Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 250 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 250

There are 14 regulatory influences for Module 250

Regulator Table (14)
Regulator Name Type
DVU3167 tf
DVU3313 tf
DVU1759 tf
DVU0277 tf
DVU1518
DVU0030
combiner
DVU0110 tf
DVU0110
DVU0569
combiner
DVU0309
DVU0653
combiner
DVU0653
DVU2251
combiner
DVU1561
DVU0230
combiner
DVU0309
DVU0110
combiner
DVU1518
DVU1561
combiner
DVU0653 tf
DVU3167
DVU0569
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
477 1.20e+03 gTgCgGcgt.g.a.caac.a.cg
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RegPredict
478 1.50e+04 ctTgcCacggaAgGG
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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 250 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 0.00e+00 1.00e-06 5/29
Metabolic pathways kegg pathway 0.00e+00 3.00e-06 15/29
Biosynthesis of secondary metabolites kegg pathway 1.39e-02 2.28e-02 4/29
Microbial metabolism in diverse environments kegg pathway 3.00e-06 1.10e-04 7/29
Carbohydrate Metabolism kegg subcategory 0.00e+00 9.00e-06 10/29
Amino Acid Metabolism kegg subcategory 4.80e-05 8.69e-04 7/29
Metabolism kegg subcategory 0.00e+00 0.00e+00 26/29
Metabolism kegg category 0.00e+00 1.00e-06 20/29
Global kegg category 0.00e+00 0.00e+00 26/29
Metabolism kegg category 3.00e-06 1.17e-04 14/29
Carbohydrate Metabolism kegg subcategory 0.00e+00 2.00e-06 9/29
Citrate cycle (TCA cycle) kegg pathway 0.00e+00 1.00e-06 5/29
Amino Acid Metabolism kegg subcategory 4.09e-03 1.54e-02 4/29
Global kegg category 0.00e+00 3.00e-06 15/29
Metabolism kegg subcategory 0.00e+00 3.00e-06 15/29
Metabolic pathways kegg pathway 0.00e+00 3.00e-06 15/29
Biosynthesis of secondary metabolites kegg pathway 1.39e-02 3.29e-02 4/29
Microbial metabolism in diverse environments kegg pathway 3.00e-06 1.10e-04 7/29

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
electron transport biological_process 1.30e-02 2.00e-02 4/29
metabolic process biological_process 1.96e-02 2.80e-02 3/29
2-oxoglutarate synthase activity molecular_function 0.00e+00 0.00e+00 5/29

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Amino acid biosynthesis tigr mainrole 4.15e-04 5.16e-03 3/29
Amino acid biosynthesis tigr mainrole 4.15e-04 8.42e-04 3/29

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Carbohydrate transport and metabolism cog subcategory 8.20e-04 1.54e-02 4/29
Amino acid transport and metabolism cog subcategory 2.87e-04 7.54e-03 7/29
Metabolism cog category 2.10e-05 5.68e-04 17/29
Metabolism cog category 4.20e-05 1.26e-04 16/29
Energy production and conversion cog subcategory 6.37e-03 1.13e-02 5/29
Carbohydrate transport and metabolism cog subcategory 8.20e-04 1.63e-03 4/29
Amino acid transport and metabolism cog subcategory 2.87e-04 6.27e-04 7/29
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 250

There are 29 genes in Module 250

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0169 CDS 2793575 chromosome 209432 210994 - oligopeptide/dipeptide ABC transporter periplasmic oligopeptide/dipeptide-binding protein False
DVU0255 CDS 2794502 chromosome 290357 290911 + hypothetical protein DVU0255 False
DVU0326 hypE CDS 2794328 chromosome 369036 370061 + hydrogenase expression/formation protein HypE False
DVU0337 CDS 2794753 chromosome 382107 384077 - hypothetical protein DVU0337 False
DVU0338 CDS 2794754 chromosome 384097 384738 - HAD superfamily hydrolase False
DVU0342 CDS 2796771 chromosome 387502 388416 - NAD-dependent epimerase/dehydratase family protein False
DVU0343 CDS 2796772 chromosome 388419 389201 - HPCH/HPAI aldolase family protein False
DVU0348 CDS 2794788 chromosome 394354 396078 - hypothetical protein DVU0348 False
DVU0349 CDS 2794676 chromosome 396098 397156 - NeuB family protein False
DVU0350 spsF CDS 2794677 chromosome 397193 397876 - spore coat polysaccharide biosynthesis protein spsF False
DVU0353 CDS 2794680 chromosome 400830 401903 - iron-containing alcohol dehydrogenase False
DVU0492 argC CDS 2793706 chromosome 561263 562327 - N-acetyl-gamma-glutamyl-phosphate reductase False
DVU1252 CDS 2794598 chromosome 1337944 1340220 + hypothetical protein DVU1252 False
DVU1424 gcvPB CDS 2794685 chromosome 1497917 1499362 - glycine dehydrogenase subunit 2 False
DVU1426 gcvH CDS 2794687 chromosome 1500705 1501088 - glycine cleavage system protein H False
DVU1772 CDS 2795819 chromosome 1836228 1838249 - pyridine nucleotide-disulfide oxidoreductase False
DVU1913 CDS 2793686 chromosome 1987690 1988916 + aspartate kinase False
DVU1945 CDS 2793517 chromosome 2017911 2019059 + 2-oxoglutarate ferredoxin oxidoreductase subunit alpha False
DVU1946 CDS 2793518 chromosome 2019067 2019897 + 2-oxoglutarate ferredoxin oxidoreductase subunit beta False
DVU2530 tkt CDS 2795716 chromosome 2640910 2642904 - transketolase False
DVU2951 glnS CDS 2796502 chromosome 3056772 3058484 + glutaminyl-tRNA synthetase False
DVU3154 CDS 2795859 chromosome 3307131 3307754 + deoxyribonucleotide triphosphate pyrophosphatase False
DVU3157 CDS 2795862 chromosome 3313723 3315165 + hypothetical protein DVU3157 False
DVU3215 CDS 2796213 chromosome 3382952 3383317 - response regulator False
DVU3348 CDS 2796360 chromosome 3519814 3520596 - pyruvate ferredoxin/flavodoxin oxidoreductase subunit beta False
DVU3349 CDS 2796361 chromosome 3520596 3521669 - 2-ketoisovalerate ferredoxin reductase False
DVU3350 CDS 2795664 chromosome 3521673 3521906 - iron-sulfur cluster-binding protein False
DVU3373 ilvD CDS 2795687 chromosome 3544991 3546655 - dihydroxy-acid dehydratase False
DVU3374 CDS 2795688 chromosome 3546687 3547520 - permease 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 250

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.