Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 125 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 125

There are 10 regulatory influences for Module 125

Regulator Table (10)
Regulator Name Type
DVU1584
DVU0269
combiner
DVU2547
DVU2989
combiner
DVU2423
DVU1419
combiner
DVU3255
DVU3186
combiner
DVU0309
DVU0621
combiner
DVU3255
DVU1156
combiner
DVU2802
DVU0539
combiner
DVU0309
DVU2989
combiner
DVU2547
DVU0539
combiner
DVU3255
DVU1584
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
241 2.10e+01 cTGcCGGcatccTGcCCgCatCa
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RegPredict
242 4.90e+00 TC.gcACa.TGcaatagaAagGg
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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 125 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 12/19
Cell Motility kegg subcategory 0.00e+00 0.00e+00 13/19
Cellular Processes kegg category 0.00e+00 0.00e+00 13/19
Cellular Processes kegg category 0.00e+00 0.00e+00 12/19
Cell Motility kegg subcategory 0.00e+00 0.00e+00 12/19
Flagellar assembly kegg pathway 0.00e+00 0.00e+00 12/19

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
ciliary or flagellar motility biological_process 0.00e+00 0.00e+00 12/19
metabolic process biological_process 4.23e-03 7.51e-03 3/19
motor activity molecular_function 0.00e+00 0.00e+00 10/19
structural molecule activity molecular_function 0.00e+00 0.00e+00 5/19
iron-sulfur cluster binding molecular_function 1.83e-03 3.35e-03 3/19

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Chemotaxis and motility tigr sub1role 0.00e+00 0.00e+00 7/19
Cellular processes tigr mainrole 0.00e+00 0.00e+00 7/19
Cellular processes tigr mainrole 0.00e+00 0.00e+00 7/19
Chemotaxis and motility tigr sub1role 0.00e+00 0.00e+00 7/19

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 10/19
Intracellular trafficking, secretion, and vesicular transport cog subcategory 4.70e-05 1.89e-03 4/19
Cellular processes and signaling cog category 0.00e+00 0.00e+00 15/19
Cellular processes and signaling cog category 2.00e-05 6.60e-05 11/19
Cell motility cog subcategory 0.00e+00 0.00e+00 10/19
Intracellular trafficking, secretion, and vesicular transport cog subcategory 4.70e-05 1.40e-04 4/19
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 125

There are 19 genes in Module 125

Gene Member Table (19)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0310 fliI CDS 2794809 chromosome 354912 356225 - flagellum-specific ATP synthase FliI False
DVU0311 CDS 2796755 chromosome 356222 356974 - flagellar assembly protein FliH False
DVU0312 fliG CDS 2796756 chromosome 356961 357977 - flagellar motor switch protein FliG False
DVU0313 fliF CDS 2796757 chromosome 357946 359562 - flagellar M-ring protein FliF False
DVU0314 fliE CDS 2796758 chromosome 359614 359949 - flagellar basal body component FliE False
DVU0315 flgC CDS 2796759 chromosome 359964 360401 - flagellar basal-body rod protein FlgC False
DVU0512 CDS 2794304 chromosome 585708 586490 + flagellar basal-body rod protein False
DVU0513 flgG CDS 2794305 chromosome 586547 587329 + flagellar basal body rod protein FlgG False
DVU0515 flgH CDS 2794307 chromosome 588330 589046 + flagellar basal body L-ring protein False
DVU0516 flgI CDS 2794308 chromosome 589056 590192 + flagellar basal body P-ring protein False
DVU0517 CDS 2794799 chromosome 590194 592026 + M24/M37 family peptidase False
DVU0519 CDS 2794801 chromosome 592514 594610 + flagellar hook-associated protein FlgK False
DVU0913 CDS 2794666 chromosome 1007363 1007800 - hypothetical protein DVU0913 False
DVU2232 CDS 2795559 chromosome 2325641 2326009 + hypothetical protein DVU2232 False
DVU3003 CDS 2793716 chromosome 3114085 3115197 - radical SAM domain-containing protein False
DVU3004 CDS 2793717 chromosome 3115376 3117250 + radical SAM domain-containing protein False
DVU3018 CDS 2793731 chromosome 3133841 3134974 - radical SAM domain-containing protein False
DVU3019 CDS 2793732 chromosome 3135056 3136513 - radical SAM/B12 binding domain-containing protein False
DVU3020 CDS 2793733 chromosome 3136549 3136917 - hypothetical protein DVU3020 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 125

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.