Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 262 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 262

There are 11 regulatory influences for Module 262

Regulator Table (11)
Regulator Name Type
DVU3313 tf
DVU2319
DVU2690		 combiner
DVU2557
DVU0936		 combiner
DVU0277
DVU1690		 combiner
DVU2557
DVU0653		 combiner
DVU0679
DVU2251		 combiner
DVU0525 tf
DVU0606
DVU2251		 combiner
DVU0277
DVU1745		 combiner
DVU3313
DVU0230		 combiner
DVU3167
DVU2251		 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
499 1.00e+02 TtGtgAAA
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 RegPredict
500 9.80e+03 Aaa.tgtGCttTccCgcTcCaTt
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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 262 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 3.00e-06 9.50e-05 6/26
Biosynthesis of secondary metabolites kegg pathway 8.73e-03 1.64e-02 4/26
Microbial metabolism in diverse environments kegg pathway 1.04e-02 1.84e-02 3/26
Membrane Transport kegg subcategory 2.10e-05 4.65e-04 6/26
Metabolism kegg subcategory 9.90e-04 7.45e-03 12/26
Environmental Information Processing kegg category 4.71e-04 4.50e-03 6/26
Global kegg category 9.90e-04 8.08e-03 12/26
Environmental Information Processing kegg category 4.43e-04 4.37e-03 6/26
Membrane Transport kegg subcategory 2.10e-05 5.31e-04 6/26
ABC transporters kegg pathway 3.00e-06 9.50e-05 6/26
Biosynthesis of secondary metabolites kegg pathway 8.73e-03 2.42e-02 4/26
Microbial metabolism in diverse environments kegg pathway 1.04e-02 2.69e-02 3/26

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
electron transport biological_process 1.99e-04 7.67e-04 6/26
transport biological_process 2.18e-04 8.26e-04 5/26
transporter activity molecular_function 3.53e-04 8.60e-04 4/26

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Electron transport tigr sub1role 5.00e-06 8.30e-05 3/26
Energy metabolism tigr mainrole 1.27e-03 1.05e-02 3/26
Transport and binding proteins tigr mainrole 2.85e-03 1.54e-02 3/26
Energy metabolism tigr mainrole 1.27e-03 2.31e-03 3/26
Electron transport tigr sub1role 5.00e-06 1.60e-05 3/26
Transport and binding proteins tigr mainrole 2.85e-03 4.64e-03 3/26

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy production and conversion cog subcategory 6.17e-04 1.26e-02 6/26
Amino acid transport and metabolism cog subcategory 2.00e-06 9.50e-05 9/26
Metabolism cog category 0.00e+00 0.00e+00 20/26
Metabolism cog category 0.00e+00 0.00e+00 20/26
Energy production and conversion cog subcategory 6.17e-04 1.26e-03 6/26
Amino acid transport and metabolism cog subcategory 2.00e-06 6.00e-06 9/26
Inorganic ion transport and metabolism cog subcategory 6.94e-03 1.23e-02 3/26
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 262

There are 26 genes in Module 262

Gene Member Table (26)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0095 CDS 2796175 chromosome 125677 126714 - polyamine ABC transporter periplasmic polyamine-binding protein False
DVU0096 potC CDS 2796176 chromosome 126716 127489 - spermidine/putrescine ABC transporter membrane protein False
DVU0386 CDS 2796744 chromosome 434628 435377 + amino acid ABC transporter periplasmic amino acid-binding protein False
DVU0477 icd CDS 2793622 chromosome 542367 543509 + isocitrate dehydrogenase, NADP-dependent False
DVU0712 CDS 2795408 chromosome 791681 792811 + amino acid ABC transporter periplasmic-binding protein False
DVU0937 CDS 2794611 chromosome 1028459 1028845 + hypothetical protein DVU0937 False
DVU1095 argG CDS 2794339 chromosome 1200783 1201973 - argininosuccinate synthase False
DVU1777 cynT CDS 2794284 chromosome 1841010 1841747 - carbonic anhydrase False
DVU1912 CDS 2793685 chromosome 1987143 1987631 + hypothetical protein DVU1912 False
DVU1934 CDS 2795311 chromosome 2007149 2007949 - phosphonate ABC transporter permease False
DVU1937 CDS 2795314 chromosome 2009605 2010618 - phosphonate ABC transporter periplasmic phosphonate-binding protein False
DVU2098 cooS CDS 2795474 chromosome 2186296 2188185 + carbon monoxide dehydrogenase False
DVU2205 CDS 2793668 chromosome 2301355 2302632 + tryptophan-specific transport protein False
DVU2342 CDS 2795516 chromosome 2437743 2438555 - amino acid ABC transporter periplasmic amino acid-binding protein False
DVU2347 argD CDS 2795521 chromosome 2440531 2441730 - acetylornithine aminotransferase False
DVU2348 dut CDS 2795522 chromosome 2441935 2442396 - deoxyuridine 5'-triphosphate nucleotidohydrolase False
DVU2364 CDS 2796523 chromosome 2461234 2462400 - class I/II aminotransferase False
DVU2529 pgk CDS 2795619 chromosome 2639592 2640773 - phosphoglycerate kinase False
DVU2792 CDS 2795378 chromosome 2894645 2895850 + electron transport complex protein RnfC False
DVU2793 CDS 2795379 chromosome 2895988 2896944 + electron transport complex protein RnfD False
DVU2794 CDS 2795380 chromosome 2896947 2897522 + electron transport complex protein RnfG False
DVU2795 CDS 2795381 chromosome 2897534 2898205 + electron transport complex RsxE subunit False
DVU2796 CDS 2795382 chromosome 2898215 2898790 + electron transport complex protein RnfA False
DVU2798 CDS 2795384 chromosome 2899744 2900754 + ApbE family protein False
DVU2931 CDS 2793969 chromosome 3034225 3036426 + sensory box histidine kinase False
DVU3171 CDS 2795876 chromosome 3327925 3328314 + cytochrome c3 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.