Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 278 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 278

There are 17 regulatory influences for Module 278

Regulator Table (17)
Regulator Name Type
DVU2557 tf
DVU1063 tf
DVU2195
DVU0629		 combiner
DVU1674
DVU1561		 combiner
DVU2547 tf
DVU0379
DVU0653		 combiner
DVU2557
DVU2195		 combiner
DVU3167 tf
DVU0653 tf
DVU1419 tf
DVU0309
DVU0653		 combiner
DVU1949 tf
DVU2686
DVU2195		 combiner
DVU1144 tf
DVU2909
DVU0569		 combiner
DVU2275
DVU0569		 combiner
DVU1561
DVU2394		 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
531 4.20e+04 cgtCCGaCtcctactttTtcag
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 RegPredict
532 1.10e+05 AAAGACTT
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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 278 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolic pathways kegg pathway 7.47e-03 1.49e-02 8/29
Biosynthesis of secondary metabolites kegg pathway 1.39e-02 2.28e-02 4/29
Amino Acid Metabolism kegg subcategory 3.60e-04 3.71e-03 6/29
Metabolism of Cofactors and Vitamins kegg subcategory 1.28e-02 4.22e-02 3/29
Metabolism kegg subcategory 9.89e-04 7.45e-03 13/29
Metabolism kegg category 2.18e-04 2.38e-03 15/29
Global kegg category 9.89e-04 8.08e-03 13/29
Metabolism kegg category 2.12e-02 4.40e-02 8/29
Metabolism of Cofactors and Vitamins kegg subcategory 1.24e-02 3.04e-02 3/29
Global kegg category 2.46e-03 1.18e-02 9/29
Metabolism kegg subcategory 2.46e-03 1.18e-02 9/29
Metabolic pathways kegg pathway 7.47e-03 2.20e-02 8/29
Biosynthesis of secondary metabolites kegg pathway 1.39e-02 3.29e-02 4/29

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
biosynthetic process biological_process 4.52e-04 1.37e-03 3/29

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Translation, ribosomal structure and biogenesis cog subcategory 6.86e-03 1.21e-02 4/29
Cell wall/membrane/envelope biogenesis cog subcategory 8.09e-03 1.42e-02 4/29
Coenzyme transport and metabolism cog subcategory 1.58e-02 2.62e-02 3/29
General function prediction only cog subcategory 2.01e-02 3.27e-02 5/29
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 278

There are 29 genes in Module 278

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0135 CDS 2794158 chromosome 171562 172473 - hypothetical protein DVU0135 False
DVU0450 ribF CDS 2793373 chromosome 514816 515760 + riboflavin biosynthesis protein RibF False
DVU0660 CDS 2794246 chromosome 731288 731854 + phosphodiesterase False
DVU0723 purT CDS 2794128 chromosome 805115 806296 + phosphoribosylglycinamide formyltransferase 2 False
DVU0724 CDS 2794129 chromosome 806523 807929 - sodium/alanine symporter family protein False
DVU0768 murI CDS 2795572 chromosome 858973 859821 - glutamate racemase False
DVU0769 CDS 2794840 chromosome 859823 860701 - pyridoxamine kinase False
DVU0808 gatA CDS 2796531 chromosome 893450 894919 - aspartyl/glutamyl-tRNA amidotransferase subunit A False
DVU0869 uppS CDS 2795168 chromosome 961920 962663 - undecaprenyl diphosphate synthase False
DVU1060 CDS 2794772 chromosome 1160947 1162050 - glycosyl transferase group 1 family protein False
DVU1215 CDS 2796673 chromosome 1305895 1306551 - PAP2 family protein False
DVU1454 ispD CDS 2794820 chromosome 1532607 1533794 - 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase False
DVU1538 CDS 2793688 chromosome 1605189 1605713 - hypothetical protein DVU1538 False
DVU1573 pth CDS 2793464 chromosome 1655955 1656560 - peptidyl-tRNA hydrolase False
DVU2209 CDS 2795356 chromosome 2304321 2305043 + hypothetical protein DVU2209 False
DVU2436 CDS 2795427 chromosome 2540394 2541026 + hypothetical protein DVU2436 False
DVU2581 CDS 2794994 chromosome 2703132 2703572 + response regulator False
DVU2756 CDS 2794029 chromosome 2864853 2865971 + radical SAM domain-containing protein False
DVU2872 CDS 2795536 chromosome 2966622 2968322 - lambda family phage portal protein False
DVU2902 pyrC CDS 2793932 chromosome 3001346 3002614 + dihydroorotase False
DVU2916 hemK CDS 2794057 chromosome 3016134 3017021 + hemK protein False
DVU2945 CDS 2796496 chromosome 3049173 3050030 + hypothetical protein DVU2945 False
DVU2995 CDS 2796309 chromosome 3105499 3106662 - glycosyl transferase group 1 family protein False
DVU3050 CDS 2796076 chromosome 3175842 3176276 - hypothetical protein DVU3050 False
DVU3109 CDS 2796601 chromosome 3258440 3258640 - iron-sulfur cluster-binding protein False
DVU3116 prfC CDS 2796608 chromosome 3264560 3266149 + peptide chain release factor 3 False
DVU3207 CDS 2796205 chromosome 3372044 3374140 + RNB-like family protein False
DVU3223 aspB CDS 2796221 chromosome 3392687 3393859 - aspartate aminotransferase False
DVU3361 CDS 2795675 chromosome 3531411 3532436 + ADP-heptose synthase 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.