Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 229 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 229

There are 6 regulatory influences for Module 229

Regulator Table (6)
Regulator Name Type
DVU1572
DVU2547		 combiner
DVU0110
DVU1144		 combiner
DVU1517 tf
DVU3313
DVU0110		 combiner
DVU1331
DVU0110		 combiner
DVU0110 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.
Click on the RegPredict links to explore the motif in RegPredict.

Motif Table (2)
Motif Id e-value Consensus Motif Logo RegPredict
437 3.40e+01 GTaTgttcGTGGTAtgaTGa
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 RegPredict
438 2.90e+02 ccATaTcCgTTgaCttgcgTg
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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 229 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Microbial metabolism in diverse environments kegg pathway 1.93e-02 2.91e-02 3/31
Carbohydrate Metabolism kegg subcategory 2.33e-02 4.75e-02 3/31
Microbial metabolism in diverse environments kegg pathway 1.93e-02 4.12e-02 3/31

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
two-component signal transduction system (phosphorelay) biological_process 2.39e-02 3.34e-02 3/31
metabolic process biological_process 2.46e-02 3.42e-02 3/31
two-component response regulator activity molecular_function 7.63e-03 1.18e-02 3/31
iron-sulfur cluster binding molecular_function 1.71e-03 3.17e-03 4/31

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 2.41e-04 3.62e-03 4/31
Energy metabolism tigr mainrole 2.41e-04 5.19e-04 4/31

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy production and conversion cog subcategory 5.30e-05 2.04e-03 8/31
Energy production and conversion cog subcategory 5.30e-05 1.51e-04 8/31
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 229

There are 31 genes in Module 229

Gene Member Table (31)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0322 eno CDS 2794445 chromosome 365096 366409 + phosphopyruvate hydratase False
DVU0407 CDS 2793708 chromosome 455770 456414 + rare lipoprotein A family protein False
DVU0627 ptB CDS 2796151 chromosome 694034 695065 + phosphotransbutyrylase False
DVU0682 CDS 2795332 chromosome 756252 757040 - DNA-binding protein True
DVU0790 CDS 2794815 chromosome 876761 877816 + radical SAM family protein False
DVU1405 CDS 2794657 chromosome 1474096 1474599 - hypothetical protein DVU1405 False
DVU1780 CDS 2794287 chromosome 1843438 1843743 - hypothetical protein DVU1780 False
DVU1781 CDS 2794288 chromosome 1843928 1844593 - hypothetical protein DVU1781 False
DVU1782 CDS 2794289 chromosome 1844586 1846013 - iron-sulfur cluster-binding protein False
DVU1783 CDS 2794290 chromosome 1846006 1846758 - hypothetical protein DVU1783 False
DVU1784 CDS 2794291 chromosome 1846930 1847691 + short chain dehydrogenase/reductase family oxidoreductase False
DVU1785 CDS 2794292 chromosome 1847895 1848497 + MarC membrane protein False
DVU1862 CDS 2793644 chromosome 1929448 1930443 + GGDEF domain-containing protein False
DVU1901 CDS 2794712 chromosome 1975298 1976344 - peptidyl-prolyl cis-trans isomerase domain-containing protein False
DVU1916 CDS 2793332 chromosome 1990842 1990973 - hypothetical protein DVU1916 False
DVU1921 hynB-1 CDS 2793337 chromosome 1994643 1995596 + periplasmic False
DVU1922 hynA-1 CDS 2793338 chromosome 1995648 1997348 + periplasmic False
DVU1923 hupD CDS 2793339 chromosome 1997717 1998214 + hydrogenase expression/formation protein HupD False
DVU1924 hypC CDS 2793340 chromosome 1998226 1998477 + hydrogenase assembly chaperone HypC/HupF False
DVU1925 CDS 2793341 chromosome 1998495 1999136 + GDSL family lipase False
DVU2013 CDS 2796735 chromosome 2090668 2092329 - hydroxylamine reductase False
DVU2014 CDS 2796736 chromosome 2092404 2093579 - metallo-beta-lactamase family protein False
DVU2021 CDS 2793356 chromosome 2100755 2101222 - hypothetical protein DVU2021 False
DVU2353 CDS 2795527 chromosome 2449172 2450980 + glycosyl transferase group 2 family protein False
DVU2416 CDS 2794357 chromosome 2524701 2525183 + hypothetical protein DVU2416 False
DVU2460 CDS 2795324 chromosome 2565584 2566177 + hypothetical protein DVU2460 False
DVU2675 CDS 2795046 chromosome 2786675 2787358 - LuxR family transcriptional regulator True
DVU2770 CDS 2796320 chromosome 2877513 2877911 + response regulator False
DVU2937 CDS 2793975 chromosome 3041307 3042662 + TPR domain/response regulator receiver domain-containing protein False
DVU3035 CDS 2796452 chromosome 3159730 3161541 + methyl-accepting chemotaxis protein False
DVU3049 CDS 2796075 chromosome 3175305 3175718 - hemerythrin family protein 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.