Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 289 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 289

There are 10 regulatory influences for Module 289

Regulator Table (10)
Regulator Name Type
DVU0230 tf
DVU0529 tf
DVU0629 tf
DVU0309 tf
DVU2359
DVU2690
combiner
DVU1754
DVU2802
combiner
DVU2036
DVU2251
combiner
DVU1754
DVU2989
combiner
DVU1967
DVU2989
combiner
DVU2359
DVUA0143
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
553 1.00e-06 acatgcaTgacAtAtGct.cc
Loader icon
RegPredict
554 1.80e+01 cggcaTcaagagCAT
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 289 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Two-component system kegg pathway 2.26e-03 7.75e-03 3/26
Bacterial chemotaxis kegg pathway 6.83e-04 4.18e-03 3/26
Signal Transduction kegg subcategory 2.26e-03 1.27e-02 3/26
Cell Motility kegg subcategory 6.26e-03 2.71e-02 3/26
Environmental Information Processing kegg category 2.87e-03 1.91e-02 5/26
Cellular Processes kegg category 6.26e-03 3.76e-02 3/26
Environmental Information Processing kegg category 2.73e-03 1.25e-02 5/26
Signal Transduction kegg subcategory 2.26e-03 1.12e-02 3/26
Two-component system kegg pathway 2.26e-03 1.12e-02 3/26
Cellular Processes kegg category 4.00e-03 1.52e-02 3/26
Cell Motility kegg subcategory 4.00e-03 1.52e-02 3/26
Bacterial chemotaxis kegg pathway 6.83e-04 5.78e-03 3/26

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
chemotaxis biological_process 4.77e-04 1.42e-03 3/26
signal transduction biological_process 8.89e-04 2.16e-03 3/26
DNA binding molecular_function 9.54e-03 1.43e-02 3/26
glutamate synthase (NADPH) activity molecular_function 0.00e+00 2.00e-06 3/26
signal transducer activity molecular_function 1.84e-04 5.22e-04 3/26

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cell motility cog subcategory 5.24e-03 4.97e-02 3/26
Amino acid transport and metabolism cog subcategory 4.53e-03 4.63e-02 5/26
Cell motility cog subcategory 5.24e-03 9.45e-03 3/26
Amino acid transport and metabolism cog subcategory 4.53e-03 8.23e-03 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 289

There are 26 genes in Module 289

Gene Member Table (26)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0093 CDS 2796242 chromosome 120692 123142 - glycosyl transferase domain-containing protein False
DVU0094 CDS 2796243 chromosome 123374 125536 + methyl-accepting chemotaxis protein False
DVU0525 CDS 2794891 chromosome 598268 598936 + MarR family transcriptional regulator True
DVU0673 CDS 2794697 chromosome 745815 745982 - hypothetical protein DVU0673 False
DVU1153 CDS 2794376 chromosome 1246834 1246944 - hypothetical protein DVU1153 False
DVU1154 CDS 2794377 chromosome 1246999 1247136 - hypothetical protein DVU1154 False
DVU1641 CDS 2796137 chromosome 1721579 1721902 + hypothetical protein DVU1641 False
DVU1642 CDS 2796138 chromosome 1721906 1722895 + hypothetical protein DVU1642 False
DVU1730 CDS 2795800 chromosome 1801234 1801539 + DNA-binding protein True
DVU1821 CDS 2793482 chromosome 1885906 1886661 - hypothetical protein DVU1821 False
DVU1822 CDS 2793483 chromosome 1886664 1887758 - glutamate synthase, amidotransferase subunit False
DVU1823 CDS 2793484 chromosome 1887773 1889296 - glutamate synthase, iron-sulfur cluster-binding subunit False
DVU2062 CDS 2796486 chromosome 2138236 2141694 + ATP-dependent DNA helicase UvrD False
DVU2072 cheA-3 CDS 2793449 chromosome 2154133 2157402 - chemotaxis protein CheA False
DVU2073 cheY-2 CDS 2793450 chromosome 2157498 2157866 - chemotaxis protein CheY False
DVU2074 CDS 2793451 chromosome 2157876 2158526 - chemotaxis protein CheW False
DVU2190 CDS 2795758 chromosome 2289318 2289512 - transcriptional regulator False
DVU2423 CDS 2794364 chromosome 2528735 2529214 + transcriptional regulator True
DVU2694 CDS 2793750 chromosome 2806364 2806798 + hypothetical protein DVU2694 False
DVU2742 livM CDS 2795944 chromosome 2847425 2848501 - high-affinity branched chain amino acid ABC transporter permease False
DVU2744 CDS 2794017 chromosome 2849554 2850711 - high-affinity branched-chain amino acid ABC transporter perisplasmic amino acid binding protein False
DVU3244 CDS 2793894 chromosome 3414449 3414784 - hypothetical protein DVU3244 False
DVU3289 CDS 2796013 chromosome 3464096 3464260 - hypothetical protein DVU3289 False
DVUA0082 CDS 2781531 pDV 109666 110697 - phage integrase family site specific recombinase False
DVUA0083 CDS 2781530 pDV 110806 110934 + hypothetical protein DVUA0083 False
DVUA0084 CDS 2781529 pDV 111110 111301 + AbrB family transcriptional regulator 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 289

Please add your comments for this module by using the form below. Your comments will be publicly available.

comments powered by Disqus
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.