Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 211 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 211

There are 10 regulatory influences for Module 211

Regulator Table (10)
Regulator Name Type
DVU2423
DVU0621		 combiner
DVU2567
DVU0621		 combiner
DVU0269
DVU2633		 combiner
DVU0309
DVU0744		 combiner
DVU0309
DVU3142		 combiner
DVU1572
DVU2106		 combiner
DVU3186
DVU2106		 combiner
DVU2686
DVU3255		 combiner
DVU2909
DVU0621		 combiner
DVU1572
DVU0936		 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
403 1.30e+00 tGccgTG.CtGacg
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 RegPredict
404 2.90e+04 agGgCAtCcgtCccG
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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 211 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
ABC transporters kegg pathway 1.02e-03 5.31e-03 4/31
Amino Acid Metabolism kegg subcategory 8.10e-05 1.31e-03 7/31
Membrane Transport kegg subcategory 6.04e-04 5.33e-03 5/31
Environmental Information Processing kegg category 1.47e-03 1.15e-02 6/31
Environmental Information Processing kegg category 6.89e-03 2.10e-02 5/31
Membrane Transport kegg subcategory 6.04e-04 5.35e-03 5/31
ABC transporters kegg pathway 1.02e-03 7.41e-03 4/31

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
DNA binding molecular_function 3.04e-03 5.26e-03 4/31

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Transport and binding proteins tigr mainrole 6.65e-04 7.10e-03 4/31
Transport and binding proteins tigr mainrole 6.65e-04 1.29e-03 4/31

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Inorganic ion transport and metabolism cog subcategory 1.30e-02 2.20e-02 3/31
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 211

There are 31 genes in Module 211

Gene Member Table (31)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0031 CDS 2793311 chromosome 38186 39172 + AzlC family protein False
DVU0032 CDS 2795101 chromosome 39162 39497 + hypothetical protein DVU0032 False
DVU0393 ung CDS 2794249 chromosome 441512 442501 + uracil-DNA glycosylase False
DVU0647 CDS 2795037 chromosome 717840 718754 - iron compound ABC transporter periplasmic iron compount-binding protein False
DVU0655 CDS 2794241 chromosome 727882 728748 - phosphotransferase domain-containing protein False
DVU0757 CDS 2793596 chromosome 848797 849117 + hypothetical protein DVU0757 False
DVU0814 CDS 2795017 chromosome 901535 902020 - bacterioferritin comigratory protein False
DVU0978 CDS 2795110 chromosome 1073542 1074396 + ABC transporter periplasmic substrate-binding protein False
DVU0982 CDS 2793324 chromosome 1079062 1079721 - hypothetical protein DVU0982 False
DVU1188 CDS 2796588 chromosome 1277104 1277325 + hypothetical protein DVU1188 False
DVU1401 CDS 2794653 chromosome 1470407 1471372 - hypothetical protein DVU1401 False
DVU1437 CDS 2795163 chromosome 1515334 1515432 + hypothetical protein DVU1437 False
DVU1445 CDS 2794572 chromosome 1522387 1523982 - flagellar hook-length control domain-containing protein False
DVU1938 CDS 2795315 chromosome 2010900 2011175 - hypothetical protein DVU1938 False
DVU2419 CDS 2794360 chromosome 2526617 2527171 - hypothetical protein DVU2419 False
DVU2477 pstS CDS 2795659 chromosome 2585915 2586727 + phosphate ABC transporter periplasmic phosphate-binding protein PstS False
DVU2479 CDS 2795661 chromosome 2587787 2588716 + phosphate ABC transporter permease False
DVU2822 CDS 2793783 chromosome 2927266 2928276 + TRAP transporter solute receptor DctP False
DVU2824 CDS 2793785 chromosome 2930367 2932853 + formate acetyltransferase False
DVU3014 CDS 2793727 chromosome 3128580 3130673 + asparagine synthetase, glutamine-hydrolyzing False
DVU3073 CDS 2796424 chromosome 3216311 3217222 + hypothetical protein DVU3073 False
DVU3209 CDS 2796207 chromosome 3375196 3375291 + hypothetical protein DVU3209 False
DVU3219 CDS 2796217 chromosome 3387054 3388256 - hypothetical protein DVU3219 False
DVU3223 aspB CDS 2796221 chromosome 3392687 3393859 - aspartate aminotransferase False
DVU3284 CDS 2796008 chromosome 3459535 3461166 - L-lactate permease False
DVU3360 CDS 2795674 chromosome 3530486 3531400 + ParB family protein False
DVU3361 CDS 2795675 chromosome 3531411 3532436 + ADP-heptose synthase False
DVUA0086 CDS 2781566 pDV 114998 116089 - response regulator False
DVUA0097 CDS 2781621 pDV 130707 132206 + radical SAM domain-containing protein False
DVUA0114 CDS 2781616 pDV 153041 153250 + hypothetical protein DVUA0114 False
DVUA0117 escJ CDS 2781475 pDV 154970 155785 + type III secretion lipoprotein 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.