Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 319 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 319

There are 7 regulatory influences for Module 319

Regulator Table (7)
Regulator Name Type
DVU2275 tf
DVU2802
DVU0057
combiner
DVU2802
DVU2799
combiner
DVU2690 tf
DVU2802
DVU0539
combiner
DVU2802
DVU2588
combiner
DVU0744
DVU2690
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
607 1.10e-01 taAttcTGtTTgAgttggaGgacA
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RegPredict
608 1.20e+02 GgTgGTGaat
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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 319 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Oxidative phosphorylation kegg pathway 0.00e+00 0.00e+00 9/16
Metabolic pathways kegg pathway 0.00e+00 0.00e+00 12/16
Microbial metabolism in diverse environments kegg pathway 1.31e-04 1.57e-03 4/16
Energy Metabolism kegg subcategory 0.00e+00 0.00e+00 13/16
Metabolism kegg subcategory 0.00e+00 0.00e+00 16/16
Metabolism kegg category 0.00e+00 0.00e+00 15/16
Global kegg category 0.00e+00 0.00e+00 16/16
Metabolism kegg category 0.00e+00 0.00e+00 13/16
Energy Metabolism kegg subcategory 0.00e+00 0.00e+00 13/16
Oxidative phosphorylation kegg pathway 0.00e+00 0.00e+00 9/16
Global kegg category 0.00e+00 0.00e+00 12/16
Metabolism kegg subcategory 0.00e+00 0.00e+00 12/16
Metabolic pathways kegg pathway 0.00e+00 0.00e+00 12/16
Microbial metabolism in diverse environments kegg pathway 1.31e-04 1.99e-03 4/16

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
electron transport biological_process 7.40e-05 3.76e-04 5/16
ATP synthesis coupled proton transport biological_process 0.00e+00 0.00e+00 7/16
hydrogen-transporting two-sector ATPase activity molecular_function 0.00e+00 0.00e+00 8/16
electron carrier activity molecular_function 5.44e-04 1.21e-03 3/16
hydrogen ion transporting ATP synthase activity, rotational mechanism molecular_function 0.00e+00 0.00e+00 8/16
proton-transporting ATPase activity, rotational mechanism molecular_function 0.00e+00 0.00e+00 8/16
iron-sulfur cluster binding molecular_function 9.19e-04 1.87e-03 3/16
CoB--CoM heterodisulfide reductase activity molecular_function 0.00e+00 0.00e+00 3/16

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
ATP-proton motive force interconversion tigr sub1role 0.00e+00 0.00e+00 6/16
Energy metabolism tigr mainrole 0.00e+00 0.00e+00 6/16
Energy metabolism tigr mainrole 0.00e+00 0.00e+00 6/16
ATP-proton motive force interconversion tigr sub1role 0.00e+00 0.00e+00 6/16

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy production and conversion cog subcategory 0.00e+00 0.00e+00 14/16
Metabolism cog category 0.00e+00 0.00e+00 14/16
Metabolism cog category 0.00e+00 0.00e+00 14/16
Energy production and conversion cog subcategory 0.00e+00 0.00e+00 14/16
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 319

There are 16 genes in Module 319

Gene Member Table (16)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0774 atpC CDS 2794845 chromosome 864389 864793 - F0F1 ATP synthase subunit epsilon False
DVU0775 atpD CDS 2794846 chromosome 864805 866217 - F0F1 ATP synthase subunit beta False
DVU0776 atpG CDS 2794847 chromosome 866236 867111 - F0F1 ATP synthase subunit gamma False
DVU0777 atpA CDS 2794762 chromosome 867128 868636 - F0F1 ATP synthase subunit alpha False
DVU0778 atpH CDS 2794763 chromosome 868641 869192 - F0F1 ATP synthase subunit delta False
DVU0779 CDS 2794764 chromosome 869189 869719 - ATP synthase F0 subunit B False
DVU0780 CDS 2794765 chromosome 869792 870187 - ATP synthase F0 subunit B' False
DVU0845 CDS 2795196 chromosome 932782 933042 - hypothetical protein DVU0845 False
DVU0846 aprB CDS 2795197 chromosome 933076 933579 + adenylylsulphate reductase subunit beta False
DVU0847 aprA CDS 2795198 chromosome 933621 935615 + adenylylsulfate reductase subunit alpha False
DVU0848 CDS 2795199 chromosome 935761 936999 + heterodisulfide reductase False
DVU0849 CDS 2795200 chromosome 937006 939282 + heterodisulfide reductase, iron-sulfur-binding subunit False
DVU0850 CDS 2795201 chromosome 939296 940450 + heterodisulfide reductase, transmembrane subunit False
DVU0851 CDS 2794180 chromosome 940540 941286 + hypothetical protein DVU0851 False
DVU0918 atpB CDS 2794254 chromosome 1010942 1011643 - ATP synthase F0 subunit A False
DVU1636 ppaC CDS 2796100 chromosome 1717621 1718541 + manganese-dependent inorganic pyrophosphatase 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 319

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.