Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 37 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 37

There are 14 regulatory influences for Module 37

Regulator Table (14)
Regulator Name Type
DVU1063 tf
DVU2359 tf
DVU2547
DVU3229
combiner
DVU2934 tf
DVU0744 tf
DVU1340 tf
DVU1949 tf
DVU3167 tf
DVU3111 tf
DVUA0100 tf
DVU2547
DVU2582
combiner
DVU3381 tf
DVU1628 tf
DVU0679 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
73 6.10e+03 ATtGCTaTCGT
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RegPredict
74 1.60e+04 CAtAtgacAGAaaCC
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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 37 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cell motility cog subcategory 2.01e-02 3.27e-02 3/38
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 37

There are 38 genes in Module 37

Gene Member Table (38)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0040 CDS 2796561 chromosome 46450 47064 + hypothetical protein DVU0040 False
DVU0140 CDS 2796556 chromosome 175592 176005 + response regulator False
DVU0145 CDS 2796578 chromosome 180029 180436 - response regulator False
DVU0147 CDS 2796580 chromosome 181386 181646 - lipoprotein False
DVU0218 CDS 2795071 chromosome 258050 259111 + tail protein False
DVU0232 CDS 2794277 chromosome 266564 266812 + hypothetical protein DVU0232 False
DVU0257 CDS 2795004 chromosome 300822 301286 + acetyltransferase False
DVU0301 CDS 2794557 chromosome 348472 348621 - hypothetical protein DVU0301 False
DVU0358 CDS 2793497 chromosome 407342 408085 + hypothetical protein DVU0358 False
DVU0381 nhaC-1 CDS 2796739 chromosome 431111 432502 - Na+/H+ antiporter NhaC False
DVU0392 CDS 2794248 chromosome 440311 441510 + aromatic aminotransferase False
DVU0425 CDS 2795218 chromosome 480810 481616 + hypothetical protein DVU0425 False
DVU0638 CDS 2794108 chromosome 707913 708779 - hypothetical protein DVU0638 False
DVU0639 pomB CDS 2794110 chromosome 709562 710335 - chemotaxis protein PomB False
DVU0641 CDS 2794333 chromosome 711092 712240 - hypothetical protein DVU0641 False
DVU1011 CDS 2794649 chromosome 1105878 1105976 - hypothetical protein DVU1011 False
DVU1126 CDS 2794737 chromosome 1229449 1229754 - lipoprotein False
DVU1360 galE CDS 2795084 chromosome 1438843 1439838 + UDP-glucose 4-epimerase False
DVU1442 CDS 2794569 chromosome 1518983 1519357 + flagellin FlaG False
DVU1604 CDS 2795959 chromosome 1686217 1686795 - hypothetical protein DVU1604 False
DVU1691 CDS 2795825 chromosome 1768959 1769066 + hypothetical protein DVU1691 False
DVU1906 CDS 2793679 chromosome 1981946 1982062 + hypothetical protein DVU1906 False
DVU1993 CDS 2793432 chromosome 2072210 2074963 - cation transporter E1-E2 family ATPase False
DVU2267 CDS 2795223 chromosome 2359130 2359423 - hypothetical protein DVU2267 False
DVU2311 CDS 2795271 chromosome 2404951 2405085 - None False
DVU2473 CDS 2795655 chromosome 2582514 2582657 - hypothetical protein DVU2473 False
DVU2498 CDS 2795466 chromosome 2609375 2609668 - hypothetical protein DVU2498 False
DVU2551 CDS 2796125 chromosome 2662087 2663322 - HD domain-containing protein False
DVU2589 CDS 2796367 chromosome 2712971 2713096 - hypothetical protein DVU2589 False
DVU2590 CDS 2796368 chromosome 2713242 2714807 + sensory box protein False
DVU2972 CDS 2796286 chromosome 3081579 3082178 - chemotaxis protein CheD False
DVU3021 CDS 2793734 chromosome 3137085 3138455 - HDIG domain-containing protein False
DVU3036 CDS 2796453 chromosome 3161724 3162716 - hypothetical protein DVU3036 False
DVU3060 CDS 2796086 chromosome 3190466 3190630 - hypothetical protein DVU3060 False
DVU3111 CDS 2796603 chromosome 3260648 3261382 - Crp/FNR family transcriptional regulator True
DVU3225 CDS 2793875 chromosome 3394894 3395316 - hypothetical protein DVU3225 False
DVU3342 CDS 2796354 chromosome 3516572 3516988 + hypothetical protein DVU3342 False
DVU3391 CDS 2796410 chromosome 3567052 3567300 + hypothetical protein DVU3391 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 37

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.