Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 10 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 10

There are 10 regulatory influences for Module 10

Regulator Table (10)
Regulator Name Type
DVU0682
DVU1584
combiner
DVU2547
DVU2394
combiner
DVU1572
DVU0063
combiner
DVU0063 tf
DVU1419 tf
DVU3255
DVU2275
combiner
DVU2275 tf
DVU0118 tf
DVU2547
DVU2086
combiner
DVU2275
DVU1949
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
19 3.10e+00 TgTCAAGa
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RegPredict
20 1.50e+03 TAtgAaCG.A.gTT
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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 10 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 1.50e-05 3.71e-04 4/25
Pyrimidine metabolism kegg pathway 1.42e-04 1.63e-03 3/25
Ribosome kegg pathway 5.46e-04 3.59e-03 3/25
Metabolic pathways kegg pathway 3.11e-02 4.34e-02 6/25
Biosynthesis of secondary metabolites kegg pathway 3.51e-02 4.80e-02 3/25
Nucleotide Metabolism kegg subcategory 0.00e+00 3.00e-06 7/25
Translation kegg subcategory 2.60e-04 3.00e-03 4/25
Folding Sorting and Degradation kegg subcategory 9.20e-05 1.44e-03 3/25
Metabolism kegg subcategory 8.27e-03 3.20e-02 10/25
Metabolism kegg category 6.19e-03 3.76e-02 11/25
Genetic Information Processing kegg category 3.10e-05 4.65e-04 7/25
Global kegg category 8.27e-03 4.53e-02 10/25
Metabolism kegg category 2.43e-02 4.91e-02 7/25
Nucleotide Metabolism kegg subcategory 0.00e+00 1.10e-05 6/25
Purine metabolism kegg pathway 1.50e-05 4.00e-04 4/25
Pyrimidine metabolism kegg pathway 1.42e-04 2.09e-03 3/25
Genetic Information Processing kegg category 1.20e-05 3.21e-04 7/25
Translation kegg subcategory 2.60e-04 3.16e-03 4/25
Ribosome kegg pathway 5.46e-04 4.93e-03 3/25
Folding Sorting and Degradation kegg subcategory 9.20e-05 1.53e-03 3/25

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
translation biological_process 1.17e-04 5.26e-04 4/25
structural constituent of ribosome molecular_function 6.69e-04 1.43e-03 3/25
GTPase activity molecular_function 0.00e+00 2.00e-06 4/25
GTP binding molecular_function 3.70e-05 1.73e-04 3/25
protein-synthesizing GTPase activity molecular_function 0.00e+00 0.00e+00 4/25

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
small_GTP tigrfam 1.00e-06 1.00e-06 3/25
Ribosomal proteins: synthesis and modification tigr sub1role 3.22e-04 1.37e-03 3/25
General tigr sub1role 1.91e-04 9.95e-04 3/25
Purines, pyrimidines, nucleosides, and nucleotides tigr mainrole 5.70e-05 1.11e-03 3/25
Transcription tigr mainrole 7.00e-06 2.07e-04 3/25
Protein synthesis tigr mainrole 8.80e-05 1.53e-03 5/25
Unknown function tigr mainrole 6.69e-04 7.10e-03 3/25
small_GTP tigrfam 1.00e-06 3.00e-06 3/25
Purines, pyrimidines, nucleosides, and nucleotides tigr mainrole 5.70e-05 1.43e-04 3/25
Transcription tigr mainrole 7.00e-06 2.10e-05 3/25
Protein synthesis tigr mainrole 8.80e-05 2.09e-04 5/25
Ribosomal proteins: synthesis and modification tigr sub1role 3.22e-04 6.73e-04 3/25
Unknown function tigr mainrole 6.69e-04 1.30e-03 3/25
General tigr sub1role 1.91e-04 4.20e-04 3/25

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Translation, ribosomal structure and biogenesis cog subcategory 0.00e+00 2.00e-06 9/25
Transcription cog subcategory 5.05e-03 4.94e-02 3/25
Nucleotide transport and metabolism cog subcategory 2.00e-06 9.40e-05 5/25
Information storage and processing cog category 0.00e+00 1.00e-06 13/25
Information storage and processing cog category 1.00e-06 3.00e-06 11/25
Translation, ribosomal structure and biogenesis cog subcategory 0.00e+00 0.00e+00 9/25
Transcription cog subcategory 5.05e-03 9.12e-03 3/25
Nucleotide transport and metabolism cog subcategory 2.00e-06 6.00e-06 5/25
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 10

There are 25 genes in Module 10

Gene Member Table (25)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0161 purF CDS 2795036 chromosome 198445 199833 - amidophosphoribosyltransferase False
DVU0162 carB CDS 2796778 chromosome 199861 203094 - carbamoyl-phosphate synthase large subunit False
DVU0399 CDS 2796541 chromosome 447708 448496 - hypothetical protein DVU0399 False
DVU0503 pnp CDS 2796763 chromosome 574964 577246 - polynucleotide phosphorylase/polyadenylase False
DVU0507 CDS 2793567 chromosome 579650 579940 - hypothetical protein DVU0507 False
DVU0508 infB CDS 2793568 chromosome 580044 583283 - translation initiation factor IF-2 False
DVU0510 nusA CDS 2793570 chromosome 583521 584807 - transcription elongation factor NusA False
DVU0511 CDS 2794303 chromosome 584848 585366 - hypothetical protein DVU0511 False
DVU0957 rpsR CDS 2795153 chromosome 1051786 1052049 + 30S ribosomal protein S18 False
DVU1077 CDS 2794455 chromosome 1179369 1180973 + inner membrane protein, 60 kDa False
DVU1078 CDS 2794456 chromosome 1181012 1182304 + R3H domain-containing protein False
DVU1202 CDS 2796659 chromosome 1293749 1294279 - cytidine/deoxycytidylate deaminase family protein False
DVU1207 fabH CDS 2796684 chromosome 1298192 1299184 - 3-oxoacyl-ACP synthase False
DVU1298 rpsL CDS 2795186 chromosome 1389633 1390004 + 30S ribosomal protein S12 False
DVU1299 rpsG CDS 2795187 chromosome 1390020 1390490 + 30S ribosomal protein S7 False
DVU1300 fusA-1 CDS 2795188 chromosome 1390506 1392581 + elongation factor G False
DVU1575 prsA CDS 2793466 chromosome 1657297 1658235 - ribose-phosphate pyrophosphokinase False
DVU1622 purQ CDS 2795883 chromosome 1706229 1707038 - phosphoribosylformylglycinamidine synthase I False
DVU2231 typA CDS 2795558 chromosome 2323364 2325205 + GTP-binding protein TypA False
DVU2913 CDS 2794054 chromosome 3013347 3014354 + lipoprotein False
DVU2914 prfA CDS 2794055 chromosome 3014361 3015434 + peptide chain release factor 1 False
DVU2923 nusG CDS 2793961 chromosome 3021239 3021790 + transcription antitermination protein NusG False
DVU3308 CDS 2796044 chromosome 3485523 3486242 + metallo-beta-lactamase family protein False
DVU3310 CDS 2796046 chromosome 3486594 3488192 + DEAD-box ATP dependent DNA helicase False
DVU3368 hisS CDS 2795682 chromosome 3539428 3540681 - histidyl-tRNA synthetase 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 10

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.