Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 169 Profile

GeneModule member RegulatorRegulator MotifMotif
Cytoscape Web
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 169

There are 8 regulatory influences for Module 169

Regulator Table (8)
Regulator Name Type
DVU3167
DVU0063
combiner
DVU1518
DVU2086
combiner
DVU2532
DVU0653
combiner
DVU0619
DVU3381
combiner
DVU0619
DVU0525
combiner
DVU0744
DVU0230
combiner
DVU3167
DVU1572
combiner
DVU2086
DVU2832
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
323 9.00e-06 AAGaGaatGagGtcTtaTaCC
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RegPredict
324 2.90e-04 aAcctGTGCaggGctggcGAcAtg
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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 169 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Fatty acid biosynthesis kegg pathway 1.00e-06 3.30e-05 3/26
Riboflavin metabolism kegg pathway 0.00e+00 4.00e-06 3/26
Metabolic pathways kegg pathway 1.54e-04 1.73e-03 10/26
Lipid Metabolism kegg subcategory 1.40e-05 3.12e-04 4/26
Nucleotide Metabolism kegg subcategory 3.39e-03 1.70e-02 3/26
Metabolism of Cofactors and Vitamins kegg subcategory 1.19e-03 8.33e-03 4/26
Translation kegg subcategory 3.11e-03 1.60e-02 3/26
Replication and Repair kegg subcategory 1.01e-03 7.51e-03 3/26
Metabolism kegg subcategory 2.33e-04 2.77e-03 13/26
Metabolism kegg category 6.00e-06 1.19e-04 16/26
Genetic Information Processing kegg category 3.33e-04 3.48e-03 6/26
Global kegg category 2.33e-04 2.49e-03 13/26
Metabolism kegg category 2.50e-05 6.02e-04 12/26
Lipid Metabolism kegg subcategory 1.35e-04 2.03e-03 3/26
Fatty acid biosynthesis kegg pathway 1.00e-06 3.00e-05 3/26
Metabolism of Cofactors and Vitamins kegg subcategory 1.14e-03 7.95e-03 4/26
Riboflavin metabolism kegg pathway 0.00e+00 4.00e-06 3/26
Genetic Information Processing kegg category 6.67e-03 2.05e-02 4/26
Translation kegg subcategory 3.11e-03 1.33e-02 3/26
Global kegg category 1.92e-04 2.56e-03 10/26
Metabolism kegg subcategory 1.92e-04 2.56e-03 10/26
Metabolic pathways kegg pathway 1.54e-04 2.22e-03 10/26

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
fatty acid biosynthetic process biological_process 0.00e+00 3.00e-06 3/26

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Biosynthesis tigr sub1role 0.00e+00 1.00e-05 3/26
Riboflavin, FMN, and FAD tigr sub1role 0.00e+00 1.00e-06 3/26
Fatty acid and phospholipid metabolism tigr mainrole 0.00e+00 2.30e-05 3/26
Protein synthesis tigr mainrole 7.91e-03 2.66e-02 3/26
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 5.53e-04 6.45e-03 3/26
Fatty acid and phospholipid metabolism tigr mainrole 0.00e+00 1.00e-06 3/26
Biosynthesis tigr sub1role 0.00e+00 1.00e-06 3/26
Protein synthesis tigr mainrole 7.91e-03 1.10e-02 3/26
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 5.53e-04 1.09e-03 3/26
Riboflavin, FMN, and FAD 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
Lipid transport and metabolism cog subcategory 2.03e-04 5.81e-03 3/26
Metabolism cog category 2.37e-02 3.79e-02 10/26
Translation, ribosomal structure and biogenesis cog subcategory 2.29e-02 3.69e-02 3/26
Coenzyme transport and metabolism cog subcategory 1.07e-02 1.84e-02 3/26
Lipid transport and metabolism cog subcategory 2.03e-04 4.60e-04 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 169

There are 26 genes in Module 169

Gene Member Table (26)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU1002 CDS 2795118 chromosome 1097829 1098284 + hypothetical protein DVU1002 False
DVU1003 CDS 2795119 chromosome 1098299 1099285 + dnaJ domain-containing protein False
DVU1194 CDS 2796594 chromosome 1285511 1286617 - hypothetical protein DVU1194 False
DVU1195 CDS 2796595 chromosome 1286583 1287101 - lipoprotein False
DVU1196 leuS CDS 2796653 chromosome 1287085 1289574 - leucyl-tRNA synthetase False
DVU1198 ribH CDS 2796655 chromosome 1290082 1290552 - 6,7-dimethyl-8-ribityllumazine synthase False
DVU1200 ribE CDS 2796657 chromosome 1291945 1292607 - riboflavin synthase subunit alpha False
DVU1201 ribD CDS 2796658 chromosome 1292613 1293746 - riboflavin biosynthesis protein RibD False
DVU1202 CDS 2796659 chromosome 1293749 1294279 - cytidine/deoxycytidylate deaminase family protein False
DVU1203 glyA CDS 2796660 chromosome 1294345 1295583 - serine hydroxymethyltransferase False
DVU1204 fabF CDS 2796661 chromosome 1295642 1296889 - 3-oxoacyl-ACP synthase False
DVU1205 acpP CDS 2796682 chromosome 1297077 1297307 - acyl carrier protein False
DVU1206 fabG CDS 2796683 chromosome 1297364 1298107 - 3-oxoacyl-ACP reductase False
DVU1207 fabH CDS 2796684 chromosome 1298192 1299184 - 3-oxoacyl-ACP synthase False
DVU1209 rpmF CDS 2796686 chromosome 1300271 1300450 - 50S ribosomal protein L32 False
DVU1210 CDS 2796687 chromosome 1300495 1301031 - hypothetical protein DVU1210 False
DVU1211 rpmB CDS 2796688 chromosome 1301234 1301443 + 50S ribosomal protein L28 False
DVU1780 CDS 2794287 chromosome 1843438 1843743 - hypothetical protein DVU1780 False
DVU1781 CDS 2794288 chromosome 1843928 1844593 - hypothetical protein DVU1781 False
DVU1782 CDS 2794289 chromosome 1844586 1846013 - iron-sulfur cluster-binding protein False
DVU1783 CDS 2794290 chromosome 1846006 1846758 - hypothetical protein DVU1783 False
DVU1784 CDS 2794291 chromosome 1846930 1847691 + short chain dehydrogenase/reductase family oxidoreductase False
DVU1785 CDS 2794292 chromosome 1847895 1848497 + MarC membrane protein False
DVU1891 CDS 2794702 chromosome 1963699 1964460 - hypothetical protein DVU1891 False
DVU3176 CDS 2793826 chromosome 3332256 3333578 + UDP-glucose/GDP-mannose dehydrogenase family protein False
DVU3177 CDS 2793827 chromosome 3333673 3333822 + hypothetical protein DVU3177 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.

Comments for Module 169

Please add your comments for this module by using the form below. Your comments will be publicly available.

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Social Help

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.

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.