Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 306 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 306

There are 11 regulatory influences for Module 306

Regulator Table (11)
Regulator Name Type
DVU1419 tf
DVU0653
DVU2275		 combiner
DVU1949 tf
DVU2423
DVU2832		 combiner
DVU2547
DVU2588		 combiner
DVU2423
DVU3381		 combiner
DVU1547
DVUA0024		 combiner
DVU3381 tf
DVU2547
DVU3142		 combiner
DVU2036
DVU2275		 combiner
DVU2547
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
585 1.50e+02 TaattaA.A.AAggcatGCaAcgC
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 RegPredict
586 1.40e+02 GTtGCgTg
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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 306 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
ABC transporters kegg pathway 4.60e-03 1.12e-02 3/27
Amino Acid Metabolism kegg subcategory 2.23e-04 2.73e-03 6/27
Translation kegg subcategory 3.59e-03 1.78e-02 3/27
Membrane Transport kegg subcategory 1.37e-02 4.39e-02 3/27
Amino Acid Metabolism kegg subcategory 1.74e-02 3.84e-02 3/27
Genetic Information Processing kegg category 7.88e-03 2.29e-02 4/27
Translation kegg subcategory 3.59e-03 1.44e-02 3/27
Membrane Transport kegg subcategory 1.37e-02 3.27e-02 3/27
ABC transporters kegg pathway 4.60e-03 1.65e-02 3/27

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
transport biological_process 2.73e-04 9.76e-04 5/27
DNA binding molecular_function 1.09e-02 1.61e-02 3/27
transporter activity molecular_function 3.91e-03 6.57e-03 3/27

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Protein synthesis tigr mainrole 1.26e-03 1.05e-02 4/27
Transport and binding proteins tigr mainrole 3.29e-03 1.69e-02 3/27
Protein synthesis tigr mainrole 1.26e-03 2.30e-03 4/27
Transport and binding proteins tigr mainrole 3.29e-03 5.26e-03 3/27

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Translation, ribosomal structure and biogenesis cog subcategory 4.99e-03 4.92e-02 4/27
Metabolism cog category 3.86e-03 7.07e-03 12/27
Translation, ribosomal structure and biogenesis cog subcategory 4.99e-03 9.03e-03 4/27
Coenzyme transport and metabolism cog subcategory 1.23e-02 2.09e-02 3/27
Function unknown cog subcategory 2.07e-02 3.36e-02 3/27
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 306

There are 27 genes in Module 306

Gene Member Table (27)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0836 trmD CDS 2794848 chromosome 924958 926235 - tRNA (guanine-N1)-methyltransferase False
DVU0867 CDS 2796164 chromosome 959615 961108 - aromatic amino acid decarboxylase False
DVU0931 thiD CDS 2794631 chromosome 1020935 1021741 + phosphomethylpyrimidine kinase False
DVU0956 rpsF CDS 2795152 chromosome 1051480 1051785 + 30S ribosomal protein S6 False
DVU0966 CDS 2794469 chromosome 1063178 1063996 + amino acid ABC transporter periplasmic amino acid-binding protein False
DVU1046 CDS 2795267 chromosome 1148991 1149128 - hypothetical protein DVU1046 False
DVU1049 CDS 2794895 chromosome 1150535 1151185 - ABC transporter ATP-binding protein False
DVU1069 CDS 2794039 chromosome 1173025 1173945 + branched chain amino acid ABC transporter permease False
DVU1237 CDS 2794414 chromosome 1325962 1326732 - His/Glu/Gln/Arg/opine ABC transporter permease False
DVU1249 fabD CDS 2795030 chromosome 1335876 1336829 - malonyl CoA-ACP transacylase False
DVU1270 CDS 2793590 chromosome 1359233 1360513 - twitching motility protein False
DVU1274 CDS 2794264 chromosome 1365953 1366396 - hypothetical protein DVU1274 False
DVU1287 CDS 2794740 chromosome 1381259 1382044 - reductase, iron-sulfur binding subunit False
DVU1288 CDS 2794741 chromosome 1382044 1382424 - cytochrome c family protein False
DVU1289 CDS 2794742 chromosome 1382427 1384037 - reductase, iron-sulfur binding subunit False
DVU1411 thiC CDS 2794955 chromosome 1480019 1481308 + thiamine biosynthesis protein ThiC False
DVU1746 CDS 2795849 chromosome 1812266 1813375 + C-5 cytosine-specific DNA methylase family protein False
DVU1848 CDS 2795911 chromosome 1916843 1917436 - hypothetical protein DVU1848 False
DVU1900 CDS 2794711 chromosome 1974260 1975201 - hypothetical protein DVU1900 False
DVU1936 CDS 2795313 chromosome 2008731 2009528 - phosphonate ABC transporter ATP-binding protein False
DVU2113 CDS 2793385 chromosome 2208084 2209415 - xanthine/uracil permease False
DVU2285 CDS 2795439 chromosome 2375226 2376746 - L-lactate permease family protein False
DVU2335 CDS 2793808 chromosome 2430361 2431911 - hypothetical protein DVU2335 False
DVU2533 pheT CDS 2795719 chromosome 2644119 2646515 - phenylalanyl-tRNA synthetase subunit beta False
DVU2927 rplL CDS 2793965 chromosome 3023830 3024213 + 50S ribosomal protein L7/L12 False
DVU2928 rpoB CDS 2793966 chromosome 3024679 3028797 + DNA-directed RNA polymerase subunit beta False
DVU3253 CDS 2793856 chromosome 3425041 3426306 + phenylacetate-coenzyme A ligase 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.