Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 62 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 62

There are 12 regulatory influences for Module 62

Regulator Table (12)
Regulator Name Type
DVU2547
DVU1730		 combiner
DVU0110 tf
DVU3080 tf
DVU1561
DVU1584		 combiner
DVU1517 tf
DVU0309
DVU3023		 combiner
DVUA0024 tf
DVU2567
DVU2675		 combiner
DVU0309
DVU1547		 combiner
DVU2960
DVU1730		 combiner
DVU3167 tf
DVU0309
DVU1340		 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
121 1.70e-05 aattt.atGCcAGCCcTA.AGT
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 RegPredict
122 3.60e+00 atAcaAaGATcAtTTTaT
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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 62 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Flagellar assembly kegg pathway 3.71e-04 2.89e-03 3/27
Metabolic pathways kegg pathway 1.54e-02 2.45e-02 7/27
Cell Motility kegg subcategory 7.19e-03 2.96e-02 3/27
Metabolism kegg subcategory 1.60e-02 4.80e-02 10/27
Cellular Processes kegg category 7.19e-03 4.14e-02 3/27
Metabolism kegg category 1.31e-02 3.16e-02 8/27
Amino Acid Metabolism kegg subcategory 1.74e-02 3.84e-02 3/27
Cellular Processes kegg category 4.60e-03 1.65e-02 3/27
Cell Motility kegg subcategory 4.60e-03 1.65e-02 3/27
Flagellar assembly kegg pathway 3.71e-04 3.88e-03 3/27
Global kegg category 1.77e-02 3.88e-02 7/27
Metabolism kegg subcategory 1.77e-02 3.88e-02 7/27
Metabolic pathways kegg pathway 1.54e-02 3.52e-02 7/27

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
metabolic process biological_process 2.49e-03 4.91e-03 4/27
iron-sulfur cluster binding molecular_function 6.94e-03 1.09e-02 3/27

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Coenzyme transport and metabolism cog subcategory 1.87e-03 2.51e-02 4/27
Cell wall/membrane/envelope biogenesis cog subcategory 2.96e-02 4.65e-02 3/27
Amino acid transport and metabolism cog subcategory 2.41e-02 3.86e-02 4/27
Coenzyme transport and metabolism cog subcategory 1.87e-03 3.52e-03 4/27
Function unknown cog subcategory 2.07e-02 3.36e-02 3/27
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 62

There are 27 genes in Module 62

Gene Member Table (27)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0247 CDS 2794295 chromosome 280944 281303 - response regulator False
DVU0250 CDS 2794298 chromosome 284703 285290 - hypothetical protein DVU0250 False
DVU0319 CDS 2794177 chromosome 362485 363510 - NAD-dependent epimerase/dehydratase False
DVU0325 hypD CDS 2794327 chromosome 367932 369029 + hydrogenase expression/formation protein HypD False
DVU0349 CDS 2794676 chromosome 396098 397156 - NeuB family protein False
DVU0394 CDS 2794250 chromosome 442741 443763 - radical SAM domain-containing protein False
DVU0499 CDS 2794727 chromosome 570496 570891 - hypothetical protein DVU0499 False
DVU0523 flgM CDS 2794889 chromosome 597294 597608 - negative regulator of flagellin synthesis FlgM False
DVU0524 CDS 2794890 chromosome 597634 598050 - hypothetical protein DVU0524 False
DVU0800 CDS 2795095 chromosome 885776 885982 - hypothetical protein DVU0800 False
DVU1670 CDS 2794392 chromosome 1749981 1750619 - hypothetical protein DVU1670 False
DVU1868 dapA CDS 2794312 chromosome 1933424 1934302 + dihydrodipicolinate synthase False
DVU1953 proA CDS 2793523 chromosome 2026227 2027486 + gamma-glutamyl phosphate reductase False
DVU2042 CDS 2794538 chromosome 2119999 2120793 + Fic family protein False
DVU2082 CDS 2793536 chromosome 2167481 2168374 + flagellin False
DVU2203 CDS 2793666 chromosome 2299312 2299686 + L-PSP family endoribonuclease False
DVU2446 panB CDS 2796623 chromosome 2550513 2551436 + 3-methyl-2-oxobutanoate hydroxymethyltransferase False
DVU2475 CDS 2795657 chromosome 2583408 2584250 + ferredoxin-NADP(+) reductase subunit alpha False
DVU2735 paaK-3 CDS 2795937 chromosome 2836219 2837517 + phenylacetate-coenzyme A ligase False
DVU2756 CDS 2794029 chromosome 2864853 2865971 + radical SAM domain-containing protein False
DVU2883 selA CDS 2795548 chromosome 2979887 2981296 + selenocysteine synthase False
DVU2884 CDS 2795549 chromosome 2981355 2982758 + aminopeptidase 1 False
DVU2897 CDS 2793927 chromosome 2995616 2996605 + hypothetical protein DVU2897 False
DVU2948 CDS 2796499 chromosome 3053486 3054334 + flagellin N-terminal domain-containing protein False
DVU3068 CDS 2796419 chromosome 3205678 3208161 + GAF domain/sensory box/EAL domain-containing protein False
DVU3208 CDS 2796206 chromosome 3374162 3375145 + membrane protein False
DVU3364 CDS 2795678 chromosome 3534750 3535673 - hypothetical protein DVU3364 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.