Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 176 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 176

There are 11 regulatory influences for Module 176

Regulator Table (11)
Regulator Name Type
DVU1561
DVU1964		 combiner
DVU3167 tf
DVUA0024 tf
DVU0619
DVU0653		 combiner
DVU0653 tf
DVU0230 tf
DVU2675 tf
DVU2567
DVU2675		 combiner
DVU1754
DVU1561		 combiner
DVU3167
DVU0569		 combiner
DVU0653
DVU2275		 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
337 2.00e-01 agtt.gCGgCGGGcgaCgacCcg
Loader icon
 RegPredict
338 4.10e+00 cC.CGgAacgcGcctTCggCgCG
Loader icon
 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 176 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Purine metabolism kegg pathway 6.12e-04 3.90e-03 3/30
Metabolic pathways kegg pathway 6.75e-04 4.14e-03 10/30
Biosynthesis of secondary metabolites kegg pathway 1.61e-02 2.53e-02 4/30
Nucleotide Metabolism kegg subcategory 6.90e-05 1.22e-03 5/30
Metabolism of Cofactors and Vitamins kegg subcategory 1.45e-02 4.54e-02 3/30
Metabolism kegg subcategory 2.00e-05 4.46e-04 16/30
Metabolism kegg category 1.35e-03 1.07e-02 14/30
Global kegg category 2.00e-05 3.30e-04 16/30
Metabolism kegg category 1.63e-04 2.32e-03 12/30
Nucleotide Metabolism kegg subcategory 2.20e-04 2.78e-03 4/30
Purine metabolism kegg pathway 6.12e-04 5.36e-03 3/30
Metabolism of Cofactors and Vitamins kegg subcategory 1.40e-02 3.30e-02 3/30
Global kegg category 8.35e-04 6.51e-03 10/30
Metabolism kegg subcategory 8.35e-04 6.51e-03 10/30
Metabolic pathways kegg pathway 6.75e-04 5.72e-03 10/30
Biosynthesis of secondary metabolites kegg pathway 1.61e-02 3.63e-02 4/30

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
ATP binding molecular_function 4.07e-02 4.96e-02 5/30
ferredoxin hydrogenase activity molecular_function 0.00e+00 1.00e-06 4/30

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Purines, pyrimidines, nucleosides, and nucleotides tigr mainrole 1.19e-04 2.00e-03 3/30
Purines, pyrimidines, nucleosides, and nucleotides tigr mainrole 1.19e-04 2.72e-04 3/30

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Nucleotide transport and metabolism cog subcategory 1.12e-03 1.87e-02 3/30
Coenzyme transport and metabolism cog subcategory 3.04e-03 3.64e-02 4/30
Metabolism cog category 2.37e-03 3.92e-02 14/30
Metabolism cog category 3.92e-03 7.18e-03 13/30
Cell wall/membrane/envelope biogenesis cog subcategory 9.37e-03 1.63e-02 4/30
Nucleotide transport and metabolism cog subcategory 1.12e-03 2.16e-03 3/30
Coenzyme transport and metabolism cog subcategory 3.04e-03 5.63e-03 4/30
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 176

There are 30 genes in Module 176

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0237 serS CDS 2795009 chromosome 270666 271940 - seryl-tRNA synthetase False
DVU0296 CDS 2795180 chromosome 341931 343001 + M24 family peptidase False
DVU0414 CDS 2795177 chromosome 463867 465186 + NADP-dependent malic enzyme-like protein False
DVU0481 rfaD CDS 2793626 chromosome 547103 548074 + ADP-L-glycero-D-mannoheptose-6-epimerase False
DVU0487 purE CDS 2796554 chromosome 554629 555129 - phosphoribosylaminoimidazole carboxylase, catalytic subunit False
DVU0489 paaK-1 CDS 2793703 chromosome 556585 557883 + phenylacetate-coenzyme A ligase False
DVU0632 CDS 2794554 chromosome 699063 699680 - cupin family protein False
DVU0633 CDS 2794555 chromosome 699680 702103 - penicillin-binding protein False
DVU0635 CDS 2794105 chromosome 702696 704282 - dolichyl-phosphate-mannose-protein mannosyltransferase family protein False
DVU0646 cobI CDS 2794338 chromosome 717068 717838 - precorrin-2 C20-methyltransferase False
DVU0648 CDS 2795038 chromosome 718732 719547 - iron compound ABC transporter ATP-binding protein False
DVU0649 CDS 2795039 chromosome 719544 720599 - iron compound ABC transporter permease False
DVU0650 CDS 2795040 chromosome 720601 721494 - chelatase False
DVU0726 tgt CDS 2794131 chromosome 810938 812065 - queuine tRNA-ribosyltransferase False
DVU0795 purC CDS 2794517 chromosome 880193 881089 - phosphoribosylaminoimidazole-succinocarboxamide synthase False
DVU1028 cmk CDS 2794525 chromosome 1132719 1133417 - cytidylate kinase False
DVU1187 CDS 2796587 chromosome 1276232 1277056 + hypothetical protein DVU1187 False
DVU1426 gcvH CDS 2794687 chromosome 1500705 1501088 - glycine cleavage system protein H False
DVU1609 dapB CDS 2796062 chromosome 1693239 1694018 + dihydrodipicolinate reductase False
DVU1769 hydA CDS 2795816 chromosome 1832483 1833748 + periplasmic False
DVU1903 mfd CDS 2793676 chromosome 1977379 1980861 - transcription-repair coupling factor False
DVU2142 surE CDS 2794221 chromosome 2239541 2240293 + acid phosphatase SurE False
DVU2209 CDS 2795356 chromosome 2304321 2305043 + hypothetical protein DVU2209 False
DVU2315 CDS 2795275 chromosome 2407645 2408373 - hypothetical protein DVU2315 False
DVU3008 CDS 2793721 chromosome 3120890 3121966 + NeuB family protein False
DVU3009 CDS 2793722 chromosome 3121963 3122946 + radical SAM domain-containing protein False
DVU3011 CDS 2793724 chromosome 3124139 3124933 + hypothetical protein DVU3011 False
DVU3064 CDS 2796090 chromosome 3198740 3200470 + sensory box protein False
DVU3190 CDS 2793840 chromosome 3349691 3351358 + hypothetical protein DVU3190 False
DVU3192 CDS 2793842 chromosome 3352605 3353765 + glycosyl transferase group 1 family protein 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.