Organism : Geobacter sulfurreducens | Module List:
Module 321 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 321

There are 10 regulatory influences for Module 321

Regulator Table (10)
Regulator Name Type
GSU0776 tf
GSU2587 tf
GSU2185 tf
GSU0655 tf
GSU1934 tf
GSU2670 tf
GSU2926 tf
GSU2571 tf
GSU0284 tf
GSU0534 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
2798 1.30e+03 CCttGaggAAAaagG
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2799 6.90e+04 AAtcgaCaCAaAA
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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 321 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 5.17e-03 1.76e-02 10/31
Carbohydrate Metabolism kegg subcategory 2.32e-02 4.69e-02 3/31
Global kegg category 2.27e-02 4.62e-02 8/31
Metabolism kegg subcategory 2.27e-02 4.62e-02 8/31
Metabolic pathways kegg pathway 1.87e-02 4.01e-02 8/31
Microbial metabolism in diverse environments kegg pathway 1.60e-02 3.63e-02 3/31

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 321

There are 31 genes in Module 321

Gene Member Table (31)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
GSU0130 fmt CDS None chromosome 144850 145803 + methionyl-tRNA formyltransferase (NCBI) False
GSU0211 GSU0211 CDS None chromosome 220056 220967 + ABC transporter, permease protein, putative (VIMSS) False
GSU0535 cysK CDS None chromosome 567299 568222 + cysteine synthase A (NCBI) False
GSU0765 GSU0765 CDS None chromosome 819967 820173 + hypothetical protein (VIMSS) False
GSU0856 htpX CDS None chromosome 915644 916507 - peptidase, M48 family (NCBI) False
GSU0874 GSU0874 CDS None chromosome 929682 932924 - hypothetical protein (VIMSS) False
GSU1337 GSU1337 CDS None chromosome 1463922 1465109 + hypothetical protein (VIMSS) False
GSU1370 GSU1370 CDS None chromosome 1498229 1499281 - oxidoreductase, aldo/keto reductase family (NCBI) False
GSU1373 GSU1373 CDS None chromosome 1501493 1501606 + hypothetical protein (VIMSS) False
GSU1402 accA CDS None chromosome 1543895 1544836 + acetyl-CoA carboxylase, carboxyl transferase, alpha subunit (NCBI) False
GSU1699 GSU1699 CDS None chromosome 1860497 1861210 - TonB-dependent receptor, putative (VIMSS) False
GSU1765 SelGGPