Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 198 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 198

There are 14 regulatory influences for Module 198

Regulator Table (14)
Regulator Name Type
DVU0916 tf
DVU2547
DVU0619
combiner
DVU2275 tf
DVU0309
DVU2275
combiner
DVU2934 tf
DVUA0151 tf
DVU0063
DVU0529
combiner
DVU2547 tf
DVU2557 tf
DVUA0143
DVU2989
combiner
DVU2547
DVU1628
combiner
DVU2547
DVU0946
combiner
DVU0529
DVU2989
combiner
DVU2036
DVU2547
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
379 3.50e+01 CAAgGAgCaca
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RegPredict
380 2.20e+04 TcTTCaGg
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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 198 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Bacterial chemotaxis kegg pathway 3.22e-03 9.24e-03 3/39
Cell Motility kegg subcategory 5.05e-03 2.29e-02 4/39
Cellular Processes kegg category 5.05e-03 3.15e-02 4/39
Cellular Processes kegg category 1.71e-02 3.78e-02 3/39
Cell Motility kegg subcategory 1.71e-02 3.78e-02 3/39
Bacterial chemotaxis kegg pathway 3.22e-03 1.35e-02 3/39

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
two-component signal transduction system (phosphorelay) biological_process 2.41e-03 4.77e-03 5/39
regulation of transcription, DNA-dependent biological_process 6.86e-03 1.14e-02 6/39
chemotaxis biological_process 2.28e-03 4.56e-03 3/39
signal transduction biological_process 4.14e-03 7.39e-03 3/39
peptidyl-histidine phosphorylation biological_process 3.66e-03 6.65e-03 3/39
two-component response regulator activity molecular_function 4.08e-04 9.65e-04 5/39
sequence-specific DNA binding transcription factor activity molecular_function 2.40e-03 4.26e-03 4/39
ATP binding molecular_function 1.66e-02 2.31e-02 7/39
transcription factor binding molecular_function 3.90e-05 1.77e-04 4/39
nucleoside-triphosphatase activity molecular_function 4.31e-04 1.00e-03 4/39

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains cog 1.42e-04 1.85e-04 3/39
Signal transduction mechanisms cog subcategory 1.00e-05 4.62e-04 11/39
Cellular processes and signaling cog category 1.01e-03 1.92e-02 16/39
Cellular processes and signaling cog category 8.23e-04 1.63e-03 15/39
Signal transduction mechanisms cog subcategory 1.00e-05 3.40e-05 11/39
Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains cog 1.42e-04 3.38e-04 3/39
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 198

There are 39 genes in Module 198

Gene Member Table (39)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0112 CDS 2794981 chromosome 145051 146475 + deoxyribodipyrimidine photolyase False
DVU0221 CDS 2795301 chromosome 260765 261208 + tail fiber assembly protein False
DVU0540 CDS 2795577 chromosome 611436 613847 - sensor histidine kinase False
DVU0608 CDS 2794094 chromosome 676751 678784 - methyl-accepting chemotaxis protein False
DVU0615 CDS 2794401 chromosome 683330 683494 + hypothetical protein DVU0615 False
DVU0619 CDS 2794405 chromosome 684470 685909 - sigma-54 dependent transcriptional regulator True
DVU0676 CDS 2794168 chromosome 748069 748956 + His/Glu/Gln/Arg/opine ABC transporter permease False
DVU0683 CDS 2795333 chromosome 757279 758130 - hflC protein False
DVU0721 CDS 2793620 chromosome 800645 803455 + sensory box histidine kinase False
DVU0741 CDS 2795257 chromosome 829146 829622 + hypothetical protein DVU0741 False
DVU0744 CDS 2795260 chromosome 832468 834177 + sigma-54 dependent transcriptional regulator/response regulator True
DVU0755 CDS 2793594 chromosome 846505 847872 - sensor histidine kinase False
DVU0803 CDS 2795098 chromosome 888532 889797 + sensor histidine kinase False
DVU0855 CDS 2794184 chromosome 944578 945681 - radical SAM domain-containing protein False
DVU0903 CDS 2795413 chromosome 994751 995608 + HD domain-containing protein False
DVU0910 fliM CDS 2794663 chromosome 1004227 1005207 + flagellar motor switch protein FliM False
DVU0992 cheV-3 CDS 2794149 chromosome 1086193 1087155 + chemotaxis protein CheV False
DVU1279 folP CDS 2794345 chromosome 1371953 1372813 + dihydropteroate synthase False
DVU1338 CDS 2794586 chromosome 1415889 1416473 - hypothetical protein DVU1338 False
DVU1447 CDS 2794574 chromosome 1525525 1527234 - CgeB family protein False
DVU1448 CDS 2794575 chromosome 1527231 1528367 - hypothetical protein DVU1448 False
DVU1549 CDS 2794865 chromosome 1625478 1626230 + hypothetical protein DVU1549 False
DVU1771 hydC CDS 2795818 chromosome 1834384 1836204 - [Fe] hydrogenase gamma [Desulfovibrio vulgaris str. Hildenborough] False
DVU1803 CDS 2796712 chromosome 1865370 1866458 - glycosyl transferase group 1 family protein False
DVU1830 CDS 2793491 chromosome 1895706 1896770 + hypothetical protein DVU1830 False
DVU1939 CDS 2795316 chromosome 2011221 2012504 - anaerobic glycerol-3-phosphate dehydrogenase subunit B False
DVU1986 CDS 2793792 chromosome 2064529 2064960 + hypothetical protein DVU1986 False
DVU2019 CDS 2793354 chromosome 2096176 2098245 - hypothetical protein DVU2019 False
DVU2091 thiE-1 CDS 2793545 chromosome 2180539 2181219 - thiamine-phosphate pyrophosphorylase False
DVU2142 surE CDS 2794221 chromosome 2239541 2240293 + acid phosphatase SurE False
DVU2361 CDS 2796520 chromosome 2459206 2459352 - hypothetical protein DVU2361 False
DVU2391 CDS 2795294 chromosome 2493730 2493873 - hypothetical protein DVU2391 False
DVU2763 CDS 2794036 chromosome 2870485 2873160 - TPR/GGDEF domain-containing protein False
DVU2813 CDS 2793774 chromosome 2917842 2917940 - hypothetical protein DVU2813 False
DVU2934 CDS 2793972 chromosome 3038778 3040196 + sigma-54 dependent transcriptional regulator/response regulator True
DVU3220 CDS 2796218 chromosome 3388327 3389706 - sigma-54 dependent transcriptional regulator/response regulator True
DVU3222 pgi CDS 2796220 chromosome 3391257 3392600 - glucose-6-phosphate isomerase False
DVU3225 CDS 2793875 chromosome 3394894 3395316 - hypothetical protein DVU3225 False
DVU3266 CDS 2793870 chromosome 3441602 3442393 - hypothetical protein DVU3266 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 198

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.