Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 146 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 146

There are 11 regulatory influences for Module 146

Regulator Table (11)
Regulator Name Type
DVU3193
DVU1690		 combiner
DVU2423
DVU1402		 combiner
DVU2557
DVU1690		 combiner
DVU0606
DVU1690		 combiner
DVU2686 tf
DVU1730 tf
DVU0525 tf
DVU1745 tf
DVU0230 tf
DVU0057 tf
DVU2423
DVU0619		 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
279 5.10e-02 GcCaGcttcTACcGGa
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 RegPredict
280 8.10e+04 C.ataCgc.T.tacTc.GtgAcgg
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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 146 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Biosynthesis of secondary metabolites kegg pathway 3.34e-03 9.46e-03 5/30
Microbial metabolism in diverse environments kegg pathway 1.72e-02 2.68e-02 3/30
Carbohydrate Metabolism kegg subcategory 6.58e-03 2.79e-02 5/30
Amino Acid Metabolism kegg subcategory 0.00e+00 3.00e-06 10/30
Metabolism kegg subcategory 4.05e-04 4.01e-03 14/30
Metabolism kegg category 3.00e-06 7.70e-05 18/30
Global kegg category 4.05e-04 4.08e-03 14/30
Amino Acid Metabolism kegg subcategory 4.77e-03 1.69e-02 4/30
Biosynthesis of secondary metabolites kegg pathway 3.34e-03 1.38e-02 5/30
Microbial metabolism in diverse environments kegg pathway 1.72e-02 3.81e-02 3/30

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 2.95e-02 4.64e-02 11/30
Amino acid transport and metabolism cog subcategory 9.47e-03 1.64e-02 5/30
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 146

There are 30 genes in Module 146

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0041 CDS 2796562 chromosome 47257 49020 - Slt family transglycosylase False
DVU0841 CDS 2794853 chromosome 929194 930375 - aspartate aminotransferase False
DVU0896 CDS 2794114 chromosome 988431 989825 + NLP/P60 family lipoprotein False
DVU0899 CDS 2794117 chromosome 992166 992426 + hypothetical protein DVU0899 False
DVU0936 CDS 2794610 chromosome 1028071 1028445 + hypothetical protein DVU0936 True
DVU0965 CDS 2794468 chromosome 1062907 1063083 + hypothetical protein DVU0965 False
DVU0966 CDS 2794469 chromosome 1063178 1063996 + amino acid ABC transporter periplasmic amino acid-binding protein False
DVU1038 hisA CDS 2796251 chromosome 1141452 1142201 - 1-(5-phosphoribosyl)-5- False
DVU1064 CDS 2794776 chromosome 1165948 1167876 + aconitate hydratase False
DVU1067 CDS 2794037 chromosome 1170790 1171938 + Bmp family membrane protein False
DVU1238 CDS 2794415 chromosome 1326839 1327579 - amino acid ABC transporter periplasmic amino acid-binding protein False
DVU1392 CDS 2794792 chromosome 1464357 1465154 + NLP/P60 family protein False
DVU1406 purM CDS 2794658 chromosome 1474610 1475662 + phosphoribosylaminoimidazole synthetase False
DVU1423 lpdA CDS 2794684 chromosome 1496557 1497927 - 2-oxoglutarate dehydrogenase, E3 component, lipoamide dehydrogenase False
DVU1615 paaK-2 CDS 2796068 chromosome 1700751 1702058 - phenylacetate-coenzyme A ligase False
DVU1910 CDS 2793683 chromosome 1984961 1986685 + YjeF-like protein False
DVU1954 nadD CDS 2793467 chromosome 2027512 2028216 + nicotinate (nicotinamide) nucleotide adenylyltransferase False
DVU1990 CDS 2793796 chromosome 2068980 2069627 + hypothetical protein DVU1990 False
DVU2056 CDS 2796480 chromosome 2133136 2133258 + hypothetical protein DVU2056 False
DVU2150 CDS 2793409 chromosome 2249277 2249639 - dnaK suppressor protein False
DVU2251 CDS 2795403 chromosome 2346940 2347500 - DNA-binding protein True
DVU2364 CDS 2796523 chromosome 2461234 2462400 - class I/II aminotransferase False
DVU2782 CDS 2796332 chromosome 2888408 2888572 - hypothetical protein DVU2782 False
DVU2783 CDS 2796333 chromosome 2888557 2889357 - hypothetical protein DVU2783 False
DVU2791 CDS 2795377 chromosome 2893852 2894631 + cytochrome c family protein False
DVU2940 CDS 2796491 chromosome 3045121 3045390 + hypothetical protein DVU2940 False
DVU3171 CDS 2795876 chromosome 3327925 3328314 + cytochrome c3 False
DVU3187 hup-4 CDS 2793837 chromosome 3347046 3347333 + DNA-binding protein HU False
DVU3238 CDS 2793888 chromosome 3409566 3409970 - response regulator False
DVU3277 CDS 2796001 chromosome 3452418 3452516 - hypothetical protein DVU3277 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.