Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 248 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 248

There are 18 regulatory influences for Module 248

Regulator Table (18)
Regulator Name Type
DVU0629 tf
DVU1744 tf
DVU2557 tf
DVU2644 tf
DVU2532
DVU1788		 combiner
DVUA0024 tf
DVU1788
DVU2275		 combiner
DVU1547 tf
DVU3167
DVU1690		 combiner
DVU3142 tf
DVU2547
DVU1628		 combiner
DVU0744
DVU2690		 combiner
DVU0619
DVU3381		 combiner
DVU2086
DVU0619		 combiner
DVU1402 tf
DVU2547
DVU2644		 combiner
DVU0653
DVU2275		 combiner
DVU3167
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
473 2.30e+02 TTtTcCG
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 RegPredict
474 4.60e+03 agTatcTT
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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 248 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Ribosome kegg pathway 0.00e+00 0.00e+00 8/16
Metabolic pathways kegg pathway 2.04e-03 7.27e-03 6/16
Nucleotide Metabolism kegg subcategory 4.98e-04 4.69e-03 3/16
Metabolism of Cofactors and Vitamins kegg subcategory 1.36e-03 9.17e-03 3/16
Translation kegg subcategory 0.00e+00 0.00e+00 8/16
Metabolism kegg subcategory 2.15e-03 1.23e-02 8/16
Metabolism kegg category 9.51e-04 8.03e-03 9/16
Genetic Information Processing kegg category 0.00e+00 0.00e+00 9/16
Global kegg category 2.15e-03 1.56e-02 8/16
Metabolism kegg category 5.32e-03 1.79e-02 6/16
Metabolism of Cofactors and Vitamins kegg subcategory 1.31e-03 8.58e-03 3/16
Genetic Information Processing kegg category 0.00e+00 0.00e+00 9/16
Translation kegg subcategory 0.00e+00 0.00e+00 8/16
Ribosome kegg pathway 0.00e+00 0.00e+00 8/16
Global kegg category 2.36e-03 1.15e-02 6/16
Metabolism kegg subcategory 2.36e-03 1.15e-02 6/16
Metabolic pathways kegg pathway 2.04e-03 1.05e-02 6/16

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
translation biological_process 0.00e+00 0.00e+00 8/16
RNA binding molecular_function 4.30e-05 1.90e-04 3/16
structural constituent of ribosome molecular_function 0.00e+00 0.00e+00 8/16

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Ribosomal proteins: synthesis and modification tigr sub1role 0.00e+00 0.00e+00 6/16
Protein synthesis tigr mainrole 0.00e+00 1.10e-05 6/16
Protein synthesis tigr mainrole 0.00e+00 1.00e-06 6/16
Ribosomal proteins: synthesis and modification tigr sub1role 0.00e+00 0.00e+00 6/16

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Translation, ribosomal structure and biogenesis cog subcategory 0.00e+00 0.00e+00 8/16
Information storage and processing cog category 0.00e+00 1.00e-06 10/16
Information storage and processing cog category 0.00e+00 0.00e+00 10/16
Translation, ribosomal structure and biogenesis cog subcategory 0.00e+00 0.00e+00 8/16
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 248

There are 16 genes in Module 248

Gene Member Table (16)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU1197 nusB CDS 2796654 chromosome 1289617 1290078 - N utilization substance protein B False
DVU1198 ribH CDS 2796655 chromosome 1290082 1290552 - 6,7-dimethyl-8-ribityllumazine synthase False
DVU1199 ribAB CDS 2796656 chromosome 1290684 1291913 - 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II False
DVU1203 glyA CDS 2796660 chromosome 1294345 1295583 - serine hydroxymethyltransferase False
DVU1204 fabF CDS 2796661 chromosome 1295642 1296889 - 3-oxoacyl-ACP synthase False
DVU1304 rplD CDS 2795192 chromosome 1394209 1394829 + 50S ribosomal protein L4 False
DVU1305 rplW CDS 2795193 chromosome 1394795 1395133 + 50S ribosomal protein L23 False
DVU1306 rplB CDS 2794189 chromosome 1395137 1395967 + 50S ribosomal protein L2 False
DVU1307 rpsS CDS 2794190 chromosome 1395977 1396258 + 30S ribosomal protein S19 False
DVU1314 rplX CDS 2794381 chromosome 1398521 1398844 + 50S ribosomal protein L24 False
DVU1315 rplE CDS 2794382 chromosome 1398856 1399395 + 50S ribosomal protein L5 False
DVU1321 rpmD CDS 2794388 chromosome 1401438 1401608 + 50S ribosomal protein L30 False
DVU1322 rplO CDS 2794617 chromosome 1401608 1402054 + 50S ribosomal protein L15 False
DVU1623 pyrG CDS 2795884 chromosome 1707295 1708938 + CTP synthetase False
DVU2226 CDS 2795553 chromosome 2318897 2320312 - acetyl-CoA carboxylase, biotin carboxylase False
DVU2929 rpoC CDS 2793967 chromosome 3028905 3033062 + DNA-directed RNA polymerase subunit beta' 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.