Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 330 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 330

There are 10 regulatory influences for Module 330

Regulator Table (10)
Regulator Name Type
DVUA0143 tf
DVU3255
DVU3186
combiner
DVU3080 tf
DVU1083
DVU0539
combiner
DVU1083
DVU2832
combiner
DVU3255
DVU1156
combiner
DVU3255 tf
DVUA0057 tf
DVU0539 tf
DVUA0057
DVU2989
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
627 2.20e+03 tcgaaataaccTcgcct.T
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RegPredict
628 1.40e+03 GcAGGCAa
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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 330 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Fructose and mannose metabolism kegg pathway 5.00e-06 1.49e-04 3/25
Amino sugar and nucleotide sugar metabolism kegg pathway 3.20e-05 6.34e-04 3/25
Phosphotransferase system (PTS) kegg pathway 0.00e+00 0.00e+00 4/25
Carbohydrate Metabolism kegg subcategory 3.97e-04 3.95e-03 6/25
Membrane Transport kegg subcategory 1.73e-04 2.30e-03 5/25
Environmental Information Processing kegg category 2.32e-03 1.64e-02 5/25
Carbohydrate Metabolism kegg subcategory 1.11e-02 2.82e-02 3/25
Fructose and mannose metabolism kegg pathway 5.00e-06 1.50e-04 3/25
Amino sugar and nucleotide sugar metabolism kegg pathway 3.20e-05 7.24e-04 3/25
Environmental Information Processing kegg category 2.20e-03 1.10e-02 5/25
Membrane Transport kegg subcategory 1.73e-04 2.40e-03 5/25
Phosphotransferase system (PTS) kegg pathway 0.00e+00 0.00e+00 4/25

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
phosphoenolpyruvate-dependent sugar phosphotransferase system biological_process 0.00e+00 0.00e+00 4/25
protein-N(PI)-phosphohistidine-sugar phosphotransferase activity molecular_function 0.00e+00 0.00e+00 3/25

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Replication, recombination and repair cog subcategory 4.87e-03 4.88e-02 3/25
Carbohydrate transport and metabolism cog subcategory 3.74e-03 4.18e-02 3/25
Replication, recombination and repair cog subcategory 4.87e-03 8.83e-03 3/25
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 330

There are 25 genes in Module 330

Gene Member Table (25)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0301 CDS 2794557 chromosome 348472 348621 - hypothetical protein DVU0301 False
DVU0528 CDS 2794894 chromosome 601058 601537 + phosphatidylglycerophosphatase False
DVU0711 CDS 2795407 chromosome 790673 791314 + hypothetical protein DVU0711 False
DVU0947 CDS 2794591 chromosome 1041478 1042383 - hypothetical protein DVU0947 False
DVU1165 CDS 2794238 chromosome 1257810 1259129 + pyridine nucleotide-disulfide oxidoreductase False
DVU1279 folP CDS 2794345 chromosome 1371953 1372813 + dihydropteroate synthase False
DVU1280 CDS 2794346 chromosome 1372822 1373568 + hypothetical protein DVU1280 False
DVU1605 uvrB CDS 2795960 chromosome 1686795 1688828 + excinuclease ABC subunit B False
DVU1606 CDS 2796059 chromosome 1688825 1689877 + TrkA family potassium uptake protein False
DVU1607 CDS 2796060 chromosome 1689878 1690624 + hypothetical protein DVU1607 False
DVU1627 CDS 2795888 chromosome 1711584 1712309 + ABC transporter ATP-binding protein False
DVU1630 CDS 2796094 chromosome 1714491 1714940 + PTS system transporter subunit IIA False
DVU1631 CDS 2796095 chromosome 1714949 1715860 + hypothetical protein DVU1631 False
DVU1632 CDS 2796096 chromosome 1715889 1716326 + PTS system transporter subunit IIA False
DVU1633 CDS 2796097 chromosome 1716328 1716789 + PTS system transporter subunit IIB False
DVU1634 CDS 2796098 chromosome 1716815 1717486 + hypothetical protein DVU1634 False
DVU2058 CDS 2796482 chromosome 2134985 2135596 + HDIG domain-containing protein False
DVU2085 CDS 2793539 chromosome 2172660 2175875 + Snf2 family protein False
DVU2265 CDS 2795221 chromosome 2358809 2358913 - hypothetical protein DVU2265 False
DVU2316 topB CDS 2795276 chromosome 2408456 2411044 + DNA topoisomerase III False
DVU2693 CDS 2793749 chromosome 2806043 2806282 + hypothetical protein DVU2693 False
DVU2699 CDS 2793755 chromosome 2808534 2809181 + transglycosylase False
DVU3122 CDS 2796614 chromosome 3270935 3271042 - hypothetical protein DVU3122 False
DVU3343 CDS 2796355 chromosome 3516985 3517404 + hypothetical protein DVU3343 False
DVU3380 CDS 2796399 chromosome 3553923 3554045 - hypothetical protein DVU3380 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 330

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.