Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 13 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 13

There are 11 regulatory influences for Module 13

Regulator Table (11)
Regulator Name Type
DVU0813 tf
DVU2423 tf
DVU0525 tf
DVU1517 tf
DVU2832 tf
DVUA0151 tf
DVUA0151
DVU1730
combiner
DVU3255
DVU2251
combiner
DVU3255
DVU0653
combiner
DVU2086
DVU2832
combiner
DVU3255
DVU0936
combiner

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.
Click on the RegPredict links to explore the motif in RegPredict.

Motif Table (2)
Motif Id e-value Consensus Motif Logo RegPredict
25 3.90e-02 acaAgcGtgTGAaag.tTtC.ACA
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RegPredict
26 2.60e+00 tTacgtcacCatTtActgGTaAAa
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RegPredict
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 13 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Two-component system kegg pathway 3.00e-06 1.00e-04 5/20
Signal Transduction kegg subcategory 3.00e-06 8.20e-05 5/20
Environmental Information Processing kegg category 6.46e-04 5.92e-03 5/20
Environmental Information Processing kegg category 6.12e-04 5.36e-03 5/20
Signal Transduction kegg subcategory 3.00e-06 1.01e-04 5/20
Two-component system kegg pathway 3.00e-06 1.01e-04 5/20

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
potassium ion transport biological_process 0.00e+00 0.00e+00 3/20
metabolic process biological_process 5.15e-03 8.84e-03 3/20
glutamate synthase (NADPH) activity molecular_function 0.00e+00 1.00e-06 3/20
potassium-transporting ATPase activity molecular_function 0.00e+00 0.00e+00 3/20

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Adaptations to atypical conditions tigr sub1role 0.00e+00 1.00e-06 3/20
Cellular processes tigr mainrole 5.00e-06 1.81e-04 4/20
Cellular processes tigr mainrole 5.00e-06 1.50e-05 4/20
Adaptations to atypical conditions tigr sub1role 0.00e+00 0.00e+00 3/20

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Transcription cog subcategory 2.16e-03 2.79e-02 3/20
Amino acid transport and metabolism cog subcategory 1.05e-03 1.82e-02 5/20
Inorganic ion transport and metabolism cog subcategory 2.58e-03 3.19e-02 3/20
Metabolism cog category 7.96e-03 1.40e-02 9/20
Transcription cog subcategory 2.16e-03 4.03e-03 3/20
Signal transduction mechanisms cog subcategory 1.17e-02 2.00e-02 4/20
Amino acid transport and metabolism cog subcategory 1.05e-03 2.04e-03 5/20
Inorganic ion transport and metabolism cog subcategory 2.58e-03 4.80e-03 3/20
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 13

There are 20 genes in Module 13

Gene Member Table (20)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0447 CDS 2796650 chromosome 507582 507899 - hypothetical protein DVU0447 False
DVU0527 maF CDS 2794893 chromosome 600433 601065 + Maf-like protein False
DVU0759 CDS 2793598 chromosome 849749 850954 - M29 family peptidase False
DVU1083 phoB CDS 2794461 chromosome 1187127 1187816 + phosphate regulon transcriptional regulator PhoB True
DVU1466 argB CDS 2794884 chromosome 1545702 1546628 - acetylglutamate kinase False
DVU1488 CDS 2794422 chromosome 1565890 1566795 - minor tail protein False
DVU1729 CDS 2795799 chromosome 1800946 1801224 + killer protein False
DVU1821 CDS 2793482 chromosome 1885906 1886661 - hypothetical protein DVU1821 False
DVU1822 CDS 2793483 chromosome 1886664 1887758 - glutamate synthase, amidotransferase subunit False
DVU1823 CDS 2793484 chromosome 1887773 1889296 - glutamate synthase, iron-sulfur cluster-binding subunit False
DVU2116 CDS 2793388 chromosome 2212101 2212274 + pilin False
DVU2986 pspC CDS 2796300 chromosome 3093874 3094296 - phage shock protein C False
DVU2987 CDS 2796301 chromosome 3094293 3094592 - hypothetical protein DVU2987 False
DVU2988 pspA CDS 2796302 chromosome 3094671 3095336 - phage shock protein A False
DVU2989 pspF CDS 2796303 chromosome 3095502 3096647 + psp operon transcriptional activator True
DVU2990 moeA CDS 2796304 chromosome 3096677 3098629 + molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein False
DVU3336 CDS 2796347 chromosome 3510381 3511520 - potassium channel histidine kinase domain-containing protein/universal stress protein False
DVU3337 kdpC CDS 2796348 chromosome 3511602 3512159 - K+-transporting ATPase subunit C False
DVU3338 kdpB CDS 2796349 chromosome 3512169 3514205 - K+-transporting ATPase subunit B False
DVU3339 kdpA CDS 2796350 chromosome 3514222 3515931 - potassium-transporting ATPase subunit A 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 13

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.