Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 113 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 113

There are 11 regulatory influences for Module 113

Regulator Table (11)
Regulator Name Type
DVU3167
DVU1584		 combiner
DVU2577
DVU0118		 combiner
DVU3167 tf
DVU2557
DVU2195		 combiner
DVU2547 tf
DVU3220 tf
DVU3167
DVU0063		 combiner
DVU2547
DVU1419		 combiner
DVU2547
DVU2394		 combiner
DVU1561
DVU0118		 combiner
DVU2557
DVU2547		 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
217 6.80e+01 TTTGcCataT
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 RegPredict
218 7.50e+04 atAtCgtagccGcgcgCCTTGC
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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 113 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Histidine metabolism kegg pathway 0.00e+00 1.40e-05 3/21
Aminoacyl-tRNA biosynthesis kegg pathway 2.10e-05 4.73e-04 3/21
Metabolic pathways kegg pathway 1.18e-02 2.00e-02 6/21
Biosynthesis of secondary metabolites kegg pathway 3.32e-03 9.40e-03 4/21
Amino Acid Metabolism kegg subcategory 1.70e-02 4.92e-02 3/21
Translation kegg subcategory 1.37e-03 9.17e-03 3/21
Metabolism kegg subcategory 1.50e-03 9.83e-03 10/21
Genetic Information Processing kegg category 4.41e-03 2.81e-02 4/21
Global kegg category 1.50e-03 1.15e-02 10/21
Amino Acid Metabolism kegg subcategory 7.08e-03 2.14e-02 3/21
Histidine metabolism kegg pathway 0.00e+00 1.30e-05 3/21
Genetic Information Processing kegg category 2.50e-03 1.19e-02 4/21
Translation kegg subcategory 1.37e-03 8.61e-03 3/21
Aminoacyl-tRNA biosynthesis kegg pathway 2.10e-05 5.20e-04 3/21
Global kegg category 1.34e-02 3.21e-02 6/21
Metabolism kegg subcategory 1.34e-02 3.21e-02 6/21
Metabolic pathways kegg pathway 1.18e-02 2.93e-02 6/21
Biosynthesis of secondary metabolites kegg pathway 3.32e-03 1.37e-02 4/21

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
histidine biosynthetic process biological_process 0.00e+00 2.00e-06 3/21
ATP binding molecular_function 3.04e-02 3.89e-02 4/21

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
tRNA aminoacylation tigr sub1role 1.60e-05 1.98e-04 3/21
Protein synthesis tigr mainrole 3.57e-03 1.77e-02 3/21
Protein synthesis tigr mainrole 3.57e-03 5.67e-03 3/21
tRNA aminoacylation tigr sub1role 1.60e-05 4.40e-05 3/21

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Translation, ribosomal structure and biogenesis cog subcategory 1.55e-03 2.23e-02 4/21
Information storage and processing cog category 1.25e-02 2.12e-02 5/21
Translation, ribosomal structure and biogenesis cog subcategory 1.55e-03 2.94e-03 4/21
Amino acid transport and metabolism cog subcategory 8.25e-03 1.44e-02 4/21
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 113

There are 21 genes in Module 113

Gene Member Table (21)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0113 hisI CDS 2794982 chromosome 147117 147497 + phosphoribosyl-AMP cyclohydrolase False
DVU0114 hisG CDS 2794983 chromosome 147494 148375 + ATP phosphoribosyltransferase False
DVU0387 CDS 2795061 chromosome 435519 436196 + His/Glu/Gln/Arg/opine ABC transporter permease False
DVU0794 fabI CDS 2794516 chromosome 879315 880079 - enoyl-ACP reductase False
DVU0796 hisD CDS 2794518 chromosome 881106 882416 - histidinol dehydrogenase False
DVU0885 CDS 2794197 chromosome 975521 976309 - amidohydrolase family protein False
DVU1042 tatB CDS 2795263 chromosome 1144695 1145063 - twin-arginine translocation protein TatB False
DVU1764 CDS 2795811 chromosome 1827038 1827307 + hypothetical protein DVU1764 False
DVU1863 CDS 2793645 chromosome 1930440 1931258 + flagellar synthesis regulator FleN False
DVU1950 CDS 2796185 chromosome 2022676 2023272 - indolepyruvate ferredoxin oxidoreductase subunit beta False
DVU1952 CDS 2793522 chromosome 2025171 2025866 - hypothetical protein DVU1952 False
DVU2051 CDS 2794547 chromosome 2127643 2128941 - hypothetical protein DVU2051 False
DVU2054 CDS 2796478 chromosome 2130967 2131065 - hypothetical protein DVU2054 False
DVU2275 CDS 2795231 chromosome 2363991 2365445 + sigma-54 dependent transcriptional regulator True
DVU2522 CDS 2795612 chromosome 2634024 2634626 + hypothetical protein DVU2522 False
DVU2552 gltX CDS 2796126 chromosome 2663659 2665050 - glutamyl-tRNA synthetase False
DVU2910 CDS 2794051 chromosome 3011248 3011853 + hypothetical protein DVU2910 False
DVU2916 hemK CDS 2794057 chromosome 3016134 3017021 + hemK protein False
DVU2917 lpxC CDS 2794058 chromosome 3017229 3018155 + UDP-3-O- False
DVU3367 aspS CDS 2795681 chromosome 3537577 3539409 - aspartyl-tRNA synthetase False
DVU3368 hisS CDS 2795682 chromosome 3539428 3540681 - histidyl-tRNA synthetase 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.