Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 348 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 348

There are 11 regulatory influences for Module 348

Regulator Table (11)
Regulator Name Type
DVU0230
DVU1949
combiner
DVU1788 tf
DVU2547
DVU0110
combiner
DVU2909 tf
DVU0653
DVU2251
combiner
DVU0277
DVU2894
combiner
DVU0277
DVU0118
combiner
DVU2547
DVU2251
combiner
DVU2547
DVU3193
combiner
DVU3220
DVU2251
combiner
DVU0946
DVU2251
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
661 6.00e+02 CtTTccaGCcgtcCcGACgtCgGa
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RegPredict
662 1.60e+03 ctgaC.tcCaTaacggtctggtac
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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 348 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Glyoxylate and dicarboxylate metabolism kegg pathway 1.60e-05 3.77e-04 3/36
Butanoate metabolism kegg pathway 9.00e-06 2.28e-04 3/36
Methane metabolism kegg pathway 6.00e-06 1.77e-04 5/36
Nitrotoluene degradation kegg pathway 0.00e+00 1.00e-06 3/36
Metabolic pathways kegg pathway 5.90e-05 9.27e-04 13/36
Biosynthesis of secondary metabolites kegg pathway 1.83e-03 6.86e-03 6/36
Microbial metabolism in diverse environments kegg pathway 0.00e+00 0.00e+00 11/36
Carbohydrate Metabolism kegg subcategory 0.00e+00 0.00e+00 14/36
Energy Metabolism kegg subcategory 0.00e+00 1.40e-05 8/36
Xenobiotics Biodegradation and Metabolism kegg subcategory 0.00e+00 1.00e-06 5/36
Metabolism kegg subcategory 0.00e+00 0.00e+00 30/36
Metabolism kegg category 0.00e+00 0.00e+00 39/36
Global kegg category 0.00e+00 0.00e+00 30/36
Metabolism kegg category 0.00e+00 0.00e+00 20/36
Carbohydrate Metabolism kegg subcategory 3.00e-06 1.05e-04 8/36
Glyoxylate and dicarboxylate metabolism kegg pathway 1.60e-05 4.09e-04 3/36
Butanoate metabolism kegg pathway 9.00e-06 2.48e-04 3/36
Energy Metabolism kegg subcategory 0.00e+00 1.70e-05 8/36
Methane metabolism kegg pathway 6.00e-06 1.88e-04 5/36
Xenobiotics Biodegradation and Metabolism kegg subcategory 0.00e+00 5.00e-06 4/36
Nitrotoluene degradation kegg pathway 0.00e+00 1.00e-06 3/36
Global kegg category 0.00e+00 4.00e-06 17/36
Metabolism kegg subcategory 0.00e+00 4.00e-06 17/36
Metabolic pathways kegg pathway 5.90e-05 1.14e-03 13/36
Biosynthesis of secondary metabolites kegg pathway 1.83e-03 9.93e-03 6/36
Microbial metabolism in diverse environments kegg pathway 0.00e+00 0.00e+00 11/36

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
electron transport biological_process 0.00e+00 0.00e+00 15/36
DNA-directed DNA polymerase activity molecular_function 0.00e+00 0.00e+00 14/36
iron ion binding molecular_function 3.15e-04 7.89e-04 3/36
ferredoxin hydrogenase activity molecular_function 0.00e+00 1.00e-06 4/36
electron carrier activity molecular_function 0.00e+00 1.00e-06 8/36
hydrogensulfite reductase activity molecular_function 0.00e+00 0.00e+00 3/36
heme binding molecular_function 5.00e-06 2.70e-05 4/36
hydrogenase (acceptor) activity molecular_function 0.00e+00 0.00e+00 4/36
iron-sulfur cluster binding molecular_function 5.80e-05 2.25e-04 6/36

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Electron transport tigr sub1role 0.00e+00 1.00e-05 4/36
TCA cycle tigr sub1role 0.00e+00 7.00e-06 3/36
Energy metabolism tigr mainrole 0.00e+00 0.00e+00 10/36
Energy metabolism tigr mainrole 0.00e+00 0.00e+00 10/36
Electron transport tigr sub1role 0.00e+00 1.00e-06 4/36
TCA cycle tigr sub1role 0.00e+00 1.00e-06 3/36

