Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 347 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 347

There are 14 regulatory influences for Module 347

Regulator Table (14)
Regulator Name Type
DVU2275 tf
DVU0653
DVU2275
combiner
DVU3255
DVU1584
combiner
DVU2836 tf
DVU2588
DVU1547
combiner
DVU3255
DVU2633
combiner
DVU3142 tf
DVU2588
DVU3381
combiner
DVU3255
DVU0936
combiner
DVU3167
DVU3255
combiner
DVU0744
DVU2832
combiner
DVU0744
DVU2690
combiner
DVU2588
DVU1419
combiner
DVU3186
DVU2275
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
659 5.00e-01 AtTgaCAaaAttGatAtaTa
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RegPredict
660 1.90e+01 T..CaGAAAg
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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 347 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
ABC transporters kegg pathway 0.00e+00 0.00e+00 11/18
Membrane Transport kegg subcategory 0.00e+00 0.00e+00 11/18
Environmental Information Processing kegg category 0.00e+00 0.00e+00 11/18
Environmental Information Processing kegg category 0.00e+00 0.00e+00 11/18
Membrane Transport kegg subcategory 0.00e+00 0.00e+00 11/18
ABC transporters kegg pathway 0.00e+00 0.00e+00 11/18

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
transport biological_process 0.00e+00 0.00e+00 8/18
transporter activity molecular_function 0.00e+00 1.00e-06 6/18
ATP binding molecular_function 3.08e-03 5.31e-03 5/18
oxidoreductase activity molecular_function 1.77e-04 5.03e-04 3/18
ATPase activity molecular_function 1.00e-06 8.00e-06 4/18

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Amino acids, peptides and amines tigr sub1role 1.00e-06 1.60e-05 3/18
Transport and binding proteins tigr mainrole 4.30e-05 9.52e-04 4/18
Transport and binding proteins tigr mainrole 4.30e-05 1.12e-04 4/18
Amino acids, peptides and amines tigr sub1role 1.00e-06 3.00e-06 3/18

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Amino acid transport and metabolism cog subcategory 0.00e+00 0.00e+00 11/18
Inorganic ion transport and metabolism cog subcategory 9.00e-06 4.27e-04 5/18
Metabolism cog category 0.00e+00 0.00e+00 18/18
Metabolism cog category 0.00e+00 0.00e+00 14/18
Amino acid transport and metabolism cog subcategory 0.00e+00 0.00e+00 11/18
Inorganic ion transport and metabolism cog subcategory 9.00e-06 3.10e-05 5/18
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 347

There are 18 genes in Module 347

Gene Member Table (18)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0165 CDS 2793571 chromosome 205350 206363 - oligopeptide/dipeptide ABC transporter ATP-binding protein False
DVU0166 CDS 2793572 chromosome 206374 207360 - oligopeptide/dipeptide ABC transporter ATP-binding protein False
DVU0167 CDS 2793573 chromosome 207363 208283 - oligopeptide/dipeptide ABC transporter permease False
DVU0168 CDS 2793574 chromosome 208285 209262 - oligopeptide/dipeptide ABC transporter permease False
DVU0279 CDS 2794210 chromosome 322378 324084 + sulfate permease family protein False
DVU0384 flr CDS 2796742 chromosome 433812 434384 - flavoredoxin False
DVU0390 CDS 2795064 chromosome 437672 439054 + glycolate oxidase subunit GlcD False
DVU0548 CDS 2794431 chromosome 618218 619126 + high-affinity branched-chain amino acid ABC transporter permease False
DVU0549 CDS 2794432 chromosome 619154 620377 + high-affinity branched-chain amino acid ABC transporter permease False
DVU0550 CDS 2794433 chromosome 620377 621165 + high-affinity branched-chain amino acid ABC transporter ATP binding protein False
DVU0551 CDS 2794434 chromosome 621158 621862 + high-affinity branched-chain amino acid ABC transporter ATP-binding protein False
DVU0713 CDS 2795409 chromosome 792889 793794 + branched-chain amino acid ABC transporter permease False
DVU0714 CDS 2795410 chromosome 793791 794744 + branched-chain amino acid ABC transporter permease False
DVU1245 CDS 2795026 chromosome 1331477 1332301 - ABC transporter ATP-binding protein False
DVU1291 CDS 2794744 chromosome 1385086 1385613 - hypothetical protein DVU1291 False
DVU2341 CDS 2795515 chromosome 2436980 2437681 - amino acid ABC transporter permease False
DVUA0069 CDS 2781597 pDV 90871 92028 - GtrA family protein, selenocysteine-containing False
DVUA0070 CDS 2781596 pDV 92091 94022 - hypothetical protein DVUA0070 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 347

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.