Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 192 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 192

There are 13 regulatory influences for Module 192

Regulator Table (13)
Regulator Name Type
DVU3066 tf
DVU2675 tf
DVU0110
DVU1419		 combiner
DVU2527
DVU1949		 combiner
DVU2547 tf
DVU2557 tf
DVU2909 tf
DVU2547
DVU0110		 combiner
DVU2275 tf
DVU1572
DVU2547		 combiner
DVU2547
DVU2799		 combiner
DVU2557
DVU2675		 combiner
DVU2547
DVU2675		 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
367 1.00e-02 gGcttTGGCGT
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 RegPredict
368 4.20e+02 GCAtCGcAtgt
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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 192 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolic pathways kegg pathway 1.39e-02 2.27e-02 9/37
Microbial metabolism in diverse environments kegg pathway 1.87e-04 1.96e-03 6/37
Carbohydrate Metabolism kegg subcategory 0.00e+00 3.00e-06 12/37
Metabolism kegg subcategory 4.30e-05 8.03e-04 18/37
Metabolism kegg category 1.20e-05 2.22e-04 20/37
Global kegg category 4.30e-05 6.08e-04 18/37
Metabolism kegg category 1.58e-02 3.59e-02 10/37
Carbohydrate Metabolism kegg subcategory 4.00e-06 1.30e-04 8/37
Energy Metabolism kegg subcategory 1.96e-02 4.18e-02 3/37
Amino Acid Metabolism kegg subcategory 1.18e-02 2.94e-02 4/37
Global kegg category 1.64e-02 3.69e-02 9/37
Metabolism kegg subcategory 1.64e-02 3.69e-02 9/37
Metabolic pathways kegg pathway 1.39e-02 3.29e-02 9/37
Microbial metabolism in diverse environments kegg pathway 1.87e-04 2.54e-03 6/37

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
electron transport biological_process 3.61e-04 1.19e-03 7/37
chemotaxis biological_process 1.87e-03 3.85e-03 3/37
signal transduction biological_process 3.41e-03 6.29e-03 3/37
peptidyl-histidine phosphorylation biological_process 3.01e-03 5.73e-03 3/37
oxidoreductase activity molecular_function 3.09e-04 7.76e-04 4/37

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 5.66e-04 6.53e-03 4/37
Energy metabolism tigr mainrole 5.66e-04 1.12e-03 4/37

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy production and conversion cog subcategory 2.38e-04 6.58e-03 8/37
Metabolism cog category 4.13e-04 8.46e-03 18/37
Cellular processes and signaling cog category 2.89e-02 4.57e-02 11/37
Metabolism cog category 1.71e-04 3.97e-04 18/37
Signal transduction mechanisms cog subcategory 1.46e-02 2.44e-02 6/37
Cell motility cog subcategory 1.83e-02 3.01e-02 3/37
Posttranslational modification, protein turnover, chaperones cog subcategory 1.27e-02 2.15e-02 3/37
Energy production and conversion cog subcategory 2.38e-04 5.28e-04 8/37
Carbohydrate transport and metabolism cog subcategory 1.54e-02 2.56e-02 3/37
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 192

There are 37 genes in Module 192

Gene Member Table (37)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0175 CDS 2795625 chromosome 219258 220889 - tungsten formylmethanofuran dehydrogenase family protein/molybdopterin binding protein False
DVU0456 CDS 2794976 chromosome 523950 524957 + DHH family protein False
DVU0580 moaA CDS 2794565 chromosome 643924 644949 + molybdenum cofactor biosynthesis protein A False
DVU0600 ldh CDS 2793528 chromosome 670757 671686 + L-lactate dehydrogenase False
DVU0626 ilvN-1 CDS 2796150 chromosome 693551 694030 + acetolactate synthase small subunit False
DVU0627 ptB CDS 2796151 chromosome 694034 695065 + phosphotransbutyrylase False
DVU0701 glcB CDS 2795485 chromosome 778761 780950 + malate synthase G False
DVU1037 CDS 2796250 chromosome 1139907 1141349 + mercuric reductase False
DVU1396 CDS 2794796 chromosome 1465764 1466021 - hypothetical protein DVU1396 False
DVU1413 CDS 2794957 chromosome 1482724 1484016 + hypothetical protein DVU1413 False
DVU1420 CDS 2794681 chromosome 1494284 1494655 + Hpt domain-containing protein False
DVU1471 CDS 2794140 chromosome 1551664 1552092 + HSP20 family protein False
DVU1472 CDS 2794141 chromosome 1552089 1554554 + ATP-dependent protease False
DVU1592 CDS 2796028 chromosome 1673985 1675727 + arginine N-succinyltransferase subunit beta False
DVU1594 cheA-1 CDS 2796030 chromosome 1676184 1678310 + chemotaxis protein CheA False
DVU1596 cheB-1 CDS 2795951 chromosome 1679212 1680285 + protein-glutamate methylesterase CheB False
DVU1613 CDS 2796066 chromosome 1698737 1699795 + glutamate synthase subunit beta False
DVU1614 CDS 2796067 chromosome 1699809 1700339 + iron-sulfur cluster-binding protein False
DVU1958 CDS 2793471 chromosome 2030405 2033002 + sensory box histidine kinase False
DVU1986 CDS 2793792 chromosome 2064529 2064960 + hypothetical protein DVU1986 False
DVU2349 CDS 2795523 chromosome 2442630 2445197 + carbohydrate phosphorylase family protein False
DVU2360 CDS 2796519 chromosome 2458415 2459221 + FAD/NAD-binding family oxidoreductase False
DVU2421 CDS 2794362 chromosome 2527924 2528121 - 4-oxalocrotonate tautomerase family protein False
DVU2422 CDS 2794363 chromosome 2528124 2528633 - nitroreductase family protein False
DVU2482 fdnG-2 CDS 2795450 chromosome 2590064 2593075 - formate dehydrogenase subunit alpha, selenocysteine-containing False
DVU2895 CDS 2793925 chromosome 2991759 2992061 + hypothetical protein DVU2895 False
DVU2968 CDS 2796282 chromosome 3073821 3075017 - sensor histidine kinase/response regulator False
DVU2976 CDS 2796290 chromosome 3084007 3085119 - hypothetical protein DVU2976 False
DVU3037 CDS 2796454 chromosome 3162817 3163689 - rhodanese-like domain-containing protein False
DVU3077 CDS 2796428 chromosome 3220001 3220762 + AhpC/TSA family protein False
DVU3147 CDS 2793997 chromosome 3297454 3298716 - 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase False
DVU3148 malQ CDS 2793998 chromosome 3299005 3300516 - 4-alpha-glucanotransferase False
DVU3217 CDS 2796215 chromosome 3385718 3386146 - hypothetical protein DVU3217 False
DVU3282 CDS 2796006 chromosome 3457225 3458124 - ADP-ribosylglycohydrolase family protein False
DVUA0021 CDS 2781542 pDV 26632 27693 - hypothetical protein DVUA0021 False
DVUA0023 CDS 2781540 pDV 28487 29617 - ABC transporter permease False
DVUA0091 katA CDS 2781562 pDV 123495 124952 + catalase 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.