Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 22 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 22

There are 11 regulatory influences for Module 22

Regulator Table (11)
Regulator Name Type
DVU3313 tf
DVU0804 tf
DVU1584
DVU1517
combiner
DVU3255
DVU1561
combiner
DVU2909
DVU0110
combiner
DVU2557
DVU2675
combiner
DVU2802
DVU0569
combiner
DVU2799 tf
DVU2909
DVU3193
combiner
DVU2802
DVU2989
combiner
DVU2675
DVU3313
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
43 1.40e-04 Gcatgct.ctTGCat
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RegPredict
44 8.70e+00 aAggGcGgGGaTGaCG.CTCTCc
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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 22 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Flagellar assembly kegg pathway 0.00e+00 0.00e+00 9/26
Cell Motility kegg subcategory 0.00e+00 0.00e+00 9/26
Cellular Processes kegg category 0.00e+00 0.00e+00 9/26
Cellular Processes kegg category 0.00e+00 0.00e+00 9/26
Cell Motility kegg subcategory 0.00e+00 0.00e+00 9/26
Flagellar assembly kegg pathway 0.00e+00 0.00e+00 9/26

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
ciliary or flagellar motility biological_process 2.00e-06 1.50e-05 4/26
flagellum assembly biological_process 0.00e+00 0.00e+00 3/26
structural molecule activity molecular_function 0.00e+00 0.00e+00 4/26

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Chemotaxis and motility tigr sub1role 0.00e+00 5.00e-06 4/26
Cellular processes tigr mainrole 2.10e-05 5.24e-04 4/26
Cellular processes tigr mainrole 2.10e-05 5.80e-05 4/26
Chemotaxis and motility tigr sub1role 0.00e+00 1.00e-06 4/26

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cell motility cog subcategory 0.00e+00 0.00e+00 10/26
Intracellular trafficking, secretion, and vesicular transport cog subcategory 2.37e-04 6.58e-03 4/26
Cellular processes and signaling cog category 0.00e+00 0.00e+00 19/26
Cellular processes and signaling cog category 9.00e-06 3.00e-05 14/26
Cell motility cog subcategory 0.00e+00 0.00e+00 10/26
Intracellular trafficking, secretion, and vesicular transport cog subcategory 2.37e-04 5.26e-04 4/26
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 22

There are 26 genes in Module 22

Gene Member Table (26)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0043 fliQ CDS 2796752 chromosome 50554 50823 - flagellar biosynthetic protein FliQ False
DVU0307 CDS 2794806 chromosome 351441 352937 + flagella basal body rod domain-containing protein False
DVU0309 CDS 2794808 chromosome 353856 354776 + LysR family transcriptional regulator True
DVU0318 CDS 2794176 chromosome 361450 362013 + hypothetical protein False
DVU0320 CDS 2794443 chromosome 363642 363902 - hypothetical protein DVU0320 False
DVU0325 hypD CDS 2794327 chromosome 367932 369029 + hydrogenase expression/formation protein HypD False
DVU0409 CDS 2793710 chromosome 458875 459225 - hypothetical protein DVU0409 False
DVU0410 CDS 2793711 chromosome 459231 459836 - hypothetical protein DVU0410 False
DVU0518 CDS 2794800 chromosome 592050 592514 + hypothetical protein DVU0518 False
DVU0520 CDS 2794802 chromosome 594622 596193 + flagellar hook-associated protein FlgL False
DVU0862 CDS 2796159 chromosome 953768 954673 - bifunctional flagellar protein FliS/hypothetical protein False
DVU0863 CDS 2796160 chromosome 954684 956411 - flagellar hook-associated protein 2 False
DVU1441 CDS 2794568 chromosome 1517815 1518711 - flagellin False
DVU1443 flgE CDS 2794570 chromosome 1519825 1521519 - flagellar hook protein FlgE False
DVU1444 flgD CDS 2794571 chromosome 1521577 1522374 - basal-body rod modification protein FlgD False
DVU1805 CDS 2796714 chromosome 1868457 1869920 + GGDEF domain-containing protein False
DVU1963 CDS 2793476 chromosome 2040758 2041039 - hypothetical protein DVU1963 False
DVU2065 CDS 2796489 chromosome 2145907 2146116 - hypothetical protein DVU2065 False
DVU2991 CDS 2796305 chromosome 3098789 3099880 + hypothetical protein DVU2991 False
DVU3001 CDS 2793714 chromosome 3112087 3112884 - hypothetical protein DVU3001 False
DVU3002 CDS 2793715 chromosome 3112881 3114029 - hypothetical protein DVU3002 False
DVU3004 CDS 2793717 chromosome 3115376 3117250 + radical SAM domain-containing protein False
DVU3005 CDS 2793718 chromosome 3117261 3118295 + aminotransferase False
DVU3006 CDS 2793719 chromosome 3118306 3119667 + polysaccharide biosynthesis protein/methyltransferase False
DVU3014 CDS 2793727 chromosome 3128580 3130673 + asparagine synthetase, glutamine-hydrolyzing False
DVU3232 flhA CDS 2793882 chromosome 3399495 3401606 - flagellar biosynthesis protein FlhA 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.