Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 5 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 5

There are 13 regulatory influences for Module 5

Regulator Table (13)
Regulator Name Type
DVU2275 tf
DVU1572
DVU2423		 combiner
DVU1572
DVU3313		 combiner
DVU1561
DVU0118		 combiner
DVU1745 tf
DVU2557 tf
DVU1730 tf
DVU1759 tf
DVU2989 tf
DVU2423
DVU3313		 combiner
DVU1759
DVU2275		 combiner
DVU2111
DVU1964		 combiner
DVU2275
DVU0057		 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
9 6.40e+00 cTtgtttG.AAG.gaaTaaat.ga
Loader icon
 RegPredict
10 2.30e+03 CtCACaCCACAaAC
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 5 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Biosynthesis of secondary metabolites kegg pathway 2.98e-02 4.21e-02 4/35

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
sequence-specific DNA binding transcription factor activity molecular_function 1.00e-02 1.50e-02 3/35
GTP binding molecular_function 1.46e-04 4.39e-04 3/35

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
General tigr sub1role 7.24e-04 2.20e-03 3/35
Transport and binding proteins tigr mainrole 1.18e-03 1.04e-02 4/35
Unknown function tigr mainrole 2.45e-03 1.40e-02 3/35
Transport and binding proteins tigr mainrole 1.18e-03 2.17e-03 4/35
Unknown function tigr mainrole 2.45e-03 4.08e-03 3/35
General tigr sub1role 7.24e-04 1.39e-03 3/35

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Transcription cog subcategory 1.68e-02 2.78e-02 3/35
Cell wall/membrane/envelope biogenesis cog subcategory 1.79e-02 2.94e-02 4/35
General function prediction only cog subcategory 1.48e-02 2.48e-02 6/35
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 5

There are 35 genes in Module 5

Gene Member Table (35)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0036 CDS 2796464 chromosome 42287 42742 - hypothetical protein DVU0036 False
DVU0052 era CDS 2794512 chromosome 56847 57773 - GTP-binding protein Era False
DVU0057 CDS 2793369 chromosome 63889 64530 + TetR family transcriptional regulator True
DVU0060 CDS 2796165 chromosome 69540 70724 + RND family efflux transporter MFP subunit False
DVU0061 CDS 2794399 chromosome 70740 73880 + multidrug resistance protein False
DVU0062 CDS 2796166 chromosome 73877 75391 + RND efflux system outer membrane lipoprotein False
DVU0063 CDS 2793612 chromosome 75421 75861 + MarR family transcriptional regulator True
DVU0064 CDS 2793613 chromosome 75950 76858 + hypothetical protein DVU0064 False
DVU0085 trpB-1 CDS 2793579 chromosome 104165 105409 + tryptophan synthase subunit beta False
DVU0602 CDS 2793363 chromosome 672841 673203 - hypothetical protein DVU0602 False
DVU0603 CDS 2793364 chromosome 673432 673698 - hypothetical protein DVU0603 False
DVU0872 CDS 2795171 chromosome 964110 964877 - glycosyl transferase group 2 family protein False
DVU1009 CDS 2794647 chromosome 1104647 1105261 - hypothetical protein DVU1009 False
DVU1454 ispD CDS 2794820 chromosome 1532607 1533794 - 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase False
DVU1571 rho CDS 2793462 chromosome 1653748 1655037 - transcription termination factor Rho False
DVU1617 CDS 2795878 chromosome 1702244 1702837 + nitroreductase family protein False
DVU1618 CDS 2795879 chromosome 1702850 1703254 + iojap-like protein False
DVU1619 gpmA CDS 2795880 chromosome 1703251 1704786 + phosphoglyceromutase False
DVU1851 CDS 2795914 chromosome 1918806 1920128 + M24/M37 family peptidase False
DVU2130 CDS 2795511 chromosome 2226864 2227526 - hypothetical protein DVU2130 False
DVU2148 CDS 2793407 chromosome 2246009 2247403 + hypothetical protein DVU2148 False
DVU2208 CDS 2793671 chromosome 2303762 2303875 - hypothetical protein DVU2208 False
DVU2274 CDS 2795230 chromosome 2363792 2363929 - hypothetical protein DVU2274 False
DVU2284 CDS 2795438 chromosome 2374291 2374803 + hypothetical protein DVU2284 False
DVU2299 CDS 2795345 chromosome 2392994 2394187 - glycine/betaine/L-proline ABC transporter ATP binding protein False
DVU2634 CDS 2795251 chromosome 2749602 2749853 + hypothetical protein DVU2634 False
DVU2671 CDS 2796238 chromosome 2781727 2783286 + phosphodiesterase False
DVU2904 CDS 2793934 chromosome 3004734 3005828 + ribosomal RNA large subunit methyltransferase N False
DVU3151 CDS 2795856 chromosome 3303547 3304839 - tRNA modifying protein False
DVU3194 engA CDS 2793844 chromosome 3355181 3356656 + GTP-binding protein EngA False
DVU3204 purA CDS 2796202 chromosome 3367232 3368512 - adenylosuccinate synthetase False
DVU3205 CDS 2796203 chromosome 3368755 3370200 + transglycosylase False
DVU3206 CDS 2796204 chromosome 3370503 3372035 + phosphoribosylaminoimidazolecarboxamide formyltransferase False
DVU3212 CDS 2796210 chromosome 3377699 3379408 + pyridine nucleotide-disulfide oxidoreductase False
DVU3313 CDS 2796049 chromosome 3489178 3490068 - LysR family transcriptional regulator True

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.