Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 274 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 274

There are 10 regulatory influences for Module 274

Regulator Table (10)
Regulator Name Type
DVU2675 tf
DVU1402 tf
DVU2547
DVU1340		 combiner
DVU3066 tf
DVU2547
DVU2394		 combiner
DVU1572
DVU2547		 combiner
DVU0309
DVU1949		 combiner
DVU0309
DVU2275		 combiner
DVU2557
DVU2675		 combiner
DVU2557
DVU2547		 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
523 1.70e+02 ATg.atcgaTgtaatGgatt
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 RegPredict
524 8.90e+03 gTaCaTggcGcAaGcctcTGaacA
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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 274 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 6.12e-04 3.90e-03 3/30
Two-component system kegg pathway 4.24e-04 3.15e-03 4/30
Bacterial chemotaxis kegg pathway 6.00e-06 1.71e-04 5/30
Microbial metabolism in diverse environments kegg pathway 2.93e-03 8.86e-03 4/30
Energy Metabolism kegg subcategory 9.80e-03 3.56e-02 3/30
Signal Transduction kegg subcategory 4.24e-04 4.14e-03 4/30
Cell Motility kegg subcategory 1.80e-04 2.34e-03 5/30
Cellular Processes kegg category 1.80e-04 2.10e-03 5/30
Energy Metabolism kegg subcategory 9.47e-03 2.55e-02 3/30
Methane metabolism kegg pathway 6.12e-04 5.36e-03 3/30
Environmental Information Processing kegg category 2.49e-02 5.00e-02 4/30
Signal Transduction kegg subcategory 4.24e-04 4.23e-03 4/30
Two-component system kegg pathway 4.24e-04 4.23e-03 4/30
Cellular Processes kegg category 9.00e-05 1.50e-03 5/30
Cell Motility kegg subcategory 9.00e-05 1.50e-03 5/30
Bacterial chemotaxis kegg pathway 6.00e-06 1.78e-04 5/30
Microbial metabolism in diverse environments kegg pathway 2.93e-03 1.29e-02 4/30

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
two-component signal transduction system (phosphorelay) biological_process 2.14e-02 3.03e-02 3/30
electron transport biological_process 9.00e-06 7.50e-05 8/30
chemotaxis biological_process 5.90e-05 3.31e-04 4/30
two-component response regulator activity molecular_function 6.78e-03 1.06e-02 3/30
oxidoreductase activity molecular_function 0.00e+00 0.00e+00 7/30
heme binding molecular_function 5.80e-05 2.26e-04 3/30

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Signal transduction mechanisms cog subcategory 9.30e-04 1.66e-02 7/30
Cell motility cog subcategory 1.36e-04 4.40e-03 5/30
Energy production and conversion cog subcategory 1.55e-03 2.23e-02 6/30
Cellular processes and signaling cog category 7.70e-05 1.76e-03 15/30
Cellular processes and signaling cog category 1.40e-02 2.36e-02 10/30
Metabolism cog category 2.95e-02 4.64e-02 11/30
Signal transduction mechanisms cog subcategory 9.30e-04 1.84e-03 7/30
Cell motility cog subcategory 1.36e-04 3.24e-04 5/30
Energy production and conversion cog subcategory 1.55e-03 2.95e-03 6/30
Inorganic ion transport and metabolism cog subcategory 1.16e-02 1.98e-02 3/30
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 274

There are 30 genes in Module 274

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0111 CDS 2794980 chromosome 144236 145042 + response regulator False
DVU0239 CDS 2795011 chromosome 272556 272792 - hypothetical protein DVU0239 False
DVU0453 CDS 2793376 chromosome 519369 522752 + ATP-dependent DNA helicase UvrD False
DVU0577 CDS 2794562 chromosome 641591 642472 + formate dehydrogenase formation protein FdhE False
DVU0579 CDS 2794564 chromosome 643259 643927 + molybdopterin-guanine dinucleotide biosynthesis protein A False
DVU0587 fdnG-1 CDS 2794164 chromosome 653387 656404 + formate dehydrogenase subunit alpha, selenocysteine-containing False
DVU0819 CDS 2795022 chromosome 908890 909507 - FMN reductase, NADPH-dependent False
DVU1396 CDS 2794796 chromosome 1465764 1466021 - hypothetical protein DVU1396 False
DVU1397 bfr CDS 2794797 chromosome 1466087 1466626 - bacterioferritin False
DVU1412 CDS 2794956 chromosome 1481630 1482610 - glycerate dehydrogenase False
DVU1564 CDS 2795735 chromosome 1647670 1647948 + hypothetical protein DVU1564 False
DVU1592 CDS 2796028 chromosome 1673985 1675727 + arginine N-succinyltransferase subunit beta False
DVU1593 cheY-1 CDS 2796029 chromosome 1675754 1676116 + chemotaxis protein CheY False
DVU1594 cheA-1 CDS 2796030 chromosome 1676184 1678310 + chemotaxis protein CheA False
DVU1595 cheR-1 CDS 2796031 chromosome 1678334 1679209 + chemotaxis protein methyltransferase False
DVU1596 cheB-1 CDS 2795951 chromosome 1679212 1680285 + protein-glutamate methylesterase CheB False
DVU1597 CDS 2795952 chromosome 1680309 1680965 + sulfite reductase, assimilatory-type False
DVU1973 CDS 2795987 chromosome 2046999 2047847 + rhodanese-like domain-containing protein False
DVU1974 CDS 2795988 chromosome 2047840 2048943 + pyridine nucleotide-disulfide oxidoreductase False
DVU2421 CDS 2794362 chromosome 2527924 2528121 - 4-oxalocrotonate tautomerase family protein False
DVU2422 CDS 2794363 chromosome 2528124 2528633 - nitroreductase family protein False
DVU2972 CDS 2796286 chromosome 3081579 3082178 - chemotaxis protein CheD False
DVU3041 CDS 2796459 chromosome 3165232 3165513 + cytochrome c553 False
DVU3042 CDS 2796460 chromosome 3165553 3165789 + lipoprotein False
DVU3076 CDS 2796427 chromosome 3218992 3219573 + hypothetical protein DVU3076 False
DVU3079 CDS 2796430 chromosome 3221509 3222111 + glyoxalase family protein False
DVU3135 CDS 2793984 chromosome 3282773 3283381 - flavodoxin-like fold domain-containing protein False
DVU3136 CDS 2793985 chromosome 3283437 3284093 - nitroreductase family protein False
DVUA0023 CDS 2781540 pDV 28487 29617 - ABC transporter permease False
DVUA0091 katA CDS 2781562 pDV 123495 124952 + catalase 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.