Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 172 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 172

There are 10 regulatory influences for Module 172

Regulator Table (10)
Regulator Name Type
DVU1674 tf
DVU0813 tf
DVU0653 tf
DVU0110 tf
DVU2086 tf
DVU1788 tf
DVU1674
DVU0525
combiner
DVU0230 tf
DVU2359
DVU2690
combiner
DVU1518
DVU1730
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
329 1.30e-02 aGCaTaCaCccCcagAaCAggAca
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RegPredict
330 7.80e-01 TAcTtaaCaTCATttCtGtGATAA
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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 172 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Purine metabolism kegg pathway 4.66e-04 3.24e-03 3/28
Metabolic pathways kegg pathway 1.50e-03 6.28e-03 9/28
Biosynthesis of secondary metabolites kegg pathway 3.66e-04 2.88e-03 6/28
Carbohydrate Metabolism kegg subcategory 8.41e-04 6.70e-03 6/28
Nucleotide Metabolism kegg subcategory 4.60e-05 8.51e-04 5/28
Amino Acid Metabolism kegg subcategory 3.60e-05 7.15e-04 7/28
Replication and Repair kegg subcategory 1.34e-03 9.14e-03 3/28
Metabolism kegg subcategory 1.00e-06 2.60e-05 17/28
Metabolism kegg category 0.00e+00 0.00e+00 20/28
Global kegg category 1.00e-06 2.10e-05 17/28
Metabolism kegg category 1.41e-03 8.83e-03 10/28
Carbohydrate Metabolism kegg subcategory 2.75e-03 1.26e-02 4/28
Nucleotide Metabolism kegg subcategory 1.79e-03 9.91e-03 3/28
Purine metabolism kegg pathway 4.66e-04 4.41e-03 3/28
Amino Acid Metabolism kegg subcategory 3.49e-03 1.42e-02 4/28
Global kegg category 4.19e-04 4.21e-03 10/28
Metabolism kegg subcategory 4.19e-04 4.21e-03 10/28
Metabolic pathways kegg pathway 1.50e-03 9.02e-03 9/28
Biosynthesis of secondary metabolites kegg pathway 3.66e-04 3.84e-03 6/28

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 14/28

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Amino acid transport and metabolism cog subcategory 2.79e-02 4.41e-02 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 172

There are 28 genes in Module 172

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0255 CDS 2794502 chromosome 290357 290911 + hypothetical protein DVU0255 False
DVU0492 argC CDS 2793706 chromosome 561263 562327 - N-acetyl-gamma-glutamyl-phosphate reductase False
DVU0495 CDS 2794723 chromosome 563891 565087 - hypothetical protein DVU0495 False
DVU0654 CDS 2794240 chromosome 726616 727842 - U32 family peptidase False
DVU0697 CDS 2794448 chromosome 771808 773226 - mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase False
DVU0876 CDS 2795130 chromosome 967948 969612 - metallo-beta-lactamase family protein False
DVU0897 CDS 2794115 chromosome 989827 991203 + RNA modification protein False
DVU0898 CDS 2794116 chromosome 991288 992169 + hypothetical protein DVU0898 False
DVU0899 CDS 2794117 chromosome 992166 992426 + hypothetical protein DVU0899 False
DVU0900 gmk CDS 2794118 chromosome 992426 993049 + guanylate kinase False
DVU1000 CDS 2795116 chromosome 1096059 1097282 - M24 family peptidase False
DVU1001 CDS 2795117 chromosome 1097428 1097832 + coenzyme A binding protein False
DVU1002 CDS 2795118 chromosome 1097829 1098284 + hypothetical protein DVU1002 False
DVU1003 CDS 2795119 chromosome 1098299 1099285 + dnaJ domain-containing protein False
DVU1182 CDS 2796667 chromosome 1272491 1273405 - hypothetical protein DVU1182 False
DVU1266 CDS 2793586 chromosome 1354391 1357828 - hypothetical protein DVU1266 False
DVU1268 CDS 2793588 chromosome 1358519 1358932 - hypothetical protein DVU1268 False
DVU1269 CDS 2793589 chromosome 1359012 1359146 + hypothetical protein DVU1269 False
DVU1353 dnaE CDS 2794919 chromosome 1430903 1434397 - DNA polymerase III subunit alpha False
DVU1914 CDS 2793687 chromosome 1988931 1990547 + alpha-isopropylmalate/homocitrate synthase family transferase False
DVU2674 CDS 2795045 chromosome 2785734 2786453 + succinate dehydrogenase and fumarate reductase iron-sulfur protein False
DVU2677 CDS 2795048 chromosome 2788003 2789466 + sensor histidine kinase/response regulator False
DVU3048 asd CDS 2796074 chromosome 3174209 3175258 - aspartate-semialdehyde dehydrogenase False
DVU3156 glmS CDS 2795861 chromosome 3311611 3313434 + glucosamine--fructose-6-phosphate aminotransferase (isomerizing) False
DVU3178 CDS 2793828 chromosome 3333906 3334529 + hypothetical protein DVU3178 False
DVU3179 ispB CDS 2793829 chromosome 3334550 3335515 + octaprenyl-diphosphate synthase False
DVU3192 CDS 2793842 chromosome 3352605 3353765 + glycosyl transferase group 1 family protein False
DVU3379 CDS 2796398 chromosome 3551477 3553810 - ribonucleotide-diphosphate reductase subunit alpha 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 172

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.