Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 188 Profile

GeneModule member RegulatorRegulator MotifMotif
Cytoscape Web
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 188

There are 11 regulatory influences for Module 188

Regulator Table (11)
Regulator Name Type
DVU1561 tf
DVU0682
DVU2275
combiner
DVU1547
DVUA0024
combiner
DVU2532
DVU2275
combiner
DVU2547
DVU2195
combiner
DVU2547
DVU2832
combiner
DVU3167
DVU2582
combiner
DVU1547
DVU0230
combiner
DVU2275 tf
DVU1547
DVU3142
combiner
DVU2547 tf

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
359 3.00e+01 CtTTtCcgaA
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RegPredict
360 4.30e+04 GCgtaccGCATcggGgCAtCcC
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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 188 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Ribosome kegg pathway 5.46e-04 3.59e-03 3/25
Carbohydrate Metabolism kegg subcategory 1.29e-02 4.22e-02 4/25
Translation kegg subcategory 2.60e-04 3.00e-03 4/25
Genetic Information Processing kegg category 3.10e-05 4.65e-04 7/25
Genetic Information Processing kegg category 1.20e-05 3.21e-04 7/25
Translation kegg subcategory 2.60e-04 3.16e-03 4/25
Ribosome kegg pathway 5.46e-04 4.93e-03 3/25

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
translation biological_process 1.44e-03 3.12e-03 3/25
structural constituent of ribosome molecular_function 6.69e-04 1.43e-03 3/25
ATP binding molecular_function 1.75e-02 2.41e-02 5/25

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Ribosomal proteins: synthesis and modification tigr sub1role 3.22e-04 1.37e-03 3/25
Protein synthesis tigr mainrole 8.80e-05 1.53e-03 5/25
Protein synthesis tigr mainrole 8.80e-05 2.09e-04 5/25
Ribosomal proteins: synthesis and modification tigr sub1role 3.22e-04 6.73e-04 3/25

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Translation, ribosomal structure and biogenesis cog subcategory 5.60e-05 2.14e-03 6/25
Replication, recombination and repair cog subcategory 4.87e-03 4.88e-02 3/25
Information storage and processing cog category 1.00e-05 3.10e-04 10/25
Information storage and processing cog category 8.00e-06 2.80e-05 10/25
Translation, ribosomal structure and biogenesis cog subcategory 5.60e-05 1.59e-04 6/25
Replication, recombination and repair cog subcategory 4.87e-03 8.83e-03 3/25
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 188

There are 25 genes in Module 188

Gene Member Table (25)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0274 CDS 2794999 chromosome 316978 317349 - hypothetical protein DVU0274 False
DVU0836 trmD CDS 2794848 chromosome 924958 926235 - tRNA (guanine-N1)-methyltransferase False
DVU0840 ffh CDS 2794852 chromosome 927439 928965 - signal recognition particle protein False
DVU0950 CDS 2794594 chromosome 1043812 1043928 + hypothetical protein DVU0950 False
DVU0957 rpsR CDS 2795153 chromosome 1051786 1052049 + 30S ribosomal protein S18 False
DVU0958 rplI CDS 2795154 chromosome 1052062 1052565 + 50S ribosomal protein L9 False
DVU0959 dnaB CDS 2795155 chromosome 1052516 1053997 + replicative DNA helicase False
DVU1021 CDS 2793744 chromosome 1124280 1125446 - hypothetical protein DVU1021 False
DVU1022 CDS 2793745 chromosome 1125448 1126224 - SUF system FeS assembly ATPase SufC False
DVU1282 glmM CDS 2794348 chromosome 1374532 1375884 + phosphoglucosamine mutase False
DVU1455 CDS 2794822 chromosome 1534209 1534952 - hypothetical protein DVU1455 False
DVU1624 kdsA CDS 2795885 chromosome 1709008 1709829 + 2-dehydro-3-deoxyphosphooctonate aldolase False
DVU1625 CDS 2795886 chromosome 1709819 1710346 + YrbI family phosphatase False
DVU1627 CDS 2795888 chromosome 1711584 1712309 + ABC transporter ATP-binding protein False
DVU1635 CDS 2796099 chromosome 1717473 1717577 + hypothetical protein DVU1635 False
DVU1841 fbp CDS 2796475 chromosome 1911438 1912451 - fructose-1,6-bisphosphatase False
DVU2252 dnaA-2 CDS 2794074 chromosome 2347717 2349192 - chromosomal replication initiator protein DnaA False
DVU2522 CDS 2795612 chromosome 2634024 2634626 + hypothetical protein DVU2522 False
DVU2903 CDS 2793933 chromosome 3002932 3004260 + HD domain-containing protein False
DVU2921 rpmG CDS 2793958 chromosome 3020701 3020850 + 50S ribosomal protein L33 False
DVU3070 CDS 2796421 chromosome 3209898 3210326 - hypothetical protein DVU3070 False
DVU3071 CDS 2796422 chromosome 3210408 3213971 - oxidoreductase False
DVU3207 CDS 2796205 chromosome 3372044 3374140 + RNB-like family protein False
DVU3274 CDS 2795998 chromosome 3451228 3451896 - hypothetical protein DVU3274 False
DVU3367 aspS CDS 2795681 chromosome 3537577 3539409 - aspartyl-tRNA synthetase 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.

Comments for Module 188

Please add your comments for this module by using the form below. Your comments will be publicly available.

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Social Help

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.

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.