Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 230 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 230

There are 9 regulatory influences for Module 230

Regulator Table (9)
Regulator Name Type
DVU2423 tf
DVU2675 tf
DVU2644 tf
DVU2527
DVU3305
combiner
DVU2275 tf
DVU2802
DVU2275
combiner
DVU1572
DVU2547
combiner
DVU2547
DVU2319
combiner
DVU2547
DVU3229
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
439 9.60e-04 aaaatCAAtAacAcatccTTTtCA
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RegPredict
440 1.30e-01 TACcgGtgACGGCA..tGgCA
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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 230 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 2.42e-03 8.03e-03 8/25
Biosynthesis of secondary metabolites kegg pathway 7.34e-03 1.49e-02 4/25
Carbohydrate Metabolism kegg subcategory 1.29e-02 4.22e-02 4/25
Metabolism kegg subcategory 2.50e-05 5.19e-04 14/25
Metabolism kegg category 4.43e-04 4.28e-03 13/25
Global kegg category 2.50e-05 3.99e-04 14/25
Metabolism kegg category 1.98e-03 1.04e-02 9/25
Amino Acid Metabolism kegg subcategory 1.33e-02 3.20e-02 3/25
Global kegg category 2.88e-03 1.27e-02 8/25
Metabolism kegg subcategory 2.88e-03 1.27e-02 8/25
Metabolic pathways kegg pathway 2.42e-03 1.17e-02 8/25
Biosynthesis of secondary metabolites kegg pathway 7.34e-03 2.19e-02 4/25

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
metabolic process biological_process 1.74e-03 3.66e-03 4/25

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 1.72e-02 2.84e-02 10/25
Amino acid transport and metabolism cog subcategory 1.75e-02 2.90e-02 4/25
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 230

There are 25 genes in Module 230

Gene Member Table (25)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0113 hisI CDS 2794982 chromosome 147117 147497 + phosphoribosyl-AMP cyclohydrolase False
DVU0335 CDS 2794751 chromosome 378977 380569 + 3-deoxy-D-manno-octulosonic-acid transferase False
DVU0477 icd CDS 2793622 chromosome 542367 543509 + isocitrate dehydrogenase, NADP-dependent False
DVU0671 CDS 2794695 chromosome 743817 745454 - hypothetical protein DVU0671 False
DVU0672 CDS 2794696 chromosome 745612 745764 + hypothetical protein DVU0672 False
DVU0704 lepB CDS 2795488 chromosome 784042 784641 + signal peptidase I False
DVU0745 CDS 2795261 chromosome 834410 835228 + ABC transporter periplasmic substrate-binding protein False
DVU0953 tyrS CDS 2795149 chromosome 1046362 1047558 + tyrosyl-tRNA synthetase False
DVU1054 CDS 2794900 chromosome 1154949 1155587 + HAD superfamily hydrolase False
DVU1186 mazG CDS 2796671 chromosome 1275312 1276115 + nucleoside triphosphate pyrophosphohydrolase False
DVU1223 CDS 2796681 chromosome 1313384 1314952 - hypothetical protein DVU1223 False
DVU1453 fadD CDS 2794819 chromosome 1530755 1532449 - long-chain-fatty-acid--CoA ligase False
DVU1469 rpsA CDS 2794138 chromosome 1549690 1551153 - 30S ribosomal protein S1 False
DVU1677 tpiA CDS 2794905 chromosome 1756281 1757036 - triosephosphate isomerase False
DVU2263 CDS 2794086 chromosome 2356696 2358621 - outer membrane autotransporter False
DVU2433 CDS 2795424 chromosome 2538257 2538379 - hypothetical protein DVU2433 False
DVU2434 CDS 2795425 chromosome 2538367 2538774 - hypothetical protein DVU2434 False
DVU2521 aroK CDS 2795611 chromosome 2633489 2634031 + shikimate kinase False
DVU2586 CDS 2796364 chromosome 2709005 2710687 - ABC transporter ATP-binding protein False
DVU2644 CDS 2795700 chromosome 2760784 2761455 - GntR family transcriptional regulator True
DVU2946 CDS 2796497 chromosome 3050421 3050663 - hypothetical protein DVU2946 False
DVU3118 CDS 2796610 chromosome 3267144 3267449 - hypothetical protein DVU3118 False
DVU3119 CDS 2796611 chromosome 3267630 3269324 + AMP-binding protein False
DVU3253 CDS 2793856 chromosome 3425041 3426306 + phenylacetate-coenzyme A ligase False
DVU3299 CDS 2796034 chromosome 3476756 3477826 - hypothetical protein DVU3299 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.