Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 321 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 321

There are 7 regulatory influences for Module 321

Regulator Table (7)
Regulator Name Type
DVU0436 tf
DVU2588
DVU0118		 combiner
DVU3186
DVU3023		 combiner
DVU2675
DVUA0024		 combiner
DVU2275 tf
DVU2588
DVU0436		 combiner
DVU1561
DVU2588		 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
611 1.20e-01 aatATCATgtC
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 RegPredict
612 1.90e+03 CagCAttgcagACG.cgcGaa
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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 321 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 1.32e-02 4.26e-02 3/32
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 1.20e-05 9.60e-05 7/32
electron transport biological_process 1.96e-02 2.80e-02 4/32
regulation of transcription, DNA-dependent biological_process 2.13e-03 4.31e-03 6/32
transport biological_process 2.46e-02 3.42e-02 3/32
chemotaxis biological_process 1.08e-03 2.48e-03 3/32
protein secretion biological_process 7.00e-06 5.80e-05 4/32
peptidyl-histidine phosphorylation biological_process 1.52e-04 6.31e-04 4/32
two-component sensor activity molecular_function 4.70e-05 2.01e-04 5/32
two-component response regulator activity molecular_function 1.31e-04 4.04e-04 5/32
transporter activity molecular_function 7.29e-03 1.14e-02 3/32
electron carrier activity molecular_function 7.91e-03 1.22e-02 3/32

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Unknown substrate tigr sub1role 3.00e-06 4.50e-05 3/32
Transport and binding proteins tigr mainrole 7.74e-04 7.85e-03 4/32
Transport and binding proteins tigr mainrole 7.74e-04 1.48e-03 4/32
Unknown substrate tigr sub1role 3.00e-06 8.00e-06 3/32

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Signal transduction mechanisms cog subcategory 2.87e-04 7.54e-03 8/32
Cell motility cog subcategory 1.66e-03 2.28e-02 4/32
Intracellular trafficking, secretion, and vesicular transport cog subcategory 0.00e+00 2.00e-05 7/32
Cellular processes and signaling cog category 0.00e+00 0.00e+00 24/32
Cellular processes and signaling cog category 0.00e+00 1.00e-06 18/32
Signal transduction mechanisms cog subcategory 2.87e-04 6.28e-04 8/32
Cell motility cog subcategory 1.66e-03 3.14e-03 4/32
Intracellular trafficking, secretion, and vesicular transport cog subcategory 0.00e+00 1.00e-06 7/32
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 321

There are 32 genes in Module 321

Gene Member Table (32)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0330 CDS 2794497 chromosome 372996 374234 - response regulator False
DVU0331 CDS 2794498 chromosome 374234 377155 - sensory box histidine kinase False
DVU0591 CDS 2794089 chromosome 659306 661264 + methyl-accepting chemotaxis protein False
DVU0592 cheW-1 CDS 2794090 chromosome 661310 661831 + chemotaxis protein CheW False
DVU0700 CDS 2794452 chromosome 776063 778519 - methyl-accepting chemotaxis protein False
DVU1474 CDS 2794143 chromosome 1555168 1555281 + hypothetical protein DVU1474 False
DVU1991 CDS 2793798 chromosome 2070224 2071219 + hypothetical protein DVU1991 False
DVU2117 CDS 2793389 chromosome 2212495 2213061 + hypothetical protein DVU2117 False
DVU2118 CDS 2793390 chromosome 2213071 2213889 + hypothetical protein DVU2118 False
DVU2119 CDS 2795500 chromosome 2213886 2215340 + type II/III secretion system protein False
DVU2121 CDS 2795502 chromosome 2215766 2216980 + response regulator False
DVU2123 CDS 2795504 chromosome 2218890 2219855 + hypothetical protein DVU2123 False
DVU2124 CDS 2795505 chromosome 2219984 2220838 + hypothetical protein DVU2124 False
DVU2126 CDS 2795507 chromosome 2222196 2222585 + hypothetical protein DVU2126 False
DVU2127 CDS 2795508 chromosome 2222596 2223858 + von Willebrand factor A False
DVU2281 CDS 2795435 chromosome 2369933 2372134 - sensor histidine kinase/response regulator False
DVU2410 sodB CDS 2794495 chromosome 2513845 2514531 + superoxide dismutase, Fe False
DVU2524 CDS 2795614 chromosome 2635568 2636065 + cytochrome c3 False
DVU2526 hynA-2 CDS 2795616 chromosome 2637049 2638698 + periplasmic False
DVU2626 CDS 2795243 chromosome 2744233 2744439 + hypothetical protein DVU2626 False
DVU2679 CDS 2795050 chromosome 2790679 2793696 - sensory box histidine kinase/response regulator False
DVU3062 CDS 2796088 chromosome 3193322 3196564 - sensor histidine kinase/response regulator False
DVU3107 CDS 2796599 chromosome 3254902 3256671 + cytochrome c family protein False
DVU3131 CDS 2793980 chromosome 3277423 3278370 + transcriptional regulator False
DVU3133 CDS 2793982 chromosome 3280115 3280870 + glycerol uptake facilitator protein False
DVU3134 glpK CDS 2793983 chromosome 3281017 3282510 + glycerol kinase False
DVU3143 CDS 2793993 chromosome 3292123 3293712 + iron-sulfur cluster-binding protein False
DVU3144 CDS 2793994 chromosome 3293742 3295370 + cytochrome c family protein False
DVU3156 glmS CDS 2795861 chromosome 3311611 3313434 + glucosamine--fructose-6-phosphate aminotransferase (isomerizing) False
DVU3246 CDS 2793896 chromosome 3415791 3417416 + RND efflux system outer membrane lipoprotein False
DVU3247 CDS 2793849 chromosome 3417458 3418627 + RND family efflux transporter MFP subunit False
DVU3248 CDS 2793850 chromosome 3418656 3421799 + AcrB/AcrD/AcrF 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.