Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 117 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 117

There are 13 regulatory influences for Module 117

Regulator Table (13)
Regulator Name Type
DVU0653 tf
DVU0946
DVU1760
combiner
DVU3167 tf
DVU3186 tf
DVU3023 tf
DVU2832
DVU1745
combiner
DVU0525 tf
DVU3186
DVU0653
combiner
DVU2788
DVU0946
combiner
DVU3167
DVU0916
combiner
DVU0946 tf
DVU0277
DVU0946
combiner
DVU0946
DVU2956
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
225 7.20e+00 cttgtcatcgctGTA
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RegPredict
226 1.30e+02 cgaTGCgctGccg.a.cggCt
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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 117 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism of Cofactors and Vitamins kegg subcategory 8.70e-03 3.30e-02 3/26
Metabolism of Cofactors and Vitamins kegg subcategory 8.43e-03 2.37e-02 3/26

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
catalytic activity molecular_function 4.50e-03 7.44e-03 3/26
ATP binding molecular_function 5.36e-03 8.66e-03 6/26

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Posttranslational modification, protein turnover, chaperones cog subcategory 3.54e-03 4.06e-02 3/26
Posttranslational modification, protein turnover, chaperones cog subcategory 3.54e-03 6.51e-03 3/26
Coenzyme transport and metabolism cog subcategory 1.07e-02 1.84e-02 3/26
General function prediction only cog subcategory 1.18e-02 2.01e-02 5/26
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 117

There are 26 genes in Module 117

Gene Member Table (26)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0007 asnC CDS 2793559 chromosome 9552 10937 - asparaginyl-tRNA synthetase False
DVU0110 CDS 2793309 chromosome 142672 144102 + sigma-54 dependent transcriptional regulator/response regulator True
DVU0156 CDS 2796698 chromosome 192240 194399 + ATP-dependent DNA helicase UvrD False
DVU0326 hypE CDS 2794328 chromosome 369036 370061 + hydrogenase expression/formation protein HypE False
DVU0413 CDS 2795176 chromosome 462411 463748 - TrkH family potassium uptake protein False
DVU0612 CDS 2794098 chromosome 681360 682580 - STAS domain-containing protein False
DVU0760 CDS 2793599 chromosome 851217 852347 - hypothetical protein DVU0760 False
DVU1376 ilvB-2 CDS 2793509 chromosome 1451544 1453235 + acetolactate synthase large subunit, biosynthetic type False
DVU1461 hemA CDS 2794879 chromosome 1540047 1541369 - glutamyl-tRNA reductase False
DVU1462 CDS 2794880 chromosome 1541371 1542102 - cytochrome c assembly protein False
DVU1463 CDS 2794881 chromosome 1542188 1542865 - siroheme synthase False
DVU1464 CDS 2794882 chromosome 1542988 1544223 + heptosyltransferase family protein False
DVU1544 CDS 2793694 chromosome 1611814 1614255 - mechanosensitive ion channel family protein False
DVU1883 CDS 2793552 chromosome 1953035 1953523 + hypothetical protein DVU1883 False
DVU2140 tmk CDS 2794219 chromosome 2237716 2238390 - thymidylate kinase False
DVU2329 hypB CDS 2793802 chromosome 2425178 2425852 + hydrogenase accessory protein HypB False
DVU2338 CDS 2793811 chromosome 2434492 2435172 - HhH-GPD family DNA repair protein False
DVU2491 CDS 2795459 chromosome 2601837 2603735 + ABC transporter ATP-binding protein False
DVU2765 CDS 2796315 chromosome 2873718 2874344 + metallo-beta-lactamase family protein False
DVU2766 CDS 2796316 chromosome 2874432 2874599 + hypothetical protein DVU2766 False
DVU2767 CDS 2796317 chromosome 2874596 2875210 + iron-sulfur flavoprotein False
DVU2932 CDS 2793970 chromosome 3036460 3037386 + hypothetical protein DVU2932 False
DVU3009 CDS 2793722 chromosome 3121963 3122946 + radical SAM domain-containing protein False
DVU3067 hypF CDS 2796418 chromosome 3202929 3205448 + [NiFe] hydrogenase maturation protein HypF [Desulfovibrio vulgaris str. Hildenborough] False
DVU3172 CDS 2795877 chromosome 3328360 3330507 + hypothetical protein DVU3172 False
DVU3216 CDS 2796214 chromosome 3383335 3385032 - sensor histidine kinase 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.