Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 105 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 105

There are 9 regulatory influences for Module 105

Regulator Table (9)
Regulator Name Type
DVU0063 tf
DVU1584
DVU2275		 combiner
DVU3220 tf
DVU2423
DVU1547		 combiner
DVU2547
DVU0539		 combiner
DVU2036
DVU2275		 combiner
DVU1561
DVU2588		 combiner
DVU2423
DVU2588		 combiner
DVU2195 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
203 4.80e+02 tcGtCGacatcCCCCTcCGgttCt
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 RegPredict
204 1.30e+01 GCcgcaa.cgcCttc.tca
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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 105 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 4.92e-03 1.17e-02 3/32
Bacterial chemotaxis kegg pathway 1.53e-03 6.36e-03 3/32
Signal Transduction kegg subcategory 4.92e-03 2.26e-02 3/32
Cell Motility kegg subcategory 2.07e-03 1.20e-02 4/32
Cellular Processes kegg category 2.07e-03 1.51e-02 4/32
Signal Transduction kegg subcategory 4.92e-03 1.71e-02 3/32
Two-component system kegg pathway 4.92e-03 1.71e-02 3/32
Cellular Processes kegg category 8.55e-03 2.38e-02 3/32
Cell Motility kegg subcategory 8.55e-03 2.38e-02 3/32
Bacterial chemotaxis kegg pathway 1.53e-03 9.15e-03 3/32

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
two-component signal transduction system (phosphorelay) biological_process 8.22e-04 2.05e-03 5/32
regulation of transcription, DNA-dependent biological_process 2.13e-03 4.31e-03 6/32
chemotaxis biological_process 1.08e-03 2.48e-03 3/32
peptidyl-histidine phosphorylation biological_process 1.52e-04 6.31e-04 4/32
two-component sensor activity molecular_function 4.48e-03 7.41e-03 3/32
two-component response regulator activity molecular_function 1.31e-04 4.04e-04 5/32

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Signal transduction histidine kinase cog 2.50e-05 4.50e-05 3/32
Signal transduction mechanisms cog subcategory 2.87e-04 7.54e-03 8/32
Cellular processes and signaling cog category 8.57e-03 1.50e-02 11/32
Signal transduction mechanisms cog subcategory 2.87e-04 6.28e-04 8/32
Signal transduction histidine kinase cog 2.50e-05 8.20e-05 3/32
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 105

There are 32 genes in Module 105

Gene Member Table (32)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0118 CDS 2796783 chromosome 152047 153411 - sigma-54 dependent transcriptional regulator/response regulator True
DVU0254 CDS 2794501 chromosome 290212 290358 - hypothetical protein DVU0254 False
DVU0289 moaC CDS 2793495 chromosome 333951 334577 - molybdenum cofactor biosynthesis protein C False
DVU0294 CDS 2795949 chromosome 338182 340326 + glycosyl transferase group 2 family protein False
DVU0482 CDS 2793627 chromosome 548195 549643 - sensory box histidine kinase/response regulator False
DVU0581 CDS 2794566 chromosome 645186 645887 - response regulator/anti-anti-sigma factor False
DVU0582 CDS 2794567 chromosome 645923 647941 - sensory box histidine kinase False
DVU0584 CDS 2794161 chromosome 649275 650213 + transposase False
DVU0608 CDS 2794094 chromosome 676751 678784 - methyl-accepting chemotaxis protein False
DVU0634 CDS 2794556 chromosome 702115 702681 - hypothetical protein DVU0634 False
DVU0640 pomA CDS 2794332 chromosome 710339 711091 - chemotaxis protein PomA False
DVU0755 CDS 2793594 chromosome 846505 847872 - sensor histidine kinase False
DVU0992 cheV-3 CDS 2794149 chromosome 1086193 1087155 + chemotaxis protein CheV False
DVU1030 CDS 2794527 chromosome 1134798 1135241 - universal stress protein False
DVU1359 CDS 2795083 chromosome 1437585 1438868 - hypothetical protein DVU1359 False
DVU1404 CDS 2794656 chromosome 1473006 1474112 - radical SAM domain-containing protein False
DVU1535 CDS 2793820 chromosome 1602447 1602968 + hypothetical protein DVU1535 False
DVU1853 CDS 2795916 chromosome 1921076 1921372 - hypothetical protein DVU1853 False
DVU2138 CDS 2794217 chromosome 2235537 2236190 - hypothetical protein DVU2138 False
DVU2141 CDS 2794220 chromosome 2238366 2239403 - nucleic acid-binding protein False
DVU2195 CDS 2795763 chromosome 2291911 2292168 + hypothetical protein DVU2195 True
DVU2312 CDS 2795272 chromosome 2405929 2406396 + hypothetical protein DVU2312 False
DVU2410 sodB CDS 2794495 chromosome 2513845 2514531 + superoxide dismutase, Fe False
DVU2429 CDS 2795420 chromosome 2533152 2533262 + hypothetical protein DVU2429 False
DVU2472 CDS 2795654 chromosome 2580029 2582368 + hypothetical protein DVU2472 False
DVU2556 CDS 2796130 chromosome 2668011 2668379 + hypothetical protein DVU2556 False
DVU2668 glmU CDS 2796235 chromosome 2779417 2780784 + bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase False
DVU2707 CDS 2793763 chromosome 2814228 2815478 + virion morphogenesis protein False
DVU2708 CDS 2793764 chromosome 2815643 2816131 + virion morphogenesis protein False
DVU3062 CDS 2796088 chromosome 3193322 3196564 - sensor histidine kinase/response regulator False
DVU3268 CDS 2793872 chromosome 3443136 3444398 + hypothetical protein DVU3268 False
DVU3388 CDS 2796407 chromosome 3562683 3563510 - lipoprotein 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.