Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 57 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 57

There are 14 regulatory influences for Module 57

Regulator Table (14)
Regulator Name Type
DVU0813 tf
DVU1788 tf
DVU2644 tf
DVU0854
DVU3111
combiner
DVU0309 tf
DVU2086 tf
DVU0110 tf
DVU0619 tf
DVU0854 tf
DVU0813
DVU1745
combiner
DVU0813
DVU0230
combiner
DVU1628
DVU0813
combiner
DVU1518
DVU0813
combiner
DVU2567
DVU0813
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
111 2.40e-01 caCcaccGatGttatAcGGaAagC
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RegPredict
112 1.40e+02 TtgTC.GGGGTgGC
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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 57 is enriched for following functions.

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
DNA replication, recombination, and repair tigr sub1role 3.90e-04 1.51e-03 3/33
DNA metabolism tigr mainrole 5.24e-04 6.24e-03 3/33
DNA metabolism tigr mainrole 5.24e-04 1.04e-03 3/33
DNA replication, recombination, and repair tigr sub1role 3.90e-04 8.01e-04 3/33

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Replication, recombination and repair cog subcategory 1.32e-02 2.24e-02 3/33
Posttranslational modification, protein turnover, chaperones cog subcategory 8.48e-03 1.48e-02 3/33
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 57

There are 33 genes in Module 57

Gene Member Table (33)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0159 CDS 2795034 chromosome 196600 197121 - thioesterase family protein False
DVU0160 CDS 2795035 chromosome 197147 198142 - carbohydrate isomerase KpsF/GutQ family protein False
DVU0243 CDS 2796724 chromosome 275444 276112 + lipoprotein False
DVU0417 speA CDS 2796700 chromosome 468657 470636 + arginine decarboxylase False
DVU0483 CDS 2796550 chromosome 549943 552177 - DNA mismatch repair protein MutL False
DVU0801 uvrC CDS 2795096 chromosome 886202 888310 + excinuclease ABC subunit C False
DVU0855 CDS 2794184 chromosome 944578 945681 - radical SAM domain-containing protein False
DVU0856 hemB CDS 2794185 chromosome 945759 946751 - delta-aminolevulinic acid dehydratase False
DVU0864 CDS 2796161 chromosome 956549 957334 - glycoprotease family protein False
DVU0982 CDS 2793324 chromosome 1079062 1079721 - hypothetical protein DVU0982 False
DVU0985 CDS 2793327 chromosome 1081606 1081863 + hypothetical protein DVU0985 False
DVU0989 CDS 2794146 chromosome 1083778 1084218 - periplasmic divalent cation tolerance protein cutA False
DVU1091 CDS 2794070 chromosome 1195859 1196965 + hypothetical protein DVU1091 False
DVU1191 CDS 2796591 chromosome 1281920 1284490 - ATP-dependent protease La False
DVU1193 radC CDS 2796593 chromosome 1284798 1285475 - DNA repair protein RadC False
DVU1380 CDS 2795121 chromosome 1455113 1455343 - hypothetical protein DVU1380 False
DVU1381 CDS 2795122 chromosome 1455324 1455539 - hypothetical protein DVU1381 False
DVU1383 CDS 2795124 chromosome 1456016 1456441 + hypothetical protein DVU1383 False
DVU1401 CDS 2794653 chromosome 1470407 1471372 - hypothetical protein DVU1401 False
DVU1432 CDS 2795158 chromosome 1510471 1513065 - radical SAM domain-containing protein False
DVU1434 CDS 2795160 chromosome 1513301 1513666 - hypothetical protein DVU1434 False
DVU1466 argB CDS 2794884 chromosome 1545702 1546628 - acetylglutamate kinase False
DVU1580 CDS 2796192 chromosome 1662846 1663289 - ribose 5-phosphate isomerase False
DVU2261 CDS 2794083 chromosome 2354254 2356068 + hypothetical protein DVU2261 False
DVU2621 CDS 2795238 chromosome 2741758 2742570 + hypothetical protein DVU2621 False
DVU2639 CDS 2795695 chromosome 2755631 2755933 + hypothetical protein DVU2639 False
DVU2909 CDS 2794050 chromosome 3010822 3011235 + MarR family transcriptional regulator True
DVU3202 CDS 2796200 chromosome 3365112 3365948 + TatD family hydrolase False
DVU3283 CDS 2796007 chromosome 3459141 3459374 + hypothetical protein DVU3283 False
DVU3314 CDS 2796050 chromosome 3490740 3492716 - U32 family peptidase False
DVU3357 CDS 2795671 chromosome 3528914 3529111 - hypothetical protein DVU3357 False
DVU3358 CDS 2795672 chromosome 3529155 3529985 + ParA family protein False
DVU3359 CDS 2795673 chromosome 3529990 3530409 - hypothetical protein DVU3359 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 57

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.