Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 81 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 81

There are 14 regulatory influences for Module 81

Regulator Table (14)
Regulator Name Type
DVU2675 tf
DVU1759 tf
DVU3023 tf
DVU2036 tf
DVU3255
DVU0569
combiner
DVU0277
DVU0744
combiner
DVU2036
DVU0569
combiner
DVU2378 tf
DVU0277
DVU0309
combiner
DVU3313
DVU1156
combiner
DVU2036
DVU0110
combiner
DVU3313
DVU1063
combiner
DVU2960
DVU0569
combiner
DVU3313 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
159 1.90e-01 CAtAcgGCagGaCaG
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RegPredict
160 3.60e+01 tGCcCCCGgtaGCagTcCCgC
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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 81 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolic pathways kegg pathway 1.80e-05 4.10e-04 12/29
Biosynthesis of secondary metabolites kegg pathway 6.40e-05 9.82e-04 7/29
Microbial metabolism in diverse environments kegg pathway 2.51e-03 8.20e-03 4/29
Carbohydrate Metabolism kegg subcategory 5.53e-03 2.44e-02 5/29
Nucleotide Metabolism kegg subcategory 5.09e-03 2.31e-02 3/29
Amino Acid Metabolism kegg subcategory 2.27e-03 1.27e-02 5/29
Cell Motility kegg subcategory 9.30e-03 3.47e-02 3/29
Metabolism kegg subcategory 0.00e+00 0.00e+00 23/29
Metabolism kegg category 2.00e-06 3.80e-05 18/29
Cellular Processes kegg category 9.30e-03 4.91e-02 3/29
Global kegg category 0.00e+00 0.00e+00 23/29
Metabolism kegg category 2.00e-05 5.11e-04 13/29
Carbohydrate Metabolism kegg subcategory 3.23e-03 1.35e-02 4/29
Amino Acid Metabolism kegg subcategory 6.05e-04 5.35e-03 5/29
Cellular Processes kegg category 5.99e-03 1.92e-02 3/29
Cell Motility kegg subcategory 5.99e-03 1.92e-02 3/29
Global kegg category 2.40e-05 5.67e-04 12/29
Metabolism kegg subcategory 2.40e-05 5.67e-04 12/29
Metabolic pathways kegg pathway 1.80e-05 4.52e-04 12/29
Biosynthesis of secondary metabolites kegg pathway 6.40e-05 1.22e-03 7/29
Microbial metabolism in diverse environments kegg pathway 2.51e-03 1.19e-02 4/29

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
metabolic process biological_process 3.46e-03 6.37e-03 4/29

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
Metabolism cog category 0.00e+00 3.00e-06 20/29
Metabolism cog category 8.00e-06 2.80e-05 17/29
Carbohydrate transport and metabolism cog subcategory 8.20e-04 1.63e-03 4/29
Amino acid transport and metabolism cog subcategory 7.98e-03 1.40e-02 5/29
Coenzyme transport and metabolism cog subcategory 1.58e-02 2.62e-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 81

There are 29 genes in Module 81

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0027 CDS 2794135 chromosome 31278 32702 - hypothetical protein DVU0027 False
DVU0097 potB CDS 2796177 chromosome 127492 128379 - polyamine ABC transporter permease False
DVU0296 CDS 2795180 chromosome 341931 343001 + M24 family peptidase False
DVU0336 CDS 2794752 chromosome 380770 382110 - aminotransferase False
DVU0337 CDS 2794753 chromosome 382107 384077 - hypothetical protein DVU0337 False
DVU0339 CDS 2796768 chromosome 384768 385673 - D-isomer specific 2-hydroxyacid dehydrogenase family protein False
DVU0340 CDS 2796769 chromosome 385816 386409 - acetyltransferase 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
DVU0344 CDS 2794784 chromosome 389669 391597 - methyl-accepting chemotaxis protein False
DVU1609 dapB CDS 2796062 chromosome 1693239 1694018 + dihydrodipicolinate reductase False
DVU1912 CDS 2793685 chromosome 1987143 1987631 + hypothetical protein DVU1912 False
DVU2370 CDS 2796103 chromosome 2465783 2466310 - outer membrane protein OmpH False
DVU2447 CDS 2796624 chromosome 2551555 2552130 - hypothetical protein DVU2447 False
DVU2448 panC CDS 2796625 chromosome 2552303 2553154 + pantoate--beta-alanine ligase False
DVU2449 metK CDS 2796626 chromosome 2553206 2554381 + S-adenosylmethionine synthetase False
DVU2530 tkt CDS 2795716 chromosome 2640910 2642904 - transketolase False
DVU2898 CDS 2793928 chromosome 2996736 2997737 + hypothetical protein DVU2898 False
DVU2947 CDS 2796498 chromosome 3050747 3052816 - anaerobic ribonucleoside triphosphate reductase False
DVU3065 CDS 2796091 chromosome 3200598 3202250 - AMP-binding protein False
DVU3119 CDS 2796611 chromosome 3267630 3269324 + AMP-binding protein False
DVU3181 purL CDS 2793831 chromosome 3338134 3341115 + phosphoribosylformylglycinamidine synthase II False
DVU3233 flhB CDS 2793883 chromosome 3401682 3402755 - flagellar biosynthesis protein FlhB False
DVU3234 CDS 2793884 chromosome 3402880 3403671 - flagellar biosynthetic protein FliR False
DVU3235 CDS 2793885 chromosome 3403776 3404378 + IMP cyclohydrolase False
DVU3347 CDS 2796359 chromosome 3519266 3519814 - pyruvate ferredoxin/flavodoxin oxidoreductase family protein False
DVU3371 metE CDS 2795685 chromosome 3542097 3544454 - 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase 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.

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.