Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 186 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 186

There are 8 regulatory influences for Module 186

Regulator Table (8)
Regulator Name Type
DVU1402 tf
DVU1561 tf
DVUA0024 tf
DVU3167
DVU2582		 combiner
DVU2547 tf
DVU0682
DVU2275		 combiner
DVU2275
DVU2251		 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
355 1.40e+03 AGTTCAagTcT
Loader icon
 RegPredict
356 6.00e+03 TTTCTTTTTaT
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 186 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Ribosome kegg pathway 0.00e+00 0.00e+00 7/23
Carbohydrate Metabolism kegg subcategory 1.57e-03 1.00e-02 5/23
Translation kegg subcategory 0.00e+00 0.00e+00 9/23
Genetic Information Processing kegg category 0.00e+00 0.00e+00 10/23
Genetic Information Processing kegg category 0.00e+00 0.00e+00 10/23
Translation kegg subcategory 0.00e+00 0.00e+00 9/23
Ribosome kegg pathway 0.00e+00 0.00e+00 7/23

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
translation biological_process 0.00e+00 0.00e+00 7/23
structural constituent of ribosome molecular_function 0.00e+00 0.00e+00 7/23

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Ribosomal proteins: synthesis and modification tigr sub1role 0.00e+00 0.00e+00 6/23
Protein synthesis tigr mainrole 0.00e+00 0.00e+00 10/23
Protein synthesis tigr mainrole 0.00e+00 0.00e+00 10/23
Ribosomal proteins: synthesis and modification tigr sub1role 0.00e+00 0.00e+00 6/23

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 0.00e+00 11/23
Information storage and processing cog category 0.00e+00 2.00e-06 12/23
Information storage and processing cog category 0.00e+00 0.00e+00 12/23
Translation, ribosomal structure and biogenesis cog subcategory 0.00e+00 0.00e+00 11/23
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 186

There are 23 genes in Module 186

Gene Member Table (23)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0873 tsf CDS 2795172 chromosome 965140 966003 - elongation factor Ts False
DVU0874 rpsB CDS 2795173 chromosome 966030 966794 - 30S ribosomal protein S2 False
DVU0958 rplI CDS 2795154 chromosome 1052062 1052565 + 50S ribosomal protein L9 False
DVU0959 dnaB CDS 2795155 chromosome 1052516 1053997 + replicative DNA helicase False
DVU1021 CDS 2793744 chromosome 1124280 1125446 - hypothetical protein DVU1021 False
DVU1022 CDS 2793745 chromosome 1125448 1126224 - SUF system FeS assembly ATPase SufC False
DVU1842 CDS 2796476 chromosome 1912544 1913500 - lipoprotein False
DVU1896 rpsT CDS 2794707 chromosome 1970096 1970359 - 30S ribosomal protein S20 False
DVU1930 CDS 2795307 chromosome 2003452 2004390 + hypothetical protein False
DVU2028 CDS 2794826 chromosome 2111168 2111395 - hypothetical protein DVU2028 False
DVU2097 CDS 2795473 chromosome 2185336 2186007 + transcriptional regulator True
DVU2143 fba CDS 2794222 chromosome 2240742 2241665 + fructose-1,6-bisphosphate aldolase, class II False
DVU2519 rpsI CDS 2795609 chromosome 2632545 2632937 + 30S ribosomal protein S9 False
DVU2531 rpe CDS 2795717 chromosome 2642995 2643663 - ribulose-phosphate 3-epimerase False
DVU2533 pheT CDS 2795719 chromosome 2644119 2646515 - phenylalanyl-tRNA synthetase subunit beta False
DVU2534 pheS CDS 2795720 chromosome 2646695 2647732 - phenylalanyl-tRNA synthetase subunit alpha False
DVU2535 rplT CDS 2795721 chromosome 2647904 2648257 - 50S ribosomal protein L20 False
DVU2536 rpmI CDS 2795722 chromosome 2648340 2648537 - 50S ribosomal protein L35 False
DVU2537 infC CDS 2795723 chromosome 2648707 2649237 - translation initiation factor IF-3 False
DVU2921 rpmG CDS 2793958 chromosome 3020701 3020850 + 50S ribosomal protein L33 False
DVU3071 CDS 2796422 chromosome 3210408 3213971 - oxidoreductase False
DVU3103 CDS 2795975 chromosome 3242725 3244095 + tolB protein False
DVU3273 CDS 2795997 chromosome 3450836 3451228 - hypothetical protein DVU3273 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.