Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 14 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 14

There are 10 regulatory influences for Module 14

Regulator Table (10)
Regulator Name Type
DVUA0143 tf
DVU2423 tf
DVU2557
DVU3255
combiner
DVU2788
DVU3255
combiner
DVU3255 tf
DVUA0151
DVU2989
combiner
DVU2423
DVU2832
combiner
DVU1754
DVU2989
combiner
DVU2557
DVU2036
combiner
DVU2989
DVU2690
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
27 1.50e+02 acACcGGCcGCACaaCgGgaGact
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RegPredict
28 1.30e+03 CaT.CAagA.GaaA
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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 14 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Citrate cycle (TCA cycle) kegg pathway 2.90e-05 6.07e-04 3/30
Metabolic pathways kegg pathway 9.50e-03 1.73e-02 8/30
Biosynthesis of secondary metabolites kegg pathway 1.61e-02 2.53e-02 4/30
Microbial metabolism in diverse environments kegg pathway 1.72e-02 2.68e-02 3/30
Carbohydrate Metabolism kegg subcategory 3.10e-05 6.27e-04 8/30
Amino Acid Metabolism kegg subcategory 2.73e-03 1.45e-02 5/30
Metabolism kegg subcategory 9.60e-05 1.48e-03 15/30
Metabolism kegg category 8.80e-05 1.14e-03 16/30
Global kegg category 9.60e-05 1.24e-03 15/30
Metabolism kegg category 9.03e-03 2.47e-02 9/30
Carbohydrate Metabolism kegg subcategory 3.77e-03 1.48e-02 4/30
Citrate cycle (TCA cycle) kegg pathway 2.90e-05 6.81e-04 3/30
Amino Acid Metabolism kegg subcategory 4.77e-03 1.69e-02 4/30
Global kegg category 1.11e-02 2.82e-02 8/30
Metabolism kegg subcategory 1.11e-02 2.82e-02 8/30
Metabolic pathways kegg pathway 9.50e-03 2.55e-02 8/30
Biosynthesis of secondary metabolites kegg pathway 1.61e-02 3.63e-02 4/30
Microbial metabolism in diverse environments kegg pathway 1.72e-02 3.81e-02 3/30

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
biosynthetic process biological_process 5.17e-04 1.50e-03 3/30
protein serine/threonine phosphatase activity molecular_function 0.00e+00 0.00e+00 3/30

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Poorly characterized cog category 5.43e-03 9.76e-03 8/30
Energy production and conversion cog subcategory 3.06e-02 4.81e-02 4/30
Function unknown cog subcategory 5.94e-03 1.06e-02 4/30
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 14

There are 30 genes in Module 14

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0072 CDS 2794887 chromosome 89105 89884 + glucose-1-phosphate cytidylyl-transferase False
DVU0076 CDS 2795015 chromosome 92916 93953 + glycosyl transferase group 2 family protein False
DVU0080 fumC CDS 2794226 chromosome 97000 98406 + fumarate hydratase False
DVU0328 CDS 2794330 chromosome 371560 372705 - glycosyl transferase group 1 family protein False
DVU0425 CDS 2795218 chromosome 480810 481616 + hypothetical protein DVU0425 False
DVU0428 CDS 2794671 chromosome 483654 483974 + hypothetical protein DVU0428 False
DVU0439 CDS 2794934 chromosome 495372 495662 + YCII-related domain-containing protein False
DVU0441 ade CDS 2796510 chromosome 497613 499340 - adenine deaminase False
DVU0478 CDS 2793623 chromosome 543608 544471 + serine/threonine protein phosphatase family protein False
DVU0638 CDS 2794108 chromosome 707913 708779 - hypothetical protein DVU0638 False
DVU0680 CDS 2794172 chromosome 752095 754167 - sensory box histidine kinase False
DVU0691 CDS 2793631 chromosome 765035 765994 + hypothetical protein DVU0691 False
DVU0699 CDS 2794450 chromosome 773972 775650 + None False
DVU0743 CDS 2795259 chromosome 830471 832468 + sensory box histidine kinase False
DVU1004 CDS 2794642 chromosome 1099427 1100311 - hypothetical protein DVU1004 False
DVU1051 ccmE CDS 2794897 chromosome 1153168 1153581 - cytochrome c-type biogenesis protein CcmE False
DVU1064 CDS 2794776 chromosome 1165948 1167876 + aconitate hydratase False
DVU1423 lpdA CDS 2794684 chromosome 1496557 1497927 - 2-oxoglutarate dehydrogenase, E3 component, lipoamide dehydrogenase False
DVU1425 gcvPA CDS 2794686 chromosome 1499359 1500690 - glycine dehydrogenase subunit 1 False
DVU1452 dtd CDS 2794818 chromosome 1530262 1530750 - D-tyrosyl-tRNA(Tyr) deacylase False
DVU1607 CDS 2796060 chromosome 1689878 1690624 + hypothetical protein DVU1607 False
DVU1926 CDS 2793342 chromosome 1999118 1999606 + hypothetical protein DVU1926 False
DVU2568 CDS 2796261 chromosome 2681380 2682618 + M20/M25/M40 family peptidase False
DVU2583 CDS 2794996 chromosome 2704465 2704971 + lipoprotein False
DVU2627 CDS 2795244 chromosome 2744482 2744859 - hypothetical protein DVU2627 False
DVU2673 CDS 2795044 chromosome 2784563 2785732 + anaerobic glycerol-3-phosphate dehydrogenase subunit A, truncation False
DVU2779 CDS 2796329 chromosome 2884963 2886348 - ABC transporter solute-binding protein False
DVU3113 carA CDS 2796605 chromosome 3262359 3263486 - carbamoyl phosphate synthase small subunit False
DVU3127 pqiB CDS 2796619 chromosome 3274537 3276168 + paraquat-inducible protein B False
DVU3296 CDS 2796020 chromosome 3473928 3474455 + hypothetical protein DVU3296 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 14

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.