Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 304 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 304

There are 10 regulatory influences for Module 304

Regulator Table (10)
Regulator Name Type
DVU2644 tf
DVU2934
DVU0621		 combiner
DVU1674
DVU3095		 combiner
DVU2319 tf
DVU3084 tf
DVU2547
DVU2934		 combiner
DVU3193
DVU2114		 combiner
DVU1645
DVU3193		 combiner
DVU2644
DVU2799		 combiner
DVU1674
DVU3186		 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
581 5.20e+04 TcCATGTCacA
Loader icon
 RegPredict
582 2.00e+04 CggaTGCCCTG
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 304 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolic pathways kegg pathway 7.47e-03 1.49e-02 8/29
Nucleotide Metabolism kegg subcategory 6.02e-04 5.33e-03 4/29
Metabolism kegg subcategory 1.05e-02 3.67e-02 11/29
Metabolism kegg category 2.12e-02 4.40e-02 8/29
Nucleotide Metabolism kegg subcategory 2.05e-03 1.06e-02 3/29
Global kegg category 8.77e-03 2.42e-02 8/29
Metabolism kegg subcategory 8.77e-03 2.42e-02 8/29
Metabolic pathways kegg pathway 7.47e-03 2.20e-02 8/29

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
iron-sulfur cluster binding molecular_function 8.99e-03 1.36e-02 3/29

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Purines, pyrimidines, nucleosides, and nucleotides tigr mainrole 1.04e-04 1.77e-03 3/29
Purines, pyrimidines, nucleosides, and nucleotides tigr mainrole 1.04e-04 2.41e-04 3/29

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Nucleotide transport and metabolism cog subcategory 7.20e-05 2.64e-03 4/29
Nucleotide transport and metabolism cog subcategory 7.20e-05 1.89e-04 4/29
Inorganic ion transport and metabolism cog subcategory 1.03e-02 1.77e-02 3/29
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 304

There are 29 genes in Module 304

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0055 ispH CDS 2794178 chromosome 61763 62635 + hydroxymethylbutenyl pyrophosphate reductase False
DVU0187 CDS 2795712 chromosome 231222 232313 - GGDEF domain-containing protein False
DVU0245 CDS 2794293 chromosome 277059 278168 - protein phosphatase False
DVU0412 CDS 2795175 chromosome 461688 462353 - potassium uptake protein TrkA False
DVU0584 CDS 2794161 chromosome 649275 650213 + transposase False
DVU0687 CDS 2795337 chromosome 761222 763006 + tungsten-containing aldehyde:ferredoxin oxidoreductase False
DVU0689 rnhA CDS 2793629 chromosome 763517 763987 + ribonuclease H False
DVU0749 CDS 2794967 chromosome 839102 840031 - DNA-binding response regulator True
DVU0897 CDS 2794115 chromosome 989827 991203 + RNA modification protein False
DVU0898 CDS 2794116 chromosome 991288 992169 + hypothetical protein DVU0898 False
DVU0900 gmk CDS 2794118 chromosome 992426 993049 + guanylate kinase False
DVU0901 pyrF CDS 2795411 chromosome 993049 993756 + orotidine 5`-phosphate decarboxylase False
DVU0922 CDS 2794258 chromosome 1013027 1013584 - cytochrome c family protein False
DVU0996 CDS 2794153 chromosome 1089448 1090323 - hypothetical protein DVU0996 False
DVU1188 CDS 2796588 chromosome 1277104 1277325 + hypothetical protein DVU1188 False
DVU1536 CDS 2793821 chromosome 1603093 1604229 + Slt family transglycosylase False
DVU2092 CDS 2795468 chromosome 2181488 2182129 - thiamine biosynthesis protein ThiF False
DVU2365 CDS 2796524 chromosome 2462435 2463259 - hypothetical protein DVU2365 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
DVU2543 CDS 2795730 chromosome 2653864 2655564 + hydroxylamine reductase False
DVU2739 CDS 2795941 chromosome 2842359 2845445 + pyruvate phosphate dikinase PEP/pyruvate binding subunit False
DVU2749 cobL CDS 2794022 chromosome 2856418 2857878 - precorrin-6Y C5,15-methyltransferase (decarboxylating) False
DVU2886 CDS 2793916 chromosome 2984227 2985066 + AraC family transcriptional regulator True
DVU2947 CDS 2796498 chromosome 3050747 3052816 - anaerobic ribonucleoside triphosphate reductase False
DVU2961 CDS 2796275 chromosome 3068386 3068733 + hypothetical protein DVU2961 False
DVU3010 CDS 2793723 chromosome 3122956 3124134 + aminotransferase False
DVU3229 fliA CDS 2793879 chromosome 3396820 3397617 - RNA polymerase sigma factor for flagellar operon FliA True
DVUA0072 CDS 2781606 pDV 96400 97737 - glycosyl transferase, group 1 family 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.