Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 206 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 206

There are 12 regulatory influences for Module 206

Regulator Table (12)
Regulator Name Type
DVU1419 tf
DVU2886 tf
DVU0679
DVU0569		 combiner
DVU2319
DVU0539		 combiner
DVU2036
DVU0946		 combiner
DVU0594
DVU3193		 combiner
DVU0057 tf
DVU0594 tf
DVU0269
DVU0569		 combiner
DVU0569 tf
DVU0539
DVU1419		 combiner
DVU0946
DVU0569		 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
395 8.80e-04 AAAactttAt.TtGccAT.tgcAa
Loader icon
 RegPredict
396 6.00e+02 cACgTaaAAGG
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 206 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Phenylalanine tyrosine and tryptophan biosynthesis kegg pathway 0.00e+00 0.00e+00 10/33
Metabolic pathways kegg pathway 0.00e+00 1.00e-06 17/33
Biosynthesis of secondary metabolites kegg pathway 0.00e+00 0.00e+00 13/33
Amino Acid Metabolism kegg subcategory 0.00e+00 0.00e+00 14/33
Metabolism kegg subcategory 0.00e+00 0.00e+00 32/33
Metabolism kegg category 0.00e+00 0.00e+00 25/33
Global kegg category 0.00e+00 0.00e+00 32/33
Metabolism kegg category 0.00e+00 5.00e-06 17/33
Amino Acid Metabolism kegg subcategory 0.00e+00 0.00e+00 12/33
Phenylalanine tyrosine and tryptophan biosynthesis kegg pathway 0.00e+00 0.00e+00 10/33
Global kegg category 0.00e+00 1.00e-06 17/33
Metabolism kegg subcategory 0.00e+00 1.00e-06 17/33
Metabolic pathways kegg pathway 0.00e+00 1.00e-06 17/33
Biosynthesis of secondary metabolites kegg pathway 0.00e+00 0.00e+00 13/33

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
tryptophan metabolic process biological_process 0.00e+00 0.00e+00 4/33
biosynthetic process biological_process 7.51e-04 1.92e-03 3/33

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Aromatic amino acid family tigr sub1role 0.00e+00 2.00e-06 3/33
Amino acid biosynthesis tigr mainrole 4.60e-05 9.52e-04 4/33
Amino acid biosynthesis tigr mainrole 4.60e-05 1.19e-04 4/33
Aromatic amino acid family tigr sub1role 0.00e+00 0.00e+00 3/33

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Amino acid transport and metabolism cog subcategory 0.00e+00 0.00e+00 13/33
Coenzyme transport and metabolism cog subcategory 9.20e-05 3.15e-03 6/33
Metabolism cog category 0.00e+00 1.40e-05 21/33
Metabolism cog category 4.00e-06 1.50e-05 19/33
Amino acid transport and metabolism cog subcategory 0.00e+00 0.00e+00 13/33
Coenzyme transport and metabolism cog subcategory 9.20e-05 2.31e-04 6/33
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 206

There are 33 genes in Module 206

Gene Member Table (33)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0012 CDS 2796416 chromosome 15099 16301 + hypothetical protein DVU0012 False
DVU0021 CDS 2794953 chromosome 23612 24658 - hypothetical protein DVU0021 False
DVU0097 potB CDS 2796177 chromosome 127492 128379 - polyamine ABC transporter permease False
DVU0121 CDS 2796786 chromosome 156057 156500 - hypothetical protein DVU0121 False
DVU0122 CDS 2794728 chromosome 156582 156680 - hypothetical protein DVU0122 False
DVU0123 CDS 2794729 chromosome 156693 157775 - hypothetical protein DVU0123 False
DVU0124 CDS 2794730 chromosome 157822 158010 + hypothetical protein DVU0124 False
DVU0335 CDS 2794751 chromosome 378977 380569 + 3-deoxy-D-manno-octulosonic-acid transferase False
DVU0460 CDS 2794473 chromosome 527671 528471 + fructose-bisphosphate aldolase False
DVU0461 CDS 2794474 chromosome 528480 529451 + 3-dehydroquinate synthase False
DVU0462 CDS 2794475 chromosome 529454 530629 + chorismate mutase/prephenate dehydratase False
DVU0463 aroA CDS 2794476 chromosome 530629 531948 + 3-phosphoshikimate 1-carboxyvinyltransferase False
DVU0464 CDS 2794477 chromosome 531954 532721 + prephenate dehydrogenase False
DVU0465 CDS 2794478 chromosome 532853 534451 + anthranilate synthase, component I False
DVU0466 trpG CDS 2793607 chromosome 534432 535061 + anthranilate synthase, glutamine amidotransferase component False
DVU0467 trpD CDS 2793608 chromosome 535058 536056 + anthranilate phosphoribosyltransferase False
DVU0468 trpC CDS 2793609 chromosome 536049 536822 + indole-3-glycerol phosphate synthase False
DVU0469 trpF-1 CDS 2793610 chromosome 536870 537724 + N-(5'-phosphoribosyl)anthranilate isomerase False
DVU0470 trpB-2 CDS 2793611 chromosome 537721 538908 + tryptophan synthase subunit beta False
DVU0471 trpA CDS 2794713 chromosome 538905 539678 + tryptophan synthase subunit alpha False
DVU0480 CDS 2793625 chromosome 546147 546878 + hypothetical protein DVU0480 False
DVU0606 CDS 2793367 chromosome 674210 675133 + ArsR family transcriptional regulator True
DVU0607 ahcY CDS 2793368 chromosome 675159 676598 + S-adenosyl-L-homocysteine hydrolase False
DVU0997 metF CDS 2794154 chromosome 1090724 1091599 + 5,10-methylenetetrahydrofolate reductase False
DVU1028 cmk CDS 2794525 chromosome 1132719 1133417 - cytidylate kinase False
DVU1065 CDS 2794777 chromosome 1167904 1169793 + peptidyl-prolyl cis-trans isomerse domain-containing protein False
DVU1847 CDS 2795910 chromosome 1915787 1916680 - hypothetical protein DVU1847 False
DVU2252 dnaA-2 CDS 2794074 chromosome 2347717 2349192 - chromosomal replication initiator protein DnaA False
DVU2448 panC CDS 2796625 chromosome 2552303 2553154 + pantoate--beta-alanine ligase False
DVU2449 metK CDS 2796626 chromosome 2553206 2554381 + S-adenosylmethionine synthetase False
DVU2930 CDS 2793968 chromosome 3033771 3034211 + hypothetical protein DVU2930 False
DVU3046 CDS 2796072 chromosome 3171427 3172533 - glycosyl transferase group 1 family protein False
DVU3193 CDS 2793843 chromosome 3354015 3355115 - DNA-binding protein True

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.