Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 77 Profile

GeneModule member RegulatorRegulator MotifMotif
Cytoscape Web
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 77

There are 14 regulatory influences for Module 77

Regulator Table (14)
Regulator Name Type
DVU0436 tf
DVU0804 tf
DVU0118 tf
DVU2097
DVU1561
combiner
DVU0309
DVU3023
combiner
DVU2394 tf
DVU0309
DVU1964
combiner
DVU0682 tf
DVU2675
DVU2588
combiner
DVU2675
DVUA0024
combiner
DVU1561
DVU0804
combiner
DVU0682
DVU0309
combiner
DVU2588
DVU2934
combiner
DVU1517 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
151 2.60e+02 caATaAtGgAaa.A
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RegPredict
152 2.40e+03 G.AAaATaAT
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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 77 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Methane metabolism kegg pathway 4.66e-04 3.24e-03 3/28
Two-component system kegg pathway 3.03e-04 2.61e-03 4/28
Bacterial chemotaxis kegg pathway 6.60e-05 9.88e-04 4/28
Microbial metabolism in diverse environments kegg pathway 1.36e-02 2.23e-02 3/28
Energy Metabolism kegg subcategory 7.65e-03 3.08e-02 3/28
Signal Transduction kegg subcategory 3.03e-04 3.22e-03 4/28
Cell Motility kegg subcategory 1.11e-03 7.94e-03 4/28
Cellular Processes kegg category 1.11e-03 8.91e-03 4/28
Carbohydrate Metabolism kegg subcategory 1.65e-02 3.69e-02 3/28
Energy Metabolism kegg subcategory 7.39e-03 2.20e-02 3/28
Methane metabolism kegg pathway 4.66e-04 4.41e-03 3/28
Environmental Information Processing kegg category 1.88e-02 4.06e-02 4/28
Signal Transduction kegg subcategory 3.03e-04 3.42e-03 4/28
Two-component system kegg pathway 3.03e-04 3.42e-03 4/28
Cellular Processes kegg category 6.26e-04 5.45e-03 4/28
Cell Motility kegg subcategory 6.26e-04 5.45e-03 4/28
Bacterial chemotaxis kegg pathway 6.60e-05 1.23e-03 4/28
Microbial metabolism in diverse environments kegg pathway 1.36e-02 3.23e-02 3/28

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
two-component signal transduction system (phosphorelay) biological_process 3.85e-04 1.25e-03 5/28
electron transport biological_process 2.12e-03 4.29e-03 5/28
regulation of transcription, DNA-dependent biological_process 2.20e-02 3.10e-02 4/28
chemotaxis biological_process 4.20e-05 2.68e-04 4/28
signal transduction biological_process 1.19e-03 2.66e-03 3/28
two-component sensor activity molecular_function 2.72e-03 4.74e-03 3/28
two-component response regulator activity molecular_function 5.27e-03 8.55e-03 3/28
signal transducer activity molecular_function 2.48e-04 6.50e-04 3/28
electron carrier activity molecular_function 5.65e-04 1.25e-03 4/28
iron-sulfur cluster binding molecular_function 7.92e-03 1.22e-02 3/28

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Transport and binding proteins tigr mainrole 3.77e-03 1.79e-02 3/28
Transport and binding proteins tigr mainrole 3.77e-03 5.91e-03 3/28

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Methyl-accepting chemotaxis protein cog 4.40e-05 7.30e-05 3/28
Signal transduction mechanisms cog subcategory 5.60e-04 1.18e-02 7/28
Cell motility cog subcategory 8.84e-04 1.61e-02 4/28
Intracellular trafficking, secretion, and vesicular transport cog subcategory 3.41e-04 8.36e-03 4/28
Energy production and conversion cog subcategory 2.10e-05 9.15e-04 8/28
Cellular processes and signaling cog category 0.00e+00 3.00e-06 18/28
Cellular processes and signaling cog category 1.43e-04 3.40e-04 13/28
Signal transduction mechanisms cog subcategory 5.60e-04 1.15e-03 7/28
Cell motility cog subcategory 8.84e-04 1.75e-03 4/28
Intracellular trafficking, secretion, and vesicular transport cog subcategory 3.41e-04 7.32e-04 4/28
Energy production and conversion cog subcategory 2.10e-05 7.00e-05 8/28
Methyl-accepting chemotaxis protein cog 4.40e-05 1.32e-04 3/28
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 77

There are 28 genes in Module 77

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0018 CDS 2794279 chromosome 20136 22385 + methyl-accepting chemotaxis protein False
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
DVU1552 CDS 2794868 chromosome 1628591 1629721 - hypothetical protein DVU1552 False
DVU1559 mop CDS 2794875 chromosome 1636751 1639471 - aldehyde oxidoreductase False
DVU1570 porB CDS 2793461 chromosome 1652439 1653293 + pyruvate ferredoxin oxidoreductase subunit beta False
DVU2020 CDS 2793355 chromosome 2098260 2100758 - hypothetical protein DVU2020 False
DVU2075 CDS 2793452 chromosome 2158520 2159296 - ParA family protein False
DVU2077 CDS 2793454 chromosome 2160222 2162150 - hypothetical protein DVU2077 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
DVU2126 CDS 2795507 chromosome 2222196 2222585 + hypothetical protein DVU2126 False
DVU2281 CDS 2795435 chromosome 2369933 2372134 - sensor histidine kinase/response regulator False
DVU2481 CDS 2795663 chromosome 2589171 2589953 - formate dehydrogenase subunit beta False
DVU2483 CDS 2795451 chromosome 2593092 2594837 - cytochrome c family protein False
DVU2524 CDS 2795614 chromosome 2635568 2636065 + cytochrome c3 False
DVU2525 hynB-2 CDS 2795615 chromosome 2636122 2637036 + periplasmic False
DVU2526 hynA-2 CDS 2795616 chromosome 2637049 2638698 + periplasmic False
DVU2626 CDS 2795243 chromosome 2744233 2744439 + hypothetical protein DVU2626 False
DVU3133 CDS 2793982 chromosome 3280115 3280870 + glycerol uptake facilitator protein False
DVU3134 glpK CDS 2793983 chromosome 3281017 3282510 + glycerol kinase 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
DVU3265 CDS 2793869 chromosome 3440787 3441338 + tartrate dehydratase subunit beta 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.

Comments for Module 77

Please add your comments for this module by using the form below. Your comments will be publicly available.

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Social Help

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.

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.