Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 31 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 31

There are 10 regulatory influences for Module 31

Regulator Table (10)
Regulator Name Type
DVU3255
DVU1690		 combiner
DVU1561
DVU0539		 combiner
DVU2423
DVU3142		 combiner
DVU0682
DVU0653		 combiner
DVU0230 tf
DVUA0151
DVU1561		 combiner
DVU0653 tf
DVU2036
DVU2114		 combiner
DVU0653
DVU2114		 combiner
DVU3142 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
61 0.00e+00 atgt.tAtTttTTt....ttgtA
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 RegPredict
62 1.20e-01 cCaTgTtgTtaaAaaAacCAcaAA
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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 31 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 2.02e-03 4.11e-03 4/26
regulation of transcription, DNA-dependent biological_process 1.62e-02 2.40e-02 4/26
peptidyl-histidine phosphorylation biological_process 5.40e-05 3.09e-04 4/26
two-component sensor activity molecular_function 1.30e-05 7.00e-05 5/26
ATP binding molecular_function 2.11e-02 2.84e-02 5/26

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
sensory_box tigrfam 2.60e-05 3.40e-05 4/26
Small molecule interactions tigr sub1role 2.80e-05 3.02e-04 4/26
Regulatory functions tigr mainrole 5.00e-06 1.81e-04 5/26
sensory_box tigrfam 2.60e-05 7.00e-05 4/26
Regulatory functions tigr mainrole 5.00e-06 1.50e-05 5/26
Small molecule interactions tigr sub1role 2.80e-05 7.70e-05 4/26

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Signal transduction mechanisms cog subcategory 1.83e-03 2.51e-02 6/26
Signal transduction mechanisms cog subcategory 1.83e-03 3.46e-03 6/26
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 31

There are 26 genes in Module 31

Gene Member Table (26)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0025 CDS 2793532 chromosome 27714 29873 - sensory box histidine kinase False
DVU0109 CDS 2793308 chromosome 141455 142687 + sensor histidine kinase False
DVU0139 CDS 2793578 chromosome 173772 175484 + sensor histidine kinase False
DVU0294 CDS 2795949 chromosome 338182 340326 + glycosyl transferase group 2 family protein False
DVU0317 CDS 2794175 chromosome 361286 361423 - hypothetical protein DVU0317 False
DVU0445 CDS 2796648 chromosome 504169 505893 - CBS domain-containing protein False
DVU0578 CDS 2794563 chromosome 642474 643262 + formate dehydrogenase accessory protein FdhD False
DVU0717 CDS 2793616 chromosome 796457 797965 - GGDEF domain/EAL domain-containing protein False
DVU1079 trmE CDS 2794457 chromosome 1182378 1183751 + tRNA modification GTPase TrmE False
DVU1228 tpX CDS 2794123 chromosome 1317780 1318298 - thiol peroxidase False
DVU1230 CDS 2794125 chromosome 1318494 1318604 + hypothetical protein DVU1230 False
DVU1231 amt CDS 2794126 chromosome 1318601 1319809 + ammonium transporter False
DVU1232 glnB-1 CDS 2794127 chromosome 1319932 1320270 + nitrogen regulatory protein P-II False
DVU1295 sat CDS 2794748 chromosome 1387712 1388995 - sulfate adenylyltransferase False
DVU1534 CDS 2793819 chromosome 1601935 1602447 + hypothetical protein DVU1534 False
DVU1535 CDS 2793820 chromosome 1602447 1602968 + hypothetical protein DVU1535 False
DVU1563 CDS 2795734 chromosome 1644419 1647538 + sensory box histidine kinase/response regulator False
DVU1654 CDS 2795925 chromosome 1735437 1736321 - phage integrase family site specific recombinase False
DVU1731 CDS 2795801 chromosome 1801647 1801817 - hypothetical protein DVU1731 False
DVU1872 CDS 2794316 chromosome 1939633 1940058 - hypothetical protein DVU1872 False
DVU2040 CDS 2794838 chromosome 2118657 2118944 + hypothetical protein DVU2040 False
DVU2268 CDS 2795224 chromosome 2359465 2359584 + hypothetical protein DVU2268 False
DVU2989 pspF CDS 2796303 chromosome 3095502 3096647 + psp operon transcriptional activator True
DVU3132 CDS 2793981 chromosome 3278367 3280007 + glycerol-3-phosphate dehydrogenase, FAD-dependent False
DVU3269 CDS 2793873 chromosome 3444526 3447045 + sensory box histidine kinase/response regulator False
DVU3385 CDS 2796404 chromosome 3559220 3559354 - hypothetical protein DVU3385 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.