Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 29 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 29

There are 11 regulatory influences for Module 29

Regulator Table (11)
Regulator Name Type
DVU0063 tf
DVU2423 tf
DVU1547
DVU3142
combiner
DVU0682 tf
DVU1572
DVU3255
combiner
DVU2275
DVU1949
combiner
DVU3255
DVU1690
combiner
DVU2547
DVU2588
combiner
DVU1949 tf
DVU0682
DVU3255
combiner
DVU2547
DVU3142
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
57 6.70e-01 aCaccGAAgaGAA.a
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RegPredict
58 3.20e+04 AaCaTAAAcTATA
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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 29 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Aminoacyl-tRNA biosynthesis kegg pathway 3.10e-05 6.12e-04 3/23
Metabolic pathways kegg pathway 5.36e-03 1.23e-02 7/23
Biosynthesis of secondary metabolites kegg pathway 2.65e-02 3.79e-02 3/23
Nucleotide Metabolism kegg subcategory 1.91e-04 2.41e-03 4/23
Translation kegg subcategory 1.95e-03 1.15e-02 3/23
Replication and Repair kegg subcategory 6.20e-04 5.38e-03 3/23
Metabolism kegg subcategory 3.80e-03 1.87e-02 10/23
Genetic Information Processing kegg category 1.50e-05 2.57e-04 7/23
Global kegg category 3.80e-03 2.47e-02 10/23
Nucleotide Metabolism kegg subcategory 8.34e-04 6.51e-03 3/23
Genetic Information Processing kegg category 5.42e-04 4.92e-03 5/23
Translation kegg subcategory 1.95e-03 1.03e-02 3/23
Aminoacyl-tRNA biosynthesis kegg pathway 3.10e-05 6.94e-04 3/23
Global kegg category 6.25e-03 1.97e-02 7/23
Metabolism kegg subcategory 6.25e-03 1.97e-02 7/23
Metabolic pathways kegg pathway 5.36e-03 1.81e-02 7/23

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
DNA-directed DNA polymerase activity molecular_function 0.00e+00 0.00e+00 14/23
ATP binding molecular_function 2.51e-03 4.41e-03 6/23

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
DNA replication, recombination, and repair tigr sub1role 9.10e-05 6.49e-04 3/23
tRNA aminoacylation tigr sub1role 2.30e-05 2.55e-04 3/23
DNA metabolism tigr mainrole 1.23e-04 2.05e-03 3/23
Protein synthesis tigr mainrole 5.81e-04 6.63e-03 4/23
DNA metabolism tigr mainrole 1.23e-04 2.82e-04 3/23
DNA replication, recombination, and repair tigr sub1role 9.10e-05 2.15e-04 3/23
Protein synthesis tigr mainrole 5.81e-04 1.14e-03 4/23
tRNA aminoacylation tigr sub1role 2.30e-05 6.30e-05 3/23

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Translation, ribosomal structure and biogenesis cog subcategory 3.02e-04 7.85e-03 5/23
Replication, recombination and repair cog subcategory 3.56e-03 4.07e-02 3/23
Information storage and processing cog category 3.10e-05 7.99e-04 9/23
Information storage and processing cog category 2.40e-05 7.90e-05 9/23
Translation, ribosomal structure and biogenesis cog subcategory 3.02e-04 6.57e-04 5/23
Replication, recombination and repair cog subcategory 3.56e-03 6.54e-03 3/23
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 29

There are 23 genes in Module 29

Gene Member Table (23)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0002 dnaN CDS 2794971 chromosome 1610 2764 + DNA polymerase III subunit beta False
DVU0003 gyrB CDS 2794972 chromosome 2766 5162 + DNA gyrase subunit B False
DVU0004 gyrA CDS 2794973 chromosome 5262 7832 + DNA gyrase subunit A False
DVU0161 purF CDS 2795036 chromosome 198445 199833 - amidophosphoribosyltransferase False
DVU0162 carB CDS 2796778 chromosome 199861 203094 - carbamoyl-phosphate synthase large subunit False
DVU0237 serS CDS 2795009 chromosome 270666 271940 - seryl-tRNA synthetase False
DVU0279 CDS 2794210 chromosome 322378 324084 + sulfate permease family protein False
DVU0502 CDS 2796762 chromosome 574371 574814 - hypothetical protein DVU0502 False
DVU0809 gatC CDS 2796532 chromosome 894941 895225 - glutamyl-tRNA(Gln) amidotransferase subunit C False
DVU0810 CDS 2796533 chromosome 895245 897305 - hypothetical protein DVU0810 False
DVU1062 CDS 2794774 chromosome 1163247 1164017 - hypothetical protein DVU1062 False
DVU1195 CDS 2796595 chromosome 1286583 1287101 - lipoprotein False
DVU1248 argS CDS 2795029 chromosome 1333990 1335645 - arginyl-tRNA synthetase False
DVU1576 ispE CDS 2796188 chromosome 1658357 1659217 - 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase False
DVU1584 CDS 2796196 chromosome 1666207 1667277 - sigma 70 family protein True
DVU1661 CDS 2795900 chromosome 1741334 1741528 + hypothetical protein DVU1661 False
DVU1666 efp CDS 2795905 chromosome 1745214 1745771 + elongation factor P False
DVU1889 gmhA CDS 2793558 chromosome 1961468 1962094 + phosphoheptose isomerase False
DVU1893 CDS 2794704 chromosome 1965307 1967727 + ATP-dependent protease False
DVU2339 CDS 2793812 chromosome 2435422 2436273 - ribosomal protein L11 methyltransferase False
DVU3275 CDS 2795999 chromosome 3451893 3452033 - hypothetical protein DVU3275 False
DVU3307 ubiX CDS 2796043 chromosome 3484853 3485416 + 3-octaprenyl-4-hydroxybenzoate carboxy-lyase False
DVU3395 CDS 2796414 chromosome 3569404 3570714 - M24/M37 family peptidase 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 29

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

comments powered by Disqus
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.