Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 236 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 236

There are 17 regulatory influences for Module 236

Regulator Table (17)
Regulator Name Type
DVU1584 tf
DVU2644
DVU3066
combiner
DVU0030 tf
DVU3167 tf
DVU0619 tf
DVU2836 tf
DVU0110
DVU1419
combiner
DVU2423
DVU0936
combiner
DVU3167
DVU0309
combiner
DVU1744 tf
DVU0110
DVU0813
combiner
DVU3167
DVU0813
combiner
DVU3193
DVU0813
combiner
DVU0653
DVU0813
combiner
DVU1645
DVU2644
combiner
DVU0110
DVU1083
combiner
DVU2423
DVU0653
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
451 2.90e+02 AgTcaTc.CATTtTT
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RegPredict
452 7.90e+03 CatcActggaGgAA
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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 236 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Methane metabolism kegg pathway 6.96e-04 4.21e-03 3/31
Metabolic pathways kegg pathway 3.56e-03 9.83e-03 9/31
Biosynthesis of secondary metabolites kegg pathway 1.08e-04 1.36e-03 7/31
Microbial metabolism in diverse environments kegg pathway 5.70e-05 9.06e-04 6/31
Carbohydrate Metabolism kegg subcategory 4.20e-05 7.98e-04 8/31
Energy Metabolism kegg subcategory 1.64e-03 1.03e-02 4/31
Amino Acid Metabolism kegg subcategory 5.59e-04 5.02e-03 6/31
Metabolism kegg subcategory 0.00e+00 0.00e+00 22/31
Metabolism kegg category 7.00e-06 1.32e-04 18/31
Global kegg category 0.00e+00 0.00e+00 22/31
Metabolism kegg category 3.64e-03 1.44e-02 10/31
Carbohydrate Metabolism kegg subcategory 6.59e-04 5.65e-03 5/31
Energy Metabolism kegg subcategory 1.57e-03 9.19e-03 4/31
Methane metabolism kegg pathway 6.96e-04 5.82e-03 3/31
Amino Acid Metabolism kegg subcategory 1.16e-04 1.82e-03 6/31
Global kegg category 4.27e-03 1.57e-02 9/31
Metabolism kegg subcategory 4.27e-03 1.57e-02 9/31
Metabolic pathways kegg pathway 3.56e-03 1.44e-02 9/31
Biosynthesis of secondary metabolites kegg pathway 1.08e-04 1.73e-03 7/31
Microbial metabolism in diverse environments kegg pathway 5.70e-05 1.10e-03 6/31

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
metabolic process biological_process 2.46e-02 3.42e-02 3/31
cell redox homeostasis biological_process 1.00e-06 1.00e-05 3/31

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 2.50e-03 1.40e-02 3/31
Energy metabolism tigr mainrole 2.50e-03 4.13e-03 3/31

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Carbohydrate transport and metabolism cog subcategory 1.13e-03 1.87e-02 4/31
Metabolism cog category 1.56e-02 2.59e-02 12/31
Carbohydrate transport and metabolism cog subcategory 1.13e-03 2.18e-03 4/31
Amino acid transport and metabolism cog subcategory 1.11e-02 1.91e-02 5/31
General function prediction only cog subcategory 2.74e-02 4.34e-02 5/31
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 236

There are 31 genes in Module 236

Gene Member Table (31)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0090 wcaG CDS 2794641 chromosome 115316 116287 + GDP-fucose synthetase False
DVU0274 CDS 2794999 chromosome 316978 317349 - hypothetical protein DVU0274 False
DVU0290 CDS 2793496 chromosome 334593 335201 - lipoprotein False
DVU0322 eno CDS 2794445 chromosome 365096 366409 + phosphopyruvate hydratase False
DVU0378 CDS 2794636 chromosome 428443 428757 - thioredoxin False
DVU0398 CDS 2796540 chromosome 445885 447711 - HMGL-like domain-containing protein False
DVU0418 lys1 CDS 2796701 chromosome 470885 472075 + saccharopine dehydrogenase False
DVU0761 CDS 2795565 chromosome 852498 853088 - lipoprotein False
DVU0870 frr CDS 2795169 chromosome 962781 963341 - ribosome recycling factor False
DVU1072 CDS 2794042 chromosome 1176605 1177267 - hypothetical protein DVU1072 False
DVU1368 CDS 2795092 chromosome 1446416 1448038 + rhodanese-like domain-containing protein False
DVU1412 CDS 2794956 chromosome 1481630 1482610 - glycerate dehydrogenase False
DVU1613 CDS 2796066 chromosome 1698737 1699795 + glutamate synthase subunit beta False
DVU1868 dapA CDS 2794312 chromosome 1933424 1934302 + dihydrodipicolinate synthase False
DVU1886 CDS 2793555 chromosome 1957910 1958587 - hypothetical protein DVU1886 False
DVU1980 CDS 2793786 chromosome 2057153 2057545 + hypothetical protein DVU1980 False
DVU2082 CDS 2793536 chromosome 2167481 2168374 + flagellin False
DVU2108 CDS 2793380 chromosome 2202492 2202851 + hypothetical protein DVU2108 False
DVU2109 CDS 2793381 chromosome 2202848 2204311 + hypothetical protein DVU2109 False
DVU2112 CDS 2793384 chromosome 2207353 2207772 + hypothetical protein DVU2112 False
DVU2143 fba CDS 2794222 chromosome 2240742 2241665 + fructose-1,6-bisphosphate aldolase, class II False
DVU2203 CDS 2793666 chromosome 2299312 2299686 + L-PSP family endoribonuclease False
DVU2313 pgl CDS 2795273 chromosome 2406614 2407363 + 6-phosphogluconolactonase False
DVU2420 CDS 2794361 chromosome 2527461 2527790 - hypothetical protein DVU2420 False
DVU2460 CDS 2795324 chromosome 2565584 2566177 + hypothetical protein DVU2460 False
DVU2490 CDS 2795458 chromosome 2601007 2601831 + histidinol phosphatase False
DVU2735 paaK-3 CDS 2795937 chromosome 2836219 2837517 + phenylacetate-coenzyme A ligase False
DVU2769 CDS 2796319 chromosome 2876621 2877403 + hypothetical protein DVU2769 False
DVU3212 CDS 2796210 chromosome 3377699 3379408 + pyridine nucleotide-disulfide oxidoreductase False
DVU3351 queA CDS 2795665 chromosome 3522270 3523385 - S-adenosylmethionine:tRNA ribosyltransferase-isomerase False
DVU3352 CDS 2795666 chromosome 3523498 3524067 + lipoprotein 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 236

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.