Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 220 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 220

There are 14 regulatory influences for Module 220

Regulator Table (14)
Regulator Name Type
DVU1759 tf
DVU2359
DVU0230		 combiner
DVU3167
DVU0309		 combiner
DVU3167
DVU0936		 combiner
DVU3167
DVUA0100		 combiner
DVU0569 tf
DVU3313
DVU0230		 combiner
DVU2532
DVU0653		 combiner
DVU0309
DVU0653		 combiner
DVU1561 tf
DVU1518
DVU1561		 combiner
DVU0230 tf
DVU0653
DVU2251		 combiner
DVU0653
DVU3305		 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
419 1.10e+02 Ctat.c.tTt.CgTTgct
Loader icon
 RegPredict
420 6.00e+02 GcCctCGTGcgGC.T
Loader icon
 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 220 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Citrate cycle (TCA cycle) kegg pathway 0.00e+00 9.00e-06 4/23
Metabolic pathways kegg pathway 5.00e-06 1.61e-04 11/23
Biosynthesis of secondary metabolites kegg pathway 5.05e-03 1.18e-02 4/23
Microbial metabolism in diverse environments kegg pathway 0.00e+00 1.00e-06 8/23
Carbohydrate Metabolism kegg subcategory 0.00e+00 7.00e-06 9/23
Amino Acid Metabolism kegg subcategory 0.00e+00 2.00e-06 9/23
Metabolism kegg subcategory 0.00e+00 0.00e+00 23/23
Metabolism kegg category 0.00e+00 0.00e+00 23/23
Global kegg category 0.00e+00 0.00e+00 23/23
Metabolism kegg category 3.00e-05 6.90e-04 11/23
Carbohydrate Metabolism kegg subcategory 1.00e-06 2.70e-05 7/23
Citrate cycle (TCA cycle) kegg pathway 0.00e+00 8.00e-06 4/23
Amino Acid Metabolism kegg subcategory 1.39e-03 8.73e-03 4/23
Global kegg category 7.00e-06 2.03e-04 11/23
Metabolism kegg subcategory 7.00e-06 2.03e-04 11/23
Metabolic pathways kegg pathway 5.00e-06 1.68e-04 11/23
Biosynthesis of secondary metabolites kegg pathway 5.05e-03 1.74e-02 4/23
Microbial metabolism in diverse environments kegg pathway 0.00e+00 1.00e-06 8/23

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
electron transport biological_process 8.40e-05 4.06e-04 6/23
electron carrier activity molecular_function 2.14e-04 5.77e-04 4/23
2-oxoglutarate synthase activity molecular_function 0.00e+00 0.00e+00 4/23
iron-sulfur cluster binding molecular_function 4.08e-04 9.65e-04 4/23

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Amino acid biosynthesis tigr mainrole 7.00e-06 2.07e-04 4/23
Amino acid biosynthesis tigr mainrole 7.00e-06 2.10e-05 4/23

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy production and conversion cog subcategory 0.00e+00 1.80e-05 9/23
Metabolism cog category 4.50e-05 1.13e-03 14/23
Metabolism cog category 1.16e-04 2.81e-04 13/23
Energy production and conversion cog subcategory 0.00e+00 1.00e-06 9/23
Amino acid transport and metabolism cog subcategory 1.23e-02 2.09e-02 4/23
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 220

There are 23 genes in Module 220

Gene Member Table (23)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU1094 argH CDS 2794073 chromosome 1199397 1200779 - argininosuccinate lyase False
DVU1095 argG CDS 2794339 chromosome 1200783 1201973 - argininosuccinate synthase False
DVU1653 CDS 2795924 chromosome 1732726 1735440 - polyA polymerase family protein False
DVU1913 CDS 2793686 chromosome 1987690 1988916 + aspartate kinase False
DVU2001 CDS 2793440 chromosome 2082778 2084039 + None False
DVU3024 CDS 2796441 chromosome 3143615 3143782 + hypothetical protein DVU3024 False
DVU3025 poR CDS 2796442 chromosome 3143767 3147414 + pyruvate-ferredoxin oxidoreductase False
DVU3026 CDS 2796443 chromosome 3147520 3149232 + L-lactate permease family protein False
DVU3027 glcD CDS 2796444 chromosome 3149407 3150792 + glycolate oxidase subunit GlcD False
DVU3028 CDS 2796445 chromosome 3150824 3152092 + iron-sulfur cluster-binding protein False
DVU3029 pta CDS 2796446 chromosome 3152216 3154330 + phosphate acetyltransferase False
DVU3030 ackA CDS 2796447 chromosome 3154356 3155564 + acetate kinase False
DVU3031 CDS 2796448 chromosome 3155664 3156755 + hypothetical protein DVU3031 False
DVU3032 CDS 2796449 chromosome 3156752 3157381 + hypothetical protein DVU3032 False
DVU3033 CDS 2796450 chromosome 3157385 3159538 + iron-sulfur cluster-binding protein False
DVU3197 ilvE CDS 2793847 chromosome 3359552 3360481 + branched-chain amino acid aminotransferase False
DVU3199 CDS 2796197 chromosome 3362483 3362794 + hypothetical protein DVU3199 False
DVU3200 recR CDS 2796198 chromosome 3362805 3363410 + recombination protein RecR False
DVU3235 CDS 2793885 chromosome 3403776 3404378 + IMP cyclohydrolase False
DVU3347 CDS 2796359 chromosome 3519266 3519814 - pyruvate ferredoxin/flavodoxin oxidoreductase family protein False
DVU3348 CDS 2796360 chromosome 3519814 3520596 - pyruvate ferredoxin/flavodoxin oxidoreductase subunit beta False
DVU3349 CDS 2796361 chromosome 3520596 3521669 - 2-ketoisovalerate ferredoxin reductase False
DVU3350 CDS 2795664 chromosome 3521673 3521906 - iron-sulfur cluster-binding protein 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.