Organism : Geobacter sulfurreducens | Module List:
Module 295 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 295

There are 7 regulatory influences for Module 295

Regulator Table (7)
Regulator Name Type
GSU3396 tf
GSU2753 tf
GSU0164 tf
GSU1320 tf
GSU1653 tf
GSU1483 tf
GSU2964 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
2748 1.20e+03 AaATctatTGATtcT
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2749 7.30e+03 TTTACATGaAaT.T
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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 295 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Carbohydrate Metabolism kegg subcategory 1.85e-02 4.01e-02 3/29
Signal Transduction kegg subcategory 6.01e-03 1.91e-02 3/29
Two-component system kegg pathway 6.01e-03 1.91e-02 3/29

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cell motility cog subcategory 1.85e-02 3.16e-02 3/29
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 295

There are 29 genes in Module 295

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
GSU0010 GSU0010 CDS None chromosome 17115 19298 + sensory box histidine kinase/response regulator (VIMSS) False
GSU0249 GSU0249 CDS None chromosome 256943 257920 + membrane protein, putative (VIMSS) False
GSU0387 GSU0387 CDS None chromosome 419107 419916 - undecaprenol kinase, putative (VIMSS) False
GSU0443 GSU0443 CDS None chromosome 475021 476166 + ribonuclease D, putative (VIMSS) False
GSU0573 GSU0573 CDS None chromosome 601211 602203 + alcohol dehydrogenase, zinc-containing (VIMSS) False
GSU1075 ruvC CDS None chromosome 1163943 1164437 + crossover junction endodeoxyribonuclease RuvC (NCBI) False
GSU1124 coaBC CDS None chromosome 1208341 1209540 + phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase (NCBI) False
GSU1172 mviN CDS None chromosome 1276965 1278530 + virulence factor mviN protein (NCBI) False
GSU1271 pyrB CDS None chromosome 1385636 1386571 + aspartate carbamoyltransferase (NCBI) False
GSU1292 GSU1292 CDS None chromosome 1408577 1409731 + sensory box histidine kinase (VIMSS) False
GSU1444 GSU1444 CDS None chromosome 1581389 1582282 - conserved hypothetical protein (VIMSS) False
GSU1460 proS CDS None chromosome 1599970 1601682 + prolyl-tRNA synthetase (NCBI) False
GSU1482 GSU1482 CDS None chromosome 1622483 1623763 - outer membrane efflux protein (VIMSS) False
GSU1653 GSU1653 CDS None chromosome 1810491 1811927 + sigma-54 dependent DNA-binding response regulator (VIMSS) True
GSU1702 GSU1702 CDS None chromosome 1864395 1865351 + ROK family protein (VIMSS) False
GSU2053 GSU2053 CDS None chromosome 2254128 2255909 - indolepyruvate ferredoxin oxidoreductase, alpha subunit, putative (VIMSS) False
GSU2092 GSU2092 CDS None chromosome 2298770 2299324 - conserved hypothetical protein (VIMSS) False
GSU2214 cheB-3 CDS None chromosome 2429043 2430158 - protein-glutamate methylesterase (NCBI) False
GSU2215 cheR-3 CDS None chromosome 2430155 2431024 - chemotaxis protein methyltransferase CheR (NCBI) False
GSU2231 GSU2231 CDS None chromosome 2446660 2447697 + conserved hypothetical protein (VIMSS) False
GSU2243 GSU2243 CDS None chromosome 2457829 2458980 - UDP-N-acetylglucosamine 2-epimerase (VIMSS) False
GSU2595 GSU2595 CDS None chromosome 2861237 2861350 + hypothetical protein (VIMSS) False
GSU2596 GSU2596 CDS None chromosome 2862308 2862982 - lipoprotein, putative (VIMSS) False
GSU2609 pilB CDS None chromosome 2877043 2878980 - type IV pilus assembly protein, putative (NCBI) False
GSU3008 cobS CDS None chromosome 3300552 3301292 - cobalamin 5'-phosphate synthase (NCBI) False
GSU3264 GSU3264 CDS None chromosome 3579874 3581100 + membrane protein, putative (VIMSS) False
GSU3265 nirB CDS None chromosome 3581132 3581809 + sulfite reductase, assimilatory-type (NCBI) False
GSU3346 GSU3346 CDS None chromosome 3675042 3676874 - potassium uptake protein, Kup system (VIMSS) False
GSU3396 GSU3396 CDS None chromosome 3735764 3736480 + transcriptional regulator, GntR family (VIMSS) True

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.