Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 139 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 139

There are 10 regulatory influences for Module 139

Regulator Table (10)
Regulator Name Type
DVU2567
DVU3313		 combiner
DVU0030 tf
DVU1759 tf
DVU2378 tf
DVU0277
DVU3305		 combiner
DVU2989 tf
DVU3313 tf
DVU0230 tf
DVU2036 tf
DVU0277
DVU0679		 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
269 3.90e-01 aACCttcaTcaatGaaaAGtTaCa
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 RegPredict
270 3.00e+01 TgcatgccgaAgtTCGTc.gG.GT
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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 139 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Methane metabolism kegg pathway 3.90e-05 7.28e-04 4/30
Energy Metabolism kegg subcategory 1.41e-03 9.40e-03 4/30
Replication and Repair kegg subcategory 1.52e-04 2.08e-03 4/30
Genetic Information Processing kegg category 4.64e-03 2.93e-02 5/30
Energy Metabolism kegg subcategory 1.34e-03 8.61e-03 4/30
Methane metabolism kegg pathway 3.90e-05 8.45e-04 4/30
Amino Acid Metabolism kegg subcategory 2.50e-02 5.00e-02 3/30

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
electron transport biological_process 1.00e-06 9.00e-06 9/30
transport biological_process 1.98e-02 2.83e-02 3/30
NADH dehydrogenase (ubiquinone) activity molecular_function 1.60e-05 8.30e-05 3/30
electron carrier activity molecular_function 7.90e-05 2.67e-04 5/30
iron-sulfur cluster binding molecular_function 1.71e-04 4.91e-04 5/30

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Electron transport tigr sub1role 0.00e+00 0.00e+00 5/30
Energy metabolism tigr mainrole 1.00e-06 3.80e-05 6/30
Energy metabolism tigr mainrole 1.00e-06 3.00e-06 6/30
Electron transport tigr sub1role 0.00e+00 0.00e+00 5/30

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy production and conversion cog subcategory 0.00e+00 0.00e+00 13/30
Metabolism cog category 0.00e+00 0.00e+00 22/30
Metabolism cog category 0.00e+00 0.00e+00 21/30
Energy production and conversion cog subcategory 0.00e+00 0.00e+00 13/30
Coenzyme transport and metabolism cog subcategory 1.77e-02 2.92e-02 3/30
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 139

There are 30 genes in Module 139

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0027 CDS 2794135 chromosome 31278 32702 - hypothetical protein DVU0027 False
DVU0095 CDS 2796175 chromosome 125677 126714 - polyamine ABC transporter periplasmic polyamine-binding protein False
DVU0096 potC CDS 2796176 chromosome 126716 127489 - spermidine/putrescine ABC transporter membrane protein False
DVU0339 CDS 2796768 chromosome 384768 385673 - D-isomer specific 2-hydroxyacid dehydrogenase family protein False
DVU0432 CDS 2794675 chromosome 486305 486778 - ech hydrogenase subunit EchC False
DVU0493 CDS 2793707 chromosome 562337 562645 - hypothetical protein DVU0493 False
DVU0953 tyrS CDS 2795149 chromosome 1046362 1047558 + tyrosyl-tRNA synthetase False
DVU1390 CDS 2794790 chromosome 1462982 1463449 - hypothetical protein DVU1390 False
DVU1411 thiC CDS 2794955 chromosome 1480019 1481308 + thiamine biosynthesis protein ThiC False
DVU1530 CDS 2793815 chromosome 1598015 1599625 + metallo-beta-lactamase family protein False
DVU1539 glpX CDS 2793689 chromosome 1605816 1606799 - fructose 1,6-bisphosphatase II False
DVU1608 ligA CDS 2796061 chromosome 1690678 1693077 + DNA ligase, NAD-dependent False
DVU1917 hysB CDS 2793333 chromosome 1991067 1992020 + periplasmic False
DVU1918 hysA CDS 2793334 chromosome 1992054 1993586 + periplasmic False
DVU2347 argD CDS 2795521 chromosome 2440531 2441730 - acetylornithine aminotransferase False
DVU2683 CDS 2795054 chromosome 2796644 2798194 + L-lactate permease family protein False
DVU2790 CDS 2795376 chromosome 2893661 2893801 - hypothetical protein DVU2790 False
DVU2791 CDS 2795377 chromosome 2893852 2894631 + cytochrome c family protein False
DVU2792 CDS 2795378 chromosome 2894645 2895850 + electron transport complex protein RnfC False
DVU2793 CDS 2795379 chromosome 2895988 2896944 + electron transport complex protein RnfD False
DVU2794 CDS 2795380 chromosome 2896947 2897522 + electron transport complex protein RnfG False
DVU2795 CDS 2795381 chromosome 2897534 2898205 + electron transport complex RsxE subunit False
DVU2796 CDS 2795382 chromosome 2898215 2898790 + electron transport complex protein RnfA False
DVU2797 CDS 2795383 chromosome 2898860 2899747 + ferredoxin False
DVU2798 CDS 2795384 chromosome 2899744 2900754 + ApbE family protein False
DVU3026 CDS 2796443 chromosome 3147520 3149232 + L-lactate permease family protein False
DVU3028 CDS 2796445 chromosome 3150824 3152092 + iron-sulfur cluster-binding protein False
DVU3033 CDS 2796450 chromosome 3157385 3159538 + iron-sulfur cluster-binding protein False
DVU3101 CDS 2795973 chromosome 3240930 3241955 + tonB protein False
DVU3371 metE CDS 2795685 chromosome 3542097 3544454 - 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase 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.