Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 342 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 342

There are 13 regulatory influences for Module 342

Regulator Table (13)
Regulator Name Type
DVUA0143 tf
DVU0606 tf
DVU1949
DVU1730		 combiner
DVU2378 tf
DVU1949 tf
DVU2675
DVU1744		 combiner
DVU0679
DVU1730		 combiner
DVU0277
DVU1744		 combiner
DVUA0143
DVU1949		 combiner
DVU2378
DVU2251		 combiner
DVU0309
DVU1949		 combiner
DVU0063
DVU0679		 combiner
DVU2378
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
649 7.10e-04 CAagCggcgTCTGtacggctaaCG
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 RegPredict
650 5.40e-01 tTtcaTcaagGTTtCAcGCatG
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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 342 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Methane metabolism kegg pathway 5.35e-04 3.55e-03 3/29
ABC transporters kegg pathway 7.30e-05 1.04e-03 5/29
Metabolic pathways kegg pathway 2.37e-02 3.44e-02 7/29
Microbial metabolism in diverse environments kegg pathway 3.30e-04 2.68e-03 5/29
Energy Metabolism kegg subcategory 8.68e-03 3.30e-02 3/29
Xenobiotics Biodegradation and Metabolism kegg subcategory 0.00e+00 7.00e-06 4/29
Membrane Transport kegg subcategory 4.13e-04 4.06e-03 5/29
Metabolism kegg subcategory 5.60e-05 9.90e-04 15/29
Metabolism kegg category 9.00e-06 1.74e-04 17/29
Environmental Information Processing kegg category 5.14e-03 3.18e-02 5/29
Global kegg category 5.60e-05 7.71e-04 15/29
Carbohydrate Metabolism kegg subcategory 1.86e-02 4.02e-02 3/29
Energy Metabolism kegg subcategory 8.38e-03 2.37e-02 3/29
Methane metabolism kegg pathway 5.35e-04 4.88e-03 3/29
Environmental Information Processing kegg category 4.89e-03 1.71e-02 5/29
Membrane Transport kegg subcategory 4.13e-04 4.17e-03 5/29
ABC transporters kegg pathway 7.30e-05 1.32e-03 5/29
Metabolic pathways kegg pathway 2.37e-02 4.80e-02 7/29
Microbial metabolism in diverse environments kegg pathway 3.30e-04 3.57e-03 5/29

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
electron transport biological_process 2.56e-03 5.02e-03 5/29
transport biological_process 1.76e-02 2.58e-02 3/29
metabolic process biological_process 1.96e-02 2.80e-02 3/29
transporter activity molecular_function 5.09e-03 8.29e-03 3/29
electron carrier activity molecular_function 6.69e-04 1.43e-03 4/29
oxidoreductase activity molecular_function 1.20e-03 2.32e-03 3/29
iron-sulfur cluster binding molecular_function 1.25e-03 2.42e-03 4/29
CoB--CoM heterodisulfide reductase activity molecular_function 0.00e+00 1.00e-06 3/29

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy production and conversion cog subcategory 1.25e-03 2.00e-02 6/29
Energy production and conversion cog subcategory 1.25e-03 2.41e-03 6/29
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 342

There are 29 genes in Module 342

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0411 CDS 2793712 chromosome 459998 461671 - heptosyltransferase family protein False
DVU0547 CDS 2794537 chromosome 616996 618114 + high-affinity branched chain amino acid ABC transporter periplasmic branched chain amino acid-binding protein False
DVU1360 galE CDS 2795084 chromosome 1438843 1439838 + UDP-glucose 4-epimerase False
DVU2067 CDS 2793444 chromosome 2147609 2148730 - GGDEF domain-containing protein False
DVU2068 CDS 2793445 chromosome 2148730 2149572 - HD domain-containing protein False
DVU2162 CDS 2796573 chromosome 2263256 2263585 - hypothetical protein DVU2162 False
DVU2384 CDS 2795286 chromosome 2485110 2487029 + ABC transporter periplasmic substrate-binding protein False
DVU2385 CDS 2795287 chromosome 2487029 2488150 + ABC transporter permease False
DVU2386 CDS 2795288 chromosome 2488147 2489178 + ABC transporter permease False
DVU2387 CDS 2795289 chromosome 2489184 2490962 + ABC transporter ATP-binding protein False
DVU2394 CDS 2795297 chromosome 2496966 2498357 - sigma-54 dependent transcriptional regulator/response regulator True
DVU2395 CDS 2795298 chromosome 2498363 2499619 - sensor histidine kinase False
DVU2396 CDS 2795299 chromosome 2499621 2500763 - iron-containing alcohol dehydrogenase False
DVU2397 CDS 2794482 chromosome 2501252 2501995 - hypothetical protein DVU2397 False
DVU2398 CDS 2794483 chromosome 2502202 2502693 - hypothetical protein DVU2398 False
DVU2399 CDS 2794484 chromosome 2502951 2503838 - hydrogenase False
DVU2400 CDS 2794485 chromosome 2503831 2504913 - hydrogenase False
DVU2401 CDS 2794486 chromosome 2504910 2506394 - hydrogenase, iron-sulfur cluster-binding subunit False
DVU2402 hdrA CDS 2794487 chromosome 2506382 2508340 - heterodisulfide reductase subunit A False
DVU2403 hdrB CDS 2794488 chromosome 2508337 2509341 - heterodisulfide reductase subunit B False
DVU2404 hdrC CDS 2794489 chromosome 2509338 2509898 - heterodisulfide reductase subunit C False
DVU2405 CDS 2794490 chromosome 2510126 2511307 - iron-containing alcohol dehydrogenase False
DVU2406 CDS 2794491 chromosome 2511342 2511548 - hypothetical protein DVU2406 False
DVU2453 CDS 2796630 chromosome 2557376 2557474 - hypothetical protein DVU2453 False
DVU2454 CDS 2796631 chromosome 2557471 2557740 - hypothetical protein DVU2454 False
DVU2455 CDS 2796632 chromosome 2557897 2558847 + NAD-dependent epimerase/dehydratase family protein False
DVU2459 CDS 2795323 chromosome 2564868 2565482 + hypothetical protein DVU2459 False
DVU2498 CDS 2795466 chromosome 2609375 2609668 - hypothetical protein DVU2498 False
DVU2551 CDS 2796125 chromosome 2662087 2663322 - HD domain-containing 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.