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy production and conversion cog subcategory 0.00e+00 0.00e+00 19/36
Metabolism cog category 0.00e+00 0.00e+00 28/36
Metabolism cog category 0.00e+00 0.00e+00 27/36
Energy production and conversion cog subcategory 0.00e+00 0.00e+00 19/36
Carbohydrate transport and metabolism cog subcategory 1.40e-02 2.35e-02 3/36
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 348

There are 36 genes in Module 348

Gene Member Table (36)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0019 ngr CDS 2794280 chromosome 22502 23110 - nigerythrin False
DVU0092 CDS 2796241 chromosome 117119 120436 - sensory box histidine kinase False
DVU0175 CDS 2795625 chromosome 219258 220889 - tungsten formylmethanofuran dehydrogenase family protein/molybdopterin binding protein False
DVU0260 CDS 2794102 chromosome 304088 304489 - response regulator False
DVU0263 CDS 2795005 chromosome 306015 306395 - acidic cytochrome c3 False
DVU0264 CDS 2795006 chromosome 306421 307740 - ferredoxin, 4Fe-4S False
DVU0402 dsvA CDS 2796152 chromosome 449888 451201 + dissimilatory sulfite reductase subunit alpha False
DVU0403 dvsB CDS 2796153 chromosome 451220 452365 + dissimilatory sulfite reductase subunit beta False
DVU0404 CDS 2796154 chromosome 452427 452663 + dissimilatory sulfite reductase B False
DVU0701 glcB CDS 2795485 chromosome 778761 780950 + malate synthase G False
DVU0979 CDS 2795111 chromosome 1074581 1075645 + dihydroxyacetone kinase subunit DhaK False
DVU0980 CDS 2793322 chromosome 1075824 1076456 + DAK2 domain-containing protein False
DVU1179 aor CDS 2796664 chromosome 1269177 1270907 + tungsten-containing aldehyde:ferredoxin oxidoreductase False
DVU1681 mreB-2 CDS 2794909 chromosome 1758877 1759899 - rod shape-determining protein MreB False
DVU1684 gcvT CDS 2794912 chromosome 1762935 1764065 + glycine cleavage system T protein False
DVU1685 CDS 2794913 chromosome 1764117 1764866 + 16S ribosomal RNA methyltransferase RsmE False
DVU1686 CDS 2794914 chromosome 1764863 1766098 + recombination factor protein RarA False
DVU1917 hysB CDS 2793333 chromosome 1991067 1992020 + periplasmic False
DVU1918 hysA CDS 2793334 chromosome 1992054 1993586 + periplasmic False
DVU1921 hynB-1 CDS 2793337 chromosome 1994643 1995596 + periplasmic False
DVU1922 hynA-1 CDS 2793338 chromosome 1995648 1997348 + periplasmic False
DVU2109 CDS 2793381 chromosome 2202848 2204311 + hypothetical protein DVU2109 False
DVU2481 CDS 2795663 chromosome 2589171 2589953 - formate dehydrogenase subunit beta False
DVU2482 fdnG-2 CDS 2795450 chromosome 2590064 2593075 - formate dehydrogenase subunit alpha, selenocysteine-containing False
DVU2483 CDS 2795451 chromosome 2593092 2594837 - cytochrome c family protein False
DVU2514 pyk CDS 2795604 chromosome 2627119 2628528 + pyruvate kinase False
DVU2557 birA CDS 2796131 chromosome 2668667 2669659 - birA bifunctional protein True
DVU3037 CDS 2796454 chromosome 3162817 3163689 - rhodanese-like domain-containing protein False
DVU3183 rbO CDS 2793833 chromosome 3343927 3344307 + desulfoferrodoxin False
DVU3184 CDS 2793834 chromosome 3344324 3344482 + rubredoxin False
DVU3185 roO CDS 2793835 chromosome 3344614 3345822 + rubredoxin-oxygen oxidoreductase False
DVU3262 fdrA CDS 2793866 chromosome 3436978 3438816 + fumarate reductase flavoprotein subunit False
DVU3263 frdB CDS 2793867 chromosome 3438819 3439562 + fumarate reductase iron-sulfur subunit False
DVU3293 CDS 2796017 chromosome 3469747 3471390 + acetolactate synthase False
DVU3294 CDS 2796018 chromosome 3471408 3472802 + aldehyde dehydrogenase family protein False
DVU3319 putA CDS 2796055 chromosome 3495296 3498316 + proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase 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 348

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.