Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 126 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 126

There are 14 regulatory influences for Module 126

Regulator Table (14)
Regulator Name Type
DVU1063 tf
DVU3023 tf
DVU2195 tf
DVU0525 tf
DVU2588
DVU1419		 combiner
DVU0539
DVU1745		 combiner
DVU3142
DVU0529		 combiner
DVU1744 tf
DVU2588
DVU1083		 combiner
DVU3142
DVU1419		 combiner
DVU3255
DVU1744		 combiner
DVU2588 tf
DVUA0151 tf
DVU1754 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
243 1.30e+03 AAAcaGgtgAaaAAt
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 RegPredict
244 6.60e+03 cAgCgtgAagA
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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 126 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
ABC transporters kegg pathway 6.00e-06 1.74e-04 6/29
Membrane Transport kegg subcategory 4.60e-05 8.55e-04 6/29
Environmental Information Processing kegg category 9.66e-04 8.03e-03 6/29
Environmental Information Processing kegg category 9.09e-04 6.91e-03 6/29
Membrane Transport kegg subcategory 4.60e-05 9.47e-04 6/29
ABC transporters kegg pathway 6.00e-06 1.82e-04 6/29

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
transport biological_process 3.01e-03 5.73e-03 4/29
transporter activity molecular_function 6.02e-04 1.32e-03 4/29

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 2.23e-02 3.59e-02 11/29
Inorganic ion transport and metabolism cog subcategory 1.03e-02 1.77e-02 3/29
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 126

There are 29 genes in Module 126

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0405 cobB-1 CDS 2796155 chromosome 452779 454185 + cobyrinic acid a,c-diamide synthase False
DVU0546 CDS 2794536 chromosome 616827 617003 - hypothetical protein DVU0546 False
DVU0548 CDS 2794431 chromosome 618218 619126 + high-affinity branched-chain amino acid ABC transporter permease False
DVU0549 CDS 2794432 chromosome 619154 620377 + high-affinity branched-chain amino acid ABC transporter permease False
DVU0550 CDS 2794433 chromosome 620377 621165 + high-affinity branched-chain amino acid ABC transporter ATP binding protein False
DVU0585 CDS 2794162 chromosome 650376 652769 - hypothetical protein DVU0585 False
DVU0653 CDS 2795043 chromosome 724910 726595 - sigma-54 dependent transcriptional regulator /response regulator True
DVU0695 CDS 2793635 chromosome 771081 771278 + None False
DVU0731 CDS 2794945 chromosome 815020 816381 - hypothetical protein DVU0731 False
DVU0746 CDS 2794964 chromosome 835639 836385 + ABC transporter permease False
DVU0781 CDS 2794766 chromosome 870276 870446 + hypothetical protein DVU0781 False
DVU0782 CDS 2794767 chromosome 870433 870552 + hypothetical protein DVU0782 False
DVU0844 CDS 2795195 chromosome 932093 932572 + None False
DVU0998 CDS 2795112 chromosome 1092123 1093178 + heptosyltransferase family protein False
DVU1081 CDS 2794459 chromosome 1184609 1186228 + iron-sulfur cluster-binding protein False
DVU1084 pstB-1 CDS 2794462 chromosome 1187844 1188611 + phosphate transporter ATP-binding protein False
DVU1171 CDS 2794859 chromosome 1263965 1264060 + hypothetical protein DVU1171 False
DVU1184 CDS 2796669 chromosome 1274264 1274716 + None False
DVU1369 CDS 2793502 chromosome 1448110 1448484 + hypothetical protein DVU1369 False
DVU1371 CDS 2793504 chromosome 1449380 1450054 + HAD family hydrolase False
DVU1393 CDS 2794793 chromosome 1465199 1465402 + hypothetical protein DVU1393 False
DVU1776 CDS 2794283 chromosome 1840788 1840901 - hypothetical protein DVU1776 False
DVU1848 CDS 2795911 chromosome 1916843 1917436 - hypothetical protein DVU1848 False
DVU2316 topB CDS 2795276 chromosome 2408456 2411044 + DNA topoisomerase III False
DVU2478 pstC CDS 2795660 chromosome 2586813 2587700 + phosphate ABC transporter permease PstC False
DVU2568 CDS 2796261 chromosome 2681380 2682618 + M20/M25/M40 family peptidase False
DVU2584 CDS 2796362 chromosome 2705433 2706365 + CorA family protein False
DVU3072 CDS 2796423 chromosome 3214138 3216072 - ABC transporter permease False
DVU3239 CDS 2793889 chromosome 3410195 3410860 - PAP2 family protein 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.