Organism : Geobacter sulfurreducens | Module List:
Module 231 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 231

There are 12 regulatory influences for Module 231

Regulator Table (12)
Regulator Name Type
GSU1201 tf
GSU2926 tf
GSU1727 tf
GSU0655 tf
GSU2945 tf
GSU1934 tf
GSU3457 tf
GSU2571 tf
GSU0079 tf
GSU2185 tf
GSU2625 tf
GSU1250 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.

Motif Table (2)
Motif Id e-value Consensus Motif Logo
2622 1.70e-01 AcGccAACggaATcA
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2623 9.40e-01 aAtCaCGCggTaCATGAAaA
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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 231 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 7.43e-03 2.20e-02 8/24
Nucleotide Metabolism kegg subcategory 7.54e-04 5.96e-03 3/24
Purine metabolism kegg pathway 1.94e-04 2.50e-03 3/24
Metabolism of Cofactors and Vitamins kegg subcategory 4.87e-04 4.52e-03 4/24
Membrane Transport kegg subcategory 4.38e-03 1.61e-02 3/24
Global kegg category 3.63e-03 1.44e-02 8/24
Metabolism kegg subcategory 3.63e-03 1.44e-02 8/24
Metabolic pathways kegg pathway 2.91e-03 1.29e-02 8/24

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Purines, pyrimidines, nucleosides, and nucleotides tigr mainrole 6.00e-05 1.55e-04 3/24
Purine ribonucleotide biosynthesis tigr sub1role 1.00e-06 4.00e-06 3/24
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 1.27e-03 2.41e-03 3/24

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 4.89e-04 1.04e-03 13/24
Nucleotide transport and metabolism cog subcategory 5.81e-04 1.22e-03 3/24
Coenzyme transport and metabolism cog subcategory 9.24e-03 1.68e-02 3/24
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 231

There are 24 genes in Module 231

Gene Member Table (24)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
GSU0021 nadA CDS None chromosome 32106 33020 - quinolinate synthetase complex, subunit A (NCBI) False
GSU0511 GSU0511 CDS None chromosome 544177 545607 + conserved domain protein (NCBI) False
GSU0604 thiC-1 CDS None chromosome 637928 639238 - thiamine biosynthesis protein ThiC (NCBI) False
GSU0606 alr CDS None chromosome 641051 642199 + alanine racemase (NCBI) False
GSU0607 selD CDS None chromosome 642216 643253 + selenide, water dikinase, selenocysteine-containing (NCBI) False
GSU0608 GSU0608 CDS None chromosome 643240 644520 + conserved domain protein (NCBI) False
GSU0609 purH CDS None chromosome 644573 646138 + phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase (NCBI) False
GSU0610 purD CDS None chromosome 646167 647438 + phosphoribosylamine--glycine ligase (NCBI) False
GSU0611 purE-1 CDS None chromosome 647453 647962 + phosphoribosylaminoimidazole carboxylase, catalytic subunit (NCBI) False
GSU1279 nikMN CDS None chromosome 1394709 1395740 + component of nickel ABCtransport system (Dmitry Rodionov) False
GSU1280 nikQ CDS None chromosome 1395768 1396580 + component of nickel ABC transport system (Dmitry Rodionov) False
GSU1432 GSU1432 CDS None chromosome 1569651 1571372 + TPR domain protein (VIMSS) False
GSU1577 cobO CDS None chromosome 1729228 1729758 + cob(I)alamin adenosyltransferase (NCBI) False
GSU1579 GSU1579 CDS None chromosome 1730261 1731220 + LAO/AO transport system ATPase (VIMSS) False
GSU2549 topA CDS None chromosome 2810320 2812593 - DNA topoisomerase I (NCBI) False
GSU2551 GSU2551 CDS None chromosome 2813764 2814771 - LysM domain protein (VIMSS) False
GSU2552 GSU2552 CDS None chromosome 2814839 2815567 - lipoprotein, putative (VIMSS) False
GSU2553 GSU2553 CDS None chromosome 2815761 2816474 + glycosyl transferase, group 2 family protein (VIMSS) False
GSU2554 GSU2554 CDS None chromosome 2816467 2816760 + conserved hypothetical protein (VIMSS) False
GSU2555 GSU2555 CDS None chromosome 2816750 2818363 + melittin resistance protein, putative (NCBI) False
GSU2619 tgt-2 CDS None chromosome 2889104 2890225 - queuine tRNA-ribosyltransferase (NCBI) False
GSU2862 GSU2862 DUMMY None chromosome 0 0 + None False
GSU3190 GSU3190 CDS None chromosome 3496433 3496669 + twin-arginine translocation protein, TatA/E family (NCBI) False
GSU3384 GSU3384 CDS None chromosome 3719386 3720963 - cardiolipin synthetase, putative (VIMSS) 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 231

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.