Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 128 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 128

There are 11 regulatory influences for Module 128

Regulator Table (11)
Regulator Name Type
DVU3167 tf
DVU0653
DVU2275
combiner
DVU0230 tf
DVU3167
DVU0269
combiner
DVU0653
DVU2251
combiner
DVU2086 tf
DVU1754 tf
DVU0525 tf
DVU1561
DVU0230
combiner
DVU3186
DVU0653
combiner
DVU0653 tf

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
247 2.10e-03 gCaAtTtcT.t.gacTTGTcaCca
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RegPredict
248 1.20e+01 GAAcgGAaCCcaaaggcAGtatAc
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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 128 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Peptidoglycan biosynthesis kegg pathway 0.00e+00 5.00e-06 4/25
Metabolic pathways kegg pathway 9.41e-03 1.72e-02 7/25
Glycan Biosynthesis and Metabolism kegg subcategory 0.00e+00 3.00e-06 5/25
Metabolism kegg subcategory 8.27e-03 3.20e-02 10/25
Metabolism kegg category 6.19e-03 3.76e-02 11/25
Global kegg category 8.27e-03 4.53e-02 10/25
Metabolism kegg category 1.98e-03 1.04e-02 9/25
Amino Acid Metabolism kegg subcategory 1.33e-02 3.20e-02 3/25
Glycan Biosynthesis and Metabolism kegg subcategory 0.00e+00 4.00e-06 5/25
Peptidoglycan biosynthesis kegg pathway 0.00e+00 5.00e-06 4/25
Global kegg category 2.88e-03 1.27e-02 8/25
Metabolism kegg subcategory 2.88e-03 1.27e-02 8/25
Metabolic pathways kegg pathway 9.41e-03 2.54e-02 7/25

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
peptidoglycan biosynthetic process biological_process 0.00e+00 0.00e+00 4/25
cell division biological_process 0.00e+00 1.00e-06 3/25
ATP binding molecular_function 1.75e-02 2.41e-02 5/25

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cell division tigr sub1role 0.00e+00 1.00e-06 3/25
Biosynthesis and degradation of murein sacculus and peptidoglycan tigr sub1role 0.00e+00 0.00e+00 5/25
Cellular processes tigr mainrole 3.22e-04 4.36e-03 3/25
Cell envelope tigr mainrole 1.00e-06 3.10e-05 5/25
Cellular processes tigr mainrole 3.22e-04 6.73e-04 3/25
Cell division tigr sub1role 0.00e+00 0.00e+00 3/25
Cell envelope tigr mainrole 1.00e-06 2.00e-06 5/25
Biosynthesis and degradation of murein sacculus and peptidoglycan tigr sub1role 0.00e+00 0.00e+00 5/25

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cell cycle control, cell division, chromosome partitioning cog subcategory 4.30e-05 1.80e-03 3/25
Cell wall/membrane/envelope biogenesis cog subcategory 7.30e-05 2.64e-03 6/25
Carbohydrate transport and metabolism cog subcategory 3.74e-03 4.18e-02 3/25
Cellular processes and signaling cog category 9.65e-03 1.67e-02 9/25
Cell cycle control, cell division, chromosome partitioning cog subcategory 4.30e-05 1.30e-04 3/25
Cell wall/membrane/envelope biogenesis cog subcategory 7.30e-05 1.91e-04 6/25
Carbohydrate transport and metabolism cog subcategory 3.74e-03 6.85e-03 3/25
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 128

There are 25 genes in Module 128

Gene Member Table (25)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0732 valS CDS 2794946 chromosome 816473 819127 + valyl-tRNA synthetase False
DVU0891 CDS 2794203 chromosome 982410 983603 - class I/II aminotransferase False
DVU1355 CDS 2794921 chromosome 1434875 1435243 + hypothetical protein DVU1355 False
DVU1647 lysA-1 CDS 2795918 chromosome 1726001 1727239 - diaminopimelate decarboxylase False
DVU1648 CDS 2795919 chromosome 1727313 1727753 - lipoprotein False
DVU1649 mutS CDS 2795920 chromosome 1727737 1730454 - DNA mismatch repair protein MutS False
DVU1651 CDS 2795922 chromosome 1731757 1732128 - hypothetical protein DVU1651 False
DVU1652 CDS 2795923 chromosome 1732139 1732663 - HIT family protein False
DVU1655 CDS 2795926 chromosome 1736595 1737761 + LL-diaminopimelate aminotransferase False
DVU1865 CDS 2794309 chromosome 1931601 1931741 + hypothetical protein DVU1865 False
DVU1886 CDS 2793555 chromosome 1957910 1958587 - hypothetical protein DVU1886 False
DVU1887 CDS 2793556 chromosome 1958609 1960351 - hypothetical protein DVU1887 False
DVU1888 CDS 2793557 chromosome 1960433 1961332 - ATP-NAD kinase domain-containing protein False
DVU1889 gmhA CDS 2793558 chromosome 1961468 1962094 + phosphoheptose isomerase False
DVU2499 ftsZ CDS 2795467 chromosome 2609897 2611246 - cell division protein FtsZ False
DVU2500 ftsA CDS 2795628 chromosome 2611296 2612522 - cell division protein FtsA False
DVU2501 CDS 2795629 chromosome 2612553 2613389 - cell division protein FtsQ False
DVU2503 murC CDS 2795631 chromosome 2614272 2615636 - UDP-N-acetylmuramate--L-alanine ligase False
DVU2504 murG CDS 2795632 chromosome 2615647 2616744 - undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase False
DVU2505 CDS 2795633 chromosome 2616748 2617881 - cell cycle protein FtsW False
DVU2506 murD CDS 2795634 chromosome 2617887 2619188 - UDP-N-acetylmuramoylalanine--D-glutamate ligase False
DVU2507 mraY CDS 2795635 chromosome 2619204 2620280 - phospho-N-acetylmuramoyl-pentapeptide-transferase False
DVU2511 CDS 2795639 chromosome 2625241 2625528 - hypothetical protein DVU2511 False
DVU2512 mraW CDS 2795640 chromosome 2625531 2626502 - S-adenosyl-methyltransferase MraW False
DVU2513 mraZ CDS 2795641 chromosome 2626516 2626965 - cell division protein MraZ 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 128

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.