Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 145 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 145

There are 9 regulatory influences for Module 145

Regulator Table (9)
Regulator Name Type
DVU0110 tf
DVU0653
DVU1690
combiner
DVU1518
DVU2086
combiner
DVU0653
DVU1063
combiner
DVU1517 tf
DVU1628 tf
DVU0230 tf
DVU1754
DVU3381
combiner
DVU2532
DVU0653
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
277 3.80e-01 atttctTgaTTgatcAaACagttt
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RegPredict
278 1.90e+02 cCcTgAccAcGcAac
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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 145 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 5.27e-03 1.22e-02 3/28
Membrane Transport kegg subcategory 1.56e-02 4.73e-02 3/28
Membrane Transport kegg subcategory 1.56e-02 3.55e-02 3/28
ABC transporters kegg pathway 5.27e-03 1.79e-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 1.69e-02 2.49e-02 3/28
peptidyl-histidine phosphorylation biological_process 1.04e-03 2.43e-03 3/28
two-component sensor activity molecular_function 2.72e-03 4.74e-03 3/28
NADH dehydrogenase (ubiquinone) activity molecular_function 1.20e-05 6.40e-05 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
Energy production and conversion cog subcategory 5.31e-03 4.97e-02 5/28
Inorganic ion transport and metabolism cog subcategory 1.27e-03 2.00e-02 4/28
Signal transduction mechanisms cog subcategory 1.28e-02 2.16e-02 5/28
Energy production and conversion cog subcategory 5.31e-03 9.55e-03 5/28
Inorganic ion transport and metabolism cog subcategory 1.27e-03 2.43e-03 4/28
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 145

There are 28 genes in Module 145

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0041 CDS 2796562 chromosome 47257 49020 - Slt family transglycosylase False
DVU0092 CDS 2796241 chromosome 117119 120436 - sensory box histidine kinase False
DVU0876 CDS 2795130 chromosome 967948 969612 - metallo-beta-lactamase family protein False
DVU0952 CDS 2795148 chromosome 1045296 1046168 + hypothetical protein DVU0952 False
DVU1057 CDS 2794903 chromosome 1158171 1158941 - cobalt ABC transporter permease False
DVU1058 cbiM CDS 2794770 chromosome 1158944 1159558 - cobalt transport protein CbiM False
DVU1460 CDS 2794878 chromosome 1539694 1540029 - hypothetical protein DVU1460 False
DVU1937 CDS 2795314 chromosome 2009605 2010618 - phosphonate ABC transporter periplasmic phosphonate-binding protein False
DVU2083 relA CDS 2793537 chromosome 2168573 2170726 - GTP pyrophosphokinase False
DVU2285 CDS 2795439 chromosome 2375226 2376746 - L-lactate permease family protein False
DVU2286 CDS 2795440 chromosome 2377289 2381050 + hydrogenase subunit CooM False
DVU2287 CDS 2795441 chromosome 2381054 2382019 + hydrogenase subunit CooK False
DVU2289 CDS 2795443 chromosome 2382468 2383103 + hydrogenase subunit CooX False
DVU2291 CDS 2795445 chromosome 2383642 2384742 + carbon monoxide-induced hydrogenase CooH False
DVU2328 CDS 2793801 chromosome 2424814 2425167 + hydrogenase nickel insertion protein HypA False
DVU2580 CDS 2794993 chromosome 2699014 2703135 + response regulator False
DVU2619 CDS 2795236 chromosome 2739486 2740214 + hypothetical protein DVU2619 False
DVU2944 CDS 2796495 chromosome 3047845 3049134 + ErfK/YbiS/YcfS/YnhG family protein False
DVU2945 CDS 2796496 chromosome 3049173 3050030 + hypothetical protein DVU2945 False
DVU2980 pssA CDS 2796294 chromosome 3086915 3087664 + CDP-diacylglycerol--serine O-phosphatidyltransferase False
DVU3005 CDS 2793718 chromosome 3117261 3118295 + aminotransferase False
DVU3157 CDS 2795862 chromosome 3313723 3315165 + hypothetical protein DVU3157 False
DVU3158 CDS 2795863 chromosome 3315162 3316049 + vacJ lipoprotein False
DVU3177 CDS 2793827 chromosome 3333673 3333822 + hypothetical protein DVU3177 False
DVU3190 CDS 2793840 chromosome 3349691 3351358 + hypothetical protein DVU3190 False
DVU3221 CDS 2796219 chromosome 3389703 3391229 - sensor histidine kinase False
DVU3273 CDS 2795997 chromosome 3450836 3451228 - hypothetical protein DVU3273 False
DVUA0138 CDS 2781579 pDV 179417 181501 - sensor histidine kinase 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.