Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 35 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 35

There are 12 regulatory influences for Module 35

Regulator Table (12)
Regulator Name Type
DVU0110 tf
DVU3167 tf
DVU2547 tf
DVU3167
DVU1340		 combiner
DVU1518
DVU1561		 combiner
DVU0309 tf
DVU0653 tf
DVU2423 tf
DVU3066 tf
DVU0749
DVU0110		 combiner
DVU2960
DVU0110		 combiner
DVU2547
DVU0110		 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
69 2.10e+04 aggAAacCGaaACgggAcaT
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 RegPredict
70 4.00e+03 ctCCccGcc.GgC..caaccc
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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 35 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Amino Acid Metabolism kegg subcategory 4.51e-04 4.35e-03 6/30
Amino Acid Metabolism kegg subcategory 2.50e-02 5.00e-02 3/30

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
regulation of transcription, DNA-dependent biological_process 7.06e-03 1.17e-02 5/30
signal transduction biological_process 1.55e-03 3.31e-03 3/30
ATP binding molecular_function 1.23e-02 1.77e-02 6/30

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
sensory_box tigrfam 7.76e-04 8.43e-04 3/30
Small molecule interactions tigr sub1role 8.37e-04 2.45e-03 3/30
Regulatory functions tigr mainrole 1.97e-03 1.32e-02 3/30
sensory_box tigrfam 7.76e-04 1.48e-03 3/30
Regulatory functions tigr mainrole 1.97e-03 3.40e-03 3/30
Small molecule interactions tigr sub1role 8.37e-04 1.59e-03 3/30

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Poorly characterized cog category 1.81e-02 2.97e-02 7/30
Amino acid transport and metabolism cog subcategory 9.47e-03 1.64e-02 5/30
General function prediction only cog subcategory 2.35e-02 3.78e-02 5/30
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 35

There are 30 genes in Module 35

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0007 asnC CDS 2793559 chromosome 9552 10937 - asparaginyl-tRNA synthetase False
DVU0247 CDS 2794295 chromosome 280944 281303 - response regulator False
DVU0291 CDS 2795946 chromosome 335226 336290 - ABC transporter ATP-binding protein False
DVU0760 CDS 2793599 chromosome 851217 852347 - hypothetical protein DVU0760 False
DVU0761 CDS 2795565 chromosome 852498 853088 - lipoprotein False
DVU0815 CDS 2795018 chromosome 902205 904310 - AsmA family protein False
DVU0983 CDS 2793325 chromosome 1079723 1080268 - hypothetical protein DVU0983 False
DVU1219 CDS 2796677 chromosome 1309280 1311475 - hypothetical protein DVU1219 False
DVU1368 CDS 2795092 chromosome 1446416 1448038 + rhodanese-like domain-containing protein False
DVU1547 CDS 2793697 chromosome 1622188 1623813 - sensory box protein True
DVU2233 CDS 2795560 chromosome 2326274 2327251 - hypothetical protein DVU2233 False
DVU2329 hypB CDS 2793802 chromosome 2425178 2425852 + hydrogenase accessory protein HypB False
DVU2330 CDS 2793803 chromosome 2425849 2426730 + MRP family protein False
DVU2490 CDS 2795458 chromosome 2601007 2601831 + histidinol phosphatase False
DVU2491 CDS 2795459 chromosome 2601837 2603735 + ABC transporter ATP-binding protein False
DVU2545 CDS 2796119 chromosome 2656906 2658066 + iron-containing alcohol dehydrogenase False
DVU2546 CDS 2796120 chromosome 2658050 2659672 + sensory box histidine kinase False
DVU2618 CDS 2793914 chromosome 2739231 2739395 + hypothetical protein DVU2618 False
DVU2636 CDS 2795253 chromosome 2751297 2752466 - hypothetical protein DVU2636 False
DVU2765 CDS 2796315 chromosome 2873718 2874344 + metallo-beta-lactamase family protein False
DVU2766 CDS 2796316 chromosome 2874432 2874599 + hypothetical protein DVU2766 False
DVU2767 CDS 2796317 chromosome 2874596 2875210 + iron-sulfur flavoprotein False
DVU2953 CDS 2796504 chromosome 3060107 3061669 + GntR family transcriptional regulator True
DVU3047 CDS 2796073 chromosome 3173003 3173950 - class IV aminotransferase False
DVU3048 asd CDS 2796074 chromosome 3174209 3175258 - aspartate-semialdehyde dehydrogenase False
DVU3049 CDS 2796075 chromosome 3175305 3175718 - hemerythrin family protein False
DVU3067 hypF CDS 2796418 chromosome 3202929 3205448 + [NiFe] hydrogenase maturation protein HypF [Desulfovibrio vulgaris str. Hildenborough] False
DVU3068 CDS 2796419 chromosome 3205678 3208161 + GAF domain/sensory box/EAL domain-containing protein False
DVU3172 CDS 2795877 chromosome 3328360 3330507 + hypothetical protein DVU3172 False
DVU3364 CDS 2795678 chromosome 3534750 3535673 - hypothetical protein DVU3364 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.