Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 136 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 136

There are 8 regulatory influences for Module 136

Regulator Table (8)
Regulator Name Type
DVU0621
DVU1744
combiner
DVU2114 tf
DVU1628 tf
DVU1674
DVU2086
combiner
DVU2527
DVU2114
combiner
DVU0030 tf
DVU1674
DVU3186
combiner
DVU2577
DVU3095
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
263 1.00e+01 CATGaAgagaGgagAaaac
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RegPredict
264 2.40e+03 GaaGaggtcAtacgc
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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 136 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Bacterial secretion system kegg pathway 0.00e+00 0.00e+00 8/28
Membrane Transport kegg subcategory 0.00e+00 8.00e-06 8/28
Environmental Information Processing kegg category 1.50e-05 2.51e-04 8/28
Environmental Information Processing kegg category 1.40e-05 3.61e-04 8/28
Membrane Transport kegg subcategory 0.00e+00 1.10e-05 8/28
Bacterial secretion system kegg pathway 0.00e+00 0.00e+00 8/28

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
protein secretion biological_process 0.00e+00 1.00e-06 5/28
protein transport biological_process 1.00e-06 8.00e-06 4/28
type III protein (virulence-related) secretor activity molecular_function 0.00e+00 0.00e+00 3/28

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Pathogenesis tigr sub1role 0.00e+00 0.00e+00 7/28
Cellular processes tigr mainrole 0.00e+00 0.00e+00 7/28
Cellular processes tigr mainrole 0.00e+00 0.00e+00 7/28
Pathogenesis tigr sub1role 0.00e+00 0.00e+00 7/28

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cell motility cog subcategory 8.84e-04 1.61e-02 4/28
Intracellular trafficking, secretion, and vesicular transport cog subcategory 0.00e+00 7.00e-06 7/28
Cellular processes and signaling cog category 4.00e-06 1.43e-04 16/28
Cellular processes and signaling cog category 6.22e-04 1.27e-03 12/28
Cell motility cog subcategory 8.84e-04 1.75e-03 4/28
Intracellular trafficking, secretion, and vesicular transport cog subcategory 0.00e+00 0.00e+00 7/28
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 136

There are 28 genes in Module 136

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0490 CDS 2793704 chromosome 558218 559487 - None False
DVUA0032 CDS 2781538 pDV 35708 36568 - hypothetical protein DVUA0032 False
DVUA0033 CDS 2781537 pDV 36600 36797 + hypothetical protein DVUA0033 False
DVUA0079 cysC CDS 2781533 pDV 105582 106268 + adenylylsulfate kinase False
DVUA0081 CDS 2781532 pDV 107247 109361 + glycosyl transferase, group 1/2 family protein False
DVUA0099 CDS 2781505 pDV 133570 135753 - HAMP domain-containing protein False
DVUA0100 CDS 2781504 pDV 136112 137839 - sigma-54 dependent transcriptional regulator True
DVUA0101 CDS 2781503 pDV 137887 138927 - hrpY/hrcU family type III secretion protein False
DVUA0104 CDS 2781593 pDV 140328 142421 - type III secretion inner membrane protein HrcV family False
DVUA0107 CDS 2781591 pDV 144885 144989 + hypothetical protein DVUA0107 False
DVUA0108 CDS 2781590 pDV 145580 146200 + hypothetical protein DVUA0108 False
DVUA0109 CDS 2781620 pDV 146209 146709 + LcrH/SycD family type III secretion system chaperone False
DVUA0111 CDS 2781619 pDV 147662 148558 + type III secretion system protein IpaC family False
DVUA0112 CDS 2781618 pDV 149369 151243 + type III secretion system protein YscC family False
DVUA0113 CDS 2781617 pDV 151240 153048 + YscD family type III secretion protein False
DVUA0114 CDS 2781616 pDV 153041 153250 + hypothetical protein DVUA0114 False
DVUA0115 CDS 2781477 pDV 153276 153527 + type III secretion system protein YscF family False
DVUA0116 CDS 2781476 pDV 153722 154087 + hypothetical protein DVUA0116 False
DVUA0117 escJ CDS 2781475 pDV 154970 155785 + type III secretion lipoprotein False
DVUA0119 CDS 2781474 pDV 157639 158955 + type III secretion system ATPase False
DVUA0121 CDS 2781473 pDV 160160 161614 + type III secretion system protein YopQ family False
DVUA0122 CDS 2781527 pDV 161611 162261 + type III secretion system protein False
DVUA0123 CDS 2781526 pDV 162292 162627 + anti-anti-sigma factor False
DVUA0124 CDS 2781525 pDV 162643 163059 + sigma factor serine-protein kinase False
DVUA0126 CDS 2781523 pDV 164796 165263 + hypothetical protein DVUA0126 False
DVUA0131 CDS 2781582 pDV 171056 172894 + CRISPR-associated Csd1 family protein False
DVUA0147 CDS 2781572 pDV 192334 193575 + hypothetical protein DVUA0147 False
DVUA0149 CDS 2781570 pDV 196632 198416 + hypothetical protein DVUA0149 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 136

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.