Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 195 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 195

There are 10 regulatory influences for Module 195

Regulator Table (10)
Regulator Name Type
DVU0529
DVU0539
combiner
DVU0653
DVU2275
combiner
DVU3167 tf
DVUA0151
DVU1561
combiner
DVU0653 tf
DVUA0057 tf
DVUA0151 tf
DVU0946 tf
DVU3167
DVU0269
combiner
DVU3381
DVU2832
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
373 3.10e-03 ATacaagAcAaGgtTtTccTga
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RegPredict
374 1.90e+02 TTcgTtgcagagGgc
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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 195 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Terpenoid backbone biosynthesis kegg pathway 0.00e+00 1.50e-05 3/24
ABC transporters kegg pathway 2.96e-03 8.91e-03 3/24
Metabolic pathways kegg pathway 7.18e-03 1.47e-02 7/24
Biosynthesis of secondary metabolites kegg pathway 6.12e-03 1.32e-02 4/24
Nucleotide Metabolism kegg subcategory 2.50e-03 1.38e-02 3/24
Metabolism of Terpenoids and Polyketides kegg subcategory 0.00e+00 4.00e-06 4/24
Membrane Transport kegg subcategory 9.02e-03 3.39e-02 3/24
Metabolism kegg subcategory 1.55e-03 1.00e-02 11/24
Global kegg category 1.55e-03 1.17e-02 11/24
Metabolism kegg category 1.89e-02 4.08e-02 7/24
Metabolism of Terpenoids and Polyketides kegg subcategory 0.00e+00 4.00e-06 4/24
Terpenoid backbone biosynthesis kegg pathway 0.00e+00 1.40e-05 3/24
Membrane Transport kegg subcategory 9.02e-03 2.47e-02 3/24
ABC transporters kegg pathway 2.96e-03 1.30e-02 3/24
Global kegg category 8.33e-03 2.37e-02 7/24
Metabolism kegg subcategory 8.33e-03 2.37e-02 7/24
Metabolic pathways kegg pathway 7.18e-03 2.16e-02 7/24
Biosynthesis of secondary metabolites kegg pathway 6.12e-03 1.95e-02 4/24

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
ATP binding molecular_function 6.27e-04 1.36e-03 7/24

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Inorganic ion transport and metabolism cog subcategory 6.03e-04 1.25e-02 4/24
Cell wall/membrane/envelope biogenesis cog subcategory 1.98e-02 3.24e-02 3/24
Inorganic ion transport and metabolism cog subcategory 6.03e-04 1.23e-03 4/24
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 195

There are 24 genes in Module 195

Gene Member Table (24)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0334 CDS 2794750 chromosome 377980 378891 + D-alanine--D-alanine ligase False
DVU0698 rfbC CDS 2794449 chromosome 773223 773795 - dTDP-4-dehydrorhamnose 3,5-epimerase False
DVU0951 CDS 2794595 chromosome 1043957 1045294 + molybdopterin biosynthesis MoeA protein False
DVU1017 CDS 2793740 chromosome 1117054 1119384 + ABC transporter ATP-binding protein/permease False
DVU1018 CDS 2793741 chromosome 1119387 1120733 + HlyD family type I secretion membrane fusion protein False
DVU1043 guaA CDS 2795264 chromosome 1145100 1146647 - GMP synthase False
DVU1046 CDS 2795267 chromosome 1148991 1149128 - hypothetical protein DVU1046 False
DVU1339 CDS 2795138 chromosome 1416774 1417604 - lipoprotein False
DVU1340 CDS 2795139 chromosome 1417766 1418260 - Fur family transcriptional regulator True
DVU1341 CDS 2795140 chromosome 1418257 1419081 - cation ABC transporter permease False
DVU1342 CDS 2795141 chromosome 1419083 1419889 - cation ABC transporter ATP-binding protein False
DVU1343 CDS 2795142 chromosome 1419892 1420899 - cation ABC transporter periplasmc-binding protein False
DVU1344 ispG CDS 2795143 chromosome 1421161 1422321 + 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase False
DVU1345 proS CDS 2795144 chromosome 1422321 1424045 + prolyl-tRNA synthetase False
DVU1346 xseA CDS 2795145 chromosome 1424092 1425489 + exodeoxyribonuclease VII large subunit False
DVU1349 CDS 2794915 chromosome 1426709 1427572 + geranylgeranyl diphosphate synthase False
DVU1350 dxs CDS 2794916 chromosome 1427612 1429537 + 1-deoxy-D-xylulose-5-phosphate synthase False
DVU2275 CDS 2795231 chromosome 2363991 2365445 + sigma-54 dependent transcriptional regulator True
DVU2425 rarD CDS 2794366 chromosome 2530647 2531534 - rarD protein False
DVU2638 CDS 2795694 chromosome 2754320 2755408 - hypothetical protein DVU2638 False
DVU2783 CDS 2796333 chromosome 2888557 2889357 - hypothetical protein DVU2783 False
DVU3011 CDS 2793724 chromosome 3124139 3124933 + hypothetical protein DVU3011 False
DVU3379 CDS 2796398 chromosome 3551477 3553810 - ribonucleotide-diphosphate reductase subunit alpha False
DVUA0111 CDS 2781619 pDV 147662 148558 + type III secretion system protein IpaC family 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 195

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.