Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 82 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 82

There are 9 regulatory influences for Module 82

Regulator Table (9)
Regulator Name Type
DVU2686 tf
DVU2423
DVU0621
combiner
DVUA0151 tf
DVU0621
DVU2690
combiner
DVU1754
DVU2802
combiner
DVU0679
DVU2690
combiner
DVU1754
DVU3305
combiner
DVU0309
DVU2832
combiner
DVU2557
DVU3080
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
161 1.40e+01 a.acaacgacc.acgCAA.Gaaac
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RegPredict
162 1.70e+04 GCgGAAGGCccgCtgGCGcC
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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 82 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 2.37e-02 3.44e-02 7/29
Carbohydrate Metabolism kegg subcategory 1.05e-03 7.58e-03 6/29
Replication and Repair kegg subcategory 8.00e-06 2.08e-04 5/29
Metabolism kegg category 2.18e-04 2.38e-03 15/29
Genetic Information Processing kegg category 6.88e-04 6.24e-03 6/29
Carbohydrate Metabolism kegg subcategory 1.86e-02 4.02e-02 3/29
Metabolic pathways kegg pathway 2.37e-02 4.80e-02 7/29

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
DNA-directed DNA polymerase activity molecular_function 0.00e+00 0.00e+00 14/29
iron-sulfur cluster binding molecular_function 8.99e-03 1.36e-02 3/29

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 2.23e-02 3.59e-02 11/29
Replication, recombination and repair cog subcategory 8.38e-03 1.47e-02 3/29
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 82

There are 29 genes in Module 82

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0066 CDS 2795213 chromosome 78122 78691 + cytidine/deoxycytidylate deaminase domain-containing protein False
DVU0099 CDS 2796545 chromosome 129890 131050 - TonB domain-containing protein False
DVU0117 CDS 2794721 chromosome 150843 151760 - glycosyl transferase group 2 family protein False
DVU0119 CDS 2796784 chromosome 153408 155072 - sensor histidine kinase False
DVU0120 CDS 2796785 chromosome 155069 156007 - ABC transporter substrate-binding protein False
DVU0171 CDS 2795601 chromosome 213725 214906 - hemolysin-like protein False
DVU0440 CDS 2796509 chromosome 496131 497462 + hypothetical protein DVU0440 False
DVU0496 polA CDS 2794724 chromosome 565280 568327 - DNA polymerase I False
DVU0643 CDS 2794335 chromosome 713684 714376 + thiF protein False
DVU0687 CDS 2795337 chromosome 761222 763006 + tungsten-containing aldehyde:ferredoxin oxidoreductase False
DVU0689 rnhA CDS 2793629 chromosome 763517 763987 + ribonuclease H False
DVU0826 CDS 2796173 chromosome 915709 917031 - glycolate oxidase, iron-sulfur subunit False
DVU0829 ptsI CDS 2795493 chromosome 919099 920871 - phosphoenolpyruvate-protein phosphotransferase False
DVU0858 CDS 2794187 chromosome 948258 948941 - lipoprotein False
DVU1079 trmE CDS 2794457 chromosome 1182378 1183751 + tRNA modification GTPase TrmE False
DVU1261 CDS 2794607 chromosome 1348254 1350014 - hypothetical protein DVU1261 False
DVU1268 CDS 2793588 chromosome 1358519 1358932 - hypothetical protein DVU1268 False
DVU1573 pth CDS 2793464 chromosome 1655955 1656560 - peptidyl-tRNA hydrolase False
DVU2115 CDS 2793387 chromosome 2211635 2211826 - hypothetical protein DVU2115 False
DVU2591 CDS 2796369 chromosome 2714953 2715462 - tail fiber assembly protein False
DVU2661 CDS 2796228 chromosome 2772423 2773988 + twin-arginine translocation pathway signal sequence domain-containing protein False
DVU2733 CDS 2795934 chromosome 2833587 2834336 + adenine specific DNA methyltransferase False
DVU2822 CDS 2793783 chromosome 2927266 2928276 + TRAP transporter solute receptor DctP False
DVU2824 CDS 2793785 chromosome 2930367 2932853 + formate acetyltransferase False
DVU3057 CDS 2796083 chromosome 3183675 3185168 + oxygen-independent coproporphyrinogen III oxidase False
DVU3058 CDS 2796084 chromosome 3185165 3188836 + sensory box histidine kinase/response regulator False
DVU3236 hflX CDS 2793886 chromosome 3404744 3406387 + GTP-binding protein HflX False
DVU3258 murA CDS 2793861 chromosome 3432618 3433871 - UDP-N-acetylglucosamine 1-carboxyvinyltransferase False
DVU3326 CDS 2796337 chromosome 3502423 3502743 - SMR family multidrug efflux pump 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 82

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.