosome 1 2553355 2554047 + conserved hypothetical membrane protein (NCBI) False
RSP_0851 RSP_0851 CDS None chromosome 1 2601717 2602646 + Putative transporter, AEC family (NCBI) False
RSP_0852 fghA CDS None chromosome 1 2602662 2603492 + S-formylglutathione hydrolase (NCBI) False
RSP_0853 RSP_0853 CDS None chromosome 1 2603485 2603973 + hypothetical protein (NCBI) False
RSP_0854 RSP_0854 CDS None chromosome 1 2603970 2604881 + Predicted ornithine cyclodeaminase (NCBI) False
RSP_1033 RSP_1033 CDS None chromosome 1 2796976 2797662 + OmpA family protein (NCBI) False
RSP_1520 prrB CDS None chromosome 1 105908 107296 + Sensor histidine kinase PrrB (RegB) (NCBI) False
RSP_1561 RSP_1561 CDS None chromosome 1 150337 151872 - AMP-forming acyl-CoA synthetase/ligase (NCBI) False
RSP_2090 pycA CDS None chromosome 1 684379 687843 - Pyruvate carboxylase (NCBI) False
RSP_2203 RSP_2203 CDS None chromosome 1 816645 817151 + hypothetical protein (NCBI) False
RSP_2253 RSP_2253 CDS None chromosome 1 869074 869898 - predicted hydrolases or acyltransferases (NCBI) False
RSP_2317 RSP_2317 CDS None chromosome 1 939220 940365 - Iron-containing alcohol dehydrogenase (NCBI) False
RSP_2318 RSP_2318 CDS None chromosome 1 940362 941750 - putative Aldehyde dehydrogenase (NCBI) False
RSP_2319 glnA CDS None chromosome 1 941763 943142 - Glutamine synthetase class-I (NCBI) False
RSP_2320 RSP_2320 CDS None chromosome 1 943218 944255 - TRAP-T family transporter, periplasmic binding protein (NCBI) False
RSP_2321 RSP_2321 CDS None chromosome 1 944312 945637 - Putative TRAP-T family transporter, DctM (12TMs) subunit (NCBI) False
RSP_2322 RSP_2322 CDS None chromosome 1 945637 946143 - TRAP-T family transporter, DctQ (4TMs) subunit (NCBI) False
RSP_2323 RSP_2323 CDS None chromosome 1 946148 946912 - hypothetical protein (NCBI) False
RSP_2324 RSP_2324 CDS None chromosome 1 947087 947953 + transcriptional regulator, RpiR family (NCBI) True
RSP_2886 glgC CDS None chromosome 1 1560042 1561313 - ADP-glucose pyrophosphorylase (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

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 16

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

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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.