Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 11 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 11

There are 12 regulatory influences for Module 11

Regulator Table (12)
Regulator Name Type
DVU2195
DVU0309		 combiner
DVU0030
DVU3080		 combiner
DVU2423 tf
DVU2557
DVU2675		 combiner
DVU0309
DVU2989		 combiner
DVU0309
DVU3334		 combiner
DVU1561
DVU2114		 combiner
DVU2557 tf
DVU0309
DVU2111		 combiner
DVU2114 tf
DVU3080 tf
DVU0309
DVU0063		 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
21 1.00e-01 ttTtcttGctaTaat
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 RegPredict
22 3.70e+03 ATgAaaATAcT
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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 11 is enriched for following functions.

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
two-component signal transduction system (phosphorelay) biological_process 1.49e-02 2.24e-02 3/27
chemotaxis biological_process 5.54e-04 1.58e-03 3/27
signal transduction biological_process 1.03e-03 2.41e-03 3/27
two-component response regulator activity molecular_function 4.60e-03 7.56e-03 3/27
signal transducer activity molecular_function 2.15e-04 5.80e-04 3/27

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Methyl-accepting chemotaxis protein cog 3.80e-05 6.40e-05 3/27
Signal transduction mechanisms cog subcategory 2.33e-03 2.95e-02 6/27
Cell motility cog subcategory 7.42e-04 1.44e-02 4/27
Posttranslational modification, protein turnover, chaperones cog subcategory 4.07e-03 4.38e-02 3/27
Cellular processes and signaling cog category 1.30e-05 3.74e-04 15/27
Cellular processes and signaling cog category 1.75e-02 2.89e-02 9/27
Signal transduction mechanisms cog subcategory 2.33e-03 4.34e-03 6/27
Cell motility cog subcategory 7.42e-04 1.49e-03 4/27
Posttranslational modification, protein turnover, chaperones cog subcategory 4.07e-03 7.45e-03 3/27
Methyl-accepting chemotaxis protein cog 3.80e-05 1.17e-04 3/27
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 11

There are 27 genes in Module 11

Gene Member Table (27)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0170 CDS 2795600 chromosome 211427 213496 + methyl-accepting chemotaxis protein False
DVU0729 CDS 2794134 chromosome 813205 813660 + hypothetical protein DVU0729 False
DVU0820 CDS 2795023 chromosome 909804 909923 + hypothetical protein DVU0820 False
DVU0821 CDS 2796167 chromosome 909911 910510 - hypothetical protein DVU0821 False
DVU0822 CDS 2796168 chromosome 910522 911178 - hypothetical protein DVU0822 False
DVU0912 CDS 2794665 chromosome 1006702 1007286 - hypothetical protein DVU0912 False
DVU0937 CDS 2794611 chromosome 1028459 1028845 + hypothetical protein DVU0937 False
DVU1121 CDS 2794732 chromosome 1225917 1226537 - hypothetical protein DVU1121 False
DVU1263 pppA CDS 2793583 chromosome 1351308 1352111 + type IV prepilin-like proteins leader peptidase False
DVU1773 CDS 2795820 chromosome 1838243 1838536 + hypothetical protein DVU1773 False
DVU1774 CDS 2794281 chromosome 1838748 1839629 + hypothetical protein DVU1774 False
DVU1811 CDS 2796640 chromosome 1875780 1876643 - protoheme IX farnesyltransferase False
DVU1812 CDS 2796641 chromosome 1876687 1877967 - cytochrome c oxidase subunit II False
DVU2107 CDS 2793379 chromosome 2201950 2202501 + hypothetical protein DVU2107 False
DVU2117 CDS 2793389 chromosome 2212495 2213061 + hypothetical protein DVU2117 False
DVU2264 CDS 2794087 chromosome 2358673 2358825 + hypothetical protein DVU2264 False
DVU2304 CDS 2795350 chromosome 2398174 2398410 + hypothetical protein DVU2304 False
DVU2345 CDS 2795519 chromosome 2439751 2440071 - hypothetical protein DVU2345 False
DVU2585 CDS 2796363 chromosome 2706604 2708484 + methyl-accepting chemotaxis protein False
DVU2615 CDS 2793911 chromosome 2733693 2734541 + solute-binding family 1 protein False
DVU2616 CDS 2793912 chromosome 2734559 2737561 + sensory box histidine kinase/response regulator False
DVU2676 CDS 2795047 chromosome 2787609 2787875 + hypothetical protein DVU2676 False
DVU2833 CDS 2796387 chromosome 2939513 2939842 + hypothetical protein DVU2833 False
DVU3045 CDS 2796071 chromosome 3168343 3171210 + sensory box histidine kinase/response regulator False
DVU3107 CDS 2796599 chromosome 3254902 3256671 + cytochrome c family protein False
DVU3155 dcrH CDS 2795860 chromosome 3308230 3311121 + methyl-accepting chemotaxis protein DcrH False
DVUA0025 CDS 2781559 pDV 30780 31241 - response regulator receiver domain-containing 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.