Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 54 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 54

There are 9 regulatory influences for Module 54

Regulator Table (9)
Regulator Name Type
DVU0606
DVU0269		 combiner
DVU1949 tf
DVU2886 tf
DVU1419
DVU2832		 combiner
DVU0057
DVU0539		 combiner
DVU3220
DVU2832		 combiner
DVU0057
DVU1419		 combiner
DVU0539
DVU1419		 combiner
DVU0606
DVU1949		 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
105 1.10e+02 aaAttacAGaaaGtTAca
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 RegPredict
106 1.00e+03 TCtcTCtTT.TGttacgC
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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 54 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Phenylalanine tyrosine and tryptophan biosynthesis kegg pathway 0.00e+00 0.00e+00 10/26
Metabolic pathways kegg pathway 0.00e+00 3.00e-06 14/26
Biosynthesis of secondary metabolites kegg pathway 0.00e+00 0.00e+00 11/26
Amino Acid Metabolism kegg subcategory 0.00e+00 0.00e+00 12/26
Metabolism kegg subcategory 0.00e+00 0.00e+00 26/26
Metabolism kegg category 6.00e-06 1.19e-04 16/26
Global kegg category 0.00e+00 0.00e+00 26/26
Metabolism kegg category 4.00e-06 1.31e-04 13/26
Amino Acid Metabolism kegg subcategory 0.00e+00 0.00e+00 10/26
Phenylalanine tyrosine and tryptophan biosynthesis kegg pathway 0.00e+00 0.00e+00 10/26
Global kegg category 0.00e+00 4.00e-06 14/26
Metabolism kegg subcategory 0.00e+00 4.00e-06 14/26
Metabolic pathways kegg pathway 0.00e+00 3.00e-06 14/26
Biosynthesis of secondary metabolites kegg pathway 0.00e+00 0.00e+00 11/26

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
proteolysis biological_process 7.31e-04 1.89e-03 3/26
tryptophan metabolic process biological_process 0.00e+00 0.00e+00 4/26

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Aromatic amino acid family tigr sub1role 0.00e+00 1.00e-06 3/26
Amino acid biosynthesis tigr mainrole 2.68e-04 3.92e-03 3/26
Amino acid biosynthesis tigr mainrole 2.68e-04 5.73e-04 3/26
Aromatic amino acid family tigr sub1role 0.00e+00 0.00e+00 3/26

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Amino acid transport and metabolism cog subcategory 0.00e+00 1.00e-06 11/26
Metabolism cog category 7.10e-05 1.65e-03 15/26
Metabolism cog category 6.70e-04 1.35e-03 13/26
Amino acid transport and metabolism cog subcategory 0.00e+00 0.00e+00 11/26
Coenzyme transport and metabolism cog subcategory 1.07e-02 1.84e-02 3/26
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 54

There are 26 genes in Module 54

Gene Member Table (26)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0236 CDS 2796585 chromosome 269283 270425 - phage integrase family site specific recombinase False
DVU0415 pepA CDS 2795178 chromosome 465244 466767 + cytosol aminopeptidase False
DVU0462 CDS 2794475 chromosome 529454 530629 + chorismate mutase/prephenate dehydratase False
DVU0463 aroA CDS 2794476 chromosome 530629 531948 + 3-phosphoshikimate 1-carboxyvinyltransferase False
DVU0464 CDS 2794477 chromosome 531954 532721 + prephenate dehydrogenase False
DVU0465 CDS 2794478 chromosome 532853 534451 + anthranilate synthase, component I False
DVU0466 trpG CDS 2793607 chromosome 534432 535061 + anthranilate synthase, glutamine amidotransferase component False
DVU0467 trpD CDS 2793608 chromosome 535058 536056 + anthranilate phosphoribosyltransferase False
DVU0468 trpC CDS 2793609 chromosome 536049 536822 + indole-3-glycerol phosphate synthase False
DVU0469 trpF-1 CDS 2793610 chromosome 536870 537724 + N-(5'-phosphoribosyl)anthranilate isomerase False
DVU0470 trpB-2 CDS 2793611 chromosome 537721 538908 + tryptophan synthase subunit beta False
DVU0471 trpA CDS 2794713 chromosome 538905 539678 + tryptophan synthase subunit alpha False
DVU0905 lipA CDS 2795415 chromosome 997479 998375 - lipoyl synthase False
DVU0908 CDS 2795418 chromosome 1001899 1003530 - iron-sulfur cluster-binding protein False
DVU0943 CDS 2794587 chromosome 1035361 1037160 + hypothetical protein DVU0943 False
DVU0944 CDS 2794588 chromosome 1037214 1037471 + hypothetical protein DVU0944 False
DVU0946 CDS 2794590 chromosome 1039992 1041422 + sigma-54 dependent transcriptional regulator/response regulator True
DVU1017 CDS 2793740 chromosome 1117054 1119384 + ABC transporter ATP-binding protein/permease False
DVU1018 CDS 2793741 chromosome 1119387 1120733 + HlyD family type I secretion membrane fusion protein False
DVU1020 CDS 2793743 chromosome 1121956 1124061 + HD domain/sensory box protein False
DVU1141 CDS 2793424 chromosome 1238043 1238474 - hypothetical protein DVU1141 False
DVU1847 CDS 2795910 chromosome 1915787 1916680 - hypothetical protein DVU1847 False
DVU2052 CDS 2794549 chromosome 2129341 2130063 + glycosyl transferase group 2 family protein False
DVU2056 CDS 2796480 chromosome 2133136 2133258 + hypothetical protein DVU2056 False
DVU2144 gap-2 CDS 2794223 chromosome 2241689 2242690 + glyceraldehyde 3-phosphate dehydrogenase False
DVU3102 CDS 2795974 chromosome 3242061 3242648 + hypothetical protein DVU3102 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.