Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 17 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 17

There are 13 regulatory influences for Module 17

Regulator Table (13)
Regulator Name Type
DVU2527
DVU3080		 combiner
DVU1730 tf
DVU2799 tf
DVU0946
DVU2960		 combiner
DVU0606
DVU1340		 combiner
DVU2886
DVU2832		 combiner
DVU0606
DVU2960		 combiner
DVU0606 tf
DVU2886
DVUA0100		 combiner
DVU2886 tf
DVUA0100
DVU2832		 combiner
DVU3334
DVUA0100		 combiner
DVU2886
DVU3334		 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
33 3.80e-05 tatcAGtAATagtTacTgtTaact
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 RegPredict
34 1.50e+02 aacTccTtgcgctt.ctCa
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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 17 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Fructose and mannose metabolism kegg pathway 0.00e+00 1.10e-05 4/31
Metabolic pathways kegg pathway 3.48e-02 4.77e-02 7/31
Biosynthesis of secondary metabolites kegg pathway 1.84e-02 2.82e-02 4/31
Carbohydrate Metabolism kegg subcategory 5.00e-06 1.45e-04 9/31
Metabolism kegg subcategory 2.21e-03 1.25e-02 13/31
Metabolism kegg category 5.93e-04 5.55e-03 15/31
Global kegg category 2.21e-03 1.58e-02 13/31
Carbohydrate Metabolism kegg subcategory 4.37e-03 1.60e-02 4/31
Fructose and mannose metabolism kegg pathway 0.00e+00 1.00e-05 4/31
Biosynthesis of secondary metabolites kegg pathway 1.84e-02 3.99e-02 4/31

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
electron transport biological_process 3.65e-03 6.65e-03 5/31
electron carrier activity molecular_function 7.05e-03 1.10e-02 3/31

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Carbohydrate transport and metabolism cog subcategory 1.23e-04 4.13e-03 5/31
Metabolism cog category 1.60e-05 4.42e-04 18/31
Metabolism cog category 2.90e-05 9.30e-05 17/31
Transcription cog subcategory 1.10e-02 1.89e-02 3/31
Energy production and conversion cog subcategory 8.93e-03 1.56e-02 5/31
Carbohydrate transport and metabolism cog subcategory 1.23e-04 2.98e-04 5/31
Coenzyme transport and metabolism cog subcategory 1.98e-02 3.24e-02 3/31
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 17

There are 31 genes in Module 17

Gene Member Table (31)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0024 CDS 2793531 chromosome 27468 27638 + hypothetical protein DVU0024 False
DVU0151 CDS 2796748 chromosome 184043 186916 + HAMP domain/sigma-54 interaction domain-containing protein False
DVU0155 CDS 2796697 chromosome 190855 192243 + type I phosphodiesterase/nucleotide pyrophosphatase family protein False
DVU0158 CDS 2795033 chromosome 195388 196386 + hypothetical protein DVU0158 False
DVU0460 CDS 2794473 chromosome 527671 528471 + fructose-bisphosphate aldolase False
DVU0461 CDS 2794474 chromosome 528480 529451 + 3-dehydroquinate synthase False
DVU0594 iciA CDS 2794092 chromosome 662909 663811 + chromosome replication initiation inhibitor protein True
DVU0685 CDS 2795335 chromosome 759320 760681 + phosphomannomutase False
DVU0711 CDS 2795407 chromosome 790673 791314 + hypothetical protein DVU0711 False
DVU0771 CDS 2794842 chromosome 862088 863158 + fused molybdenum-pterin binding domain-containing protein/site-specific recombinase phage integrase family False
DVU0772 CDS 2794843 chromosome 863400 863747 - hypothetical protein DVU0772 False
DVU0903 CDS 2795413 chromosome 994751 995608 + HD domain-containing protein False
DVU0971 CDS 2795103 chromosome 1067552 1068331 + molybdenum cofactor biosynthesis protein False
DVU1677 tpiA CDS 2794905 chromosome 1756281 1757036 - triosephosphate isomerase False
DVU2230 deoD CDS 2795557 chromosome 2322336 2323160 + purine nucleoside phosphorylase False
DVU2239 CDS 2795391 chromosome 2330937 2332382 - glycosy hydrolase family protein False
DVU2241 pdxA CDS 2795393 chromosome 2334036 2335256 - pyridoxal phosphate biosynthetic protein PdxA False
DVU2246 CDS 2795398 chromosome 2341713 2343884 + S1 RNA-binding domain-containing protein False
DVU2247 CDS 2795399 chromosome 2344057 2344671 - anti-oxidant AhpCTSA family protein False
DVU2248 CDS 2795400 chromosome 2344699 2344803 + hypothetical protein DVU2248 False
DVU2318 CDS 2795278 chromosome 2413715 2414209 + rubrerythrin False
DVU2462 CDS 2795326 chromosome 2567205 2568107 + oligopeptide ABC transporter permease False
DVU2672 CDS 2796239 chromosome 2783384 2784007 + hypothetical protein DVU2672 False
DVU3093 rdl CDS 2795965 chromosome 3236518 3236745 - rubredoxin-like protein False
DVU3094 rr CDS 2795966 chromosome 3236764 3237339 - rubrerythrin False
DVU3095 CDS 2795967 chromosome 3237384 3237770 - Fur family transcriptional regulator True
DVU3096 CDS 2795968 chromosome 3237800 3238051 - hypothetical protein DVU3096 False
DVU3240 CDS 2793890 chromosome 3410878 3411867 - M24/M37 family peptidase False
DVU3270 cydB CDS 2795994 chromosome 3447306 3448331 - cytochrome d ubiquinol oxidase subunit II False
DVU3271 cydA CDS 2795995 chromosome 3448377 3449678 - cytochrome d ubiquinol oxidase subunit I False
DVU3330 CDS 2796341 chromosome 3503964 3504239 + hypothetical protein DVU3330 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.