Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 291 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 291

There are 8 regulatory influences for Module 291

Regulator Table (8)
Regulator Name Type
DVU3066 tf
DVU0379
DVU1949
combiner
DVU2086
DVU2251
combiner
DVU3193
DVU0230
combiner
DVU2788
DVU2086
combiner
DVU3193
DVU2819
combiner
DVUA0100
DVU1949
combiner
DVU3193
DVU2832
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
557 2.20e+02 TgcCgTtgtCgcccggcCcGtgTt
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RegPredict
558 8.90e+03 tTTcCATgTgaAtC
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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 291 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolic pathways kegg pathway 3.48e-02 4.77e-02 7/31
Microbial metabolism in diverse environments kegg pathway 3.40e-03 9.54e-03 4/31
Amino Acid Metabolism kegg subcategory 3.25e-03 1.65e-02 5/31
Metabolism of Cofactors and Vitamins kegg subcategory 3.65e-04 3.73e-03 5/31
Metabolism kegg subcategory 6.86e-03 2.85e-02 12/31
Metabolism kegg category 1.52e-04 1.85e-03 16/31
Global kegg category 6.86e-03 4.00e-02 12/31
Metabolism kegg category 3.64e-03 1.44e-02 10/31
Metabolism of Cofactors and Vitamins kegg subcategory 3.47e-04 3.70e-03 5/31
Global kegg category 1.39e-02 3.29e-02 8/31
Metabolism kegg subcategory 1.39e-02 3.29e-02 8/31
Microbial metabolism in diverse environments kegg pathway 3.40e-03 1.39e-02 4/31

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
two-component signal transduction system (phosphorelay) biological_process 4.52e-03 7.92e-03 4/31
regulation of transcription, DNA-dependent biological_process 1.75e-03 3.68e-03 6/31
two-component sensor activity molecular_function 3.98e-03 6.67e-03 3/31
two-component response regulator activity molecular_function 1.02e-03 2.03e-03 4/31
RNA binding molecular_function 6.40e-04 1.39e-03 3/31
iron-sulfur cluster binding molecular_function 1.14e-02 1.67e-02 3/31

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Protein synthesis tigr mainrole 1.48e-02 3.84e-02 3/31
Protein synthesis tigr mainrole 1.48e-02 1.91e-02 3/31

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Coenzyme transport and metabolism cog subcategory 5.06e-04 1.07e-02 5/31
Metabolism cog category 5.65e-03 1.01e-02 13/31
Signal transduction mechanisms cog subcategory 5.38e-03 9.67e-03 6/31
Coenzyme transport and metabolism cog subcategory 5.06e-04 1.05e-03 5/31
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 291

There are 31 genes in Module 291

Gene Member Table (31)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0022 CDS 2794596 chromosome 24857 27238 - HAMP domain/GGDEF domain/EAL domain-containing protein False
DVU0364 pabA CDS 2793562 chromosome 413780 414334 - para-aminobenzoate/anthranilate synthase glutamine amidotransferase False
DVU0614 CDS 2794400 chromosome 683049 683330 - hypothetical protein DVU0614 False
DVU0679 CDS 2794171 chromosome 750641 752107 - sigma-54 dependent transcriptional regulator/response regulator True
DVU0680 CDS 2794172 chromosome 752095 754167 - sensory box histidine kinase False
DVU0681 CDS 2795331 chromosome 754029 756032 - sensor histidine kinase/response regulator False
DVU0733 CDS 2794947 chromosome 819244 819732 + hypothetical protein DVU0733 False
DVU0826 CDS 2796173 chromosome 915709 917031 - glycolate oxidase, iron-sulfur subunit False
DVU0827 CDS 2796174 chromosome 917179 918594 - glycolate oxidase subunit GlcD False
DVU0828 smpB CDS 2795492 chromosome 918623 919087 - SsrA-binding protein False
DVU0829 ptsI CDS 2795493 chromosome 919099 920871 - phosphoenolpyruvate-protein phosphotransferase False
DVU0890 hom CDS 2794202 chromosome 981134 982408 - homoserine dehydrogenase False
DVU0905 lipA CDS 2795415 chromosome 997479 998375 - lipoyl synthase False
DVU0924 rumA CDS 2794260 chromosome 1014520 1015926 - 23S rRNA (uracil-5-)-methyltransferase RumA False
DVU0933 CDS 2794633 chromosome 1023539 1024783 + response regulator False
DVU1352 CDS 2794918 chromosome 1430512 1430901 - 6-pyruvoyl tetrahydrobiopterin synthase False
DVU1386 CDS 2795127 chromosome 1457330 1458880 - hypothetical protein DVU1386 False
DVU1403 cobO CDS 2794655 chromosome 1472525 1473028 - cob(I)alamin adenosyltransferase False
DVU1999 CDS 2793438 chromosome 2079560 2081704 + sulfate transporter family protein False
DVU2036 CDS 2794834 chromosome 2116661 2116900 - CopG family transcriptinal regulator True
DVU2131 CDS 2795512 chromosome 2227823 2228302 + hypothetical protein DVU2131 False
DVU2314 CDS 2795274 chromosome 2407508 2407648 + hypothetical protein DVU2314 False
DVU2331 CDS 2793804 chromosome 2427033 2428262 + Smr family protein False
DVU2433 CDS 2795424 chromosome 2538257 2538379 - hypothetical protein DVU2433 False
DVU2525 hynB-2 CDS 2795615 chromosome 2636122 2637036 + periplasmic False
DVU2620 CDS 2795237 chromosome 2740315 2741475 + hypothetical protein DVU2620 False
DVU2748 cobM CDS 2794021 chromosome 2855627 2856400 - precorrin-4 C11-methyltransferase False
DVU2934 CDS 2793972 chromosome 3038778 3040196 + sigma-54 dependent transcriptional regulator/response regulator True
DVU3051 mutT CDS 2796077 chromosome 3176498 3176887 - mutator mutT protein False
DVU3237 CDS 2793887 chromosome 3406865 3409276 - phosphoenolpyruvate synthase-like protein False
DVU3363 sun CDS 2795677 chromosome 3532995 3534518 - sun protein 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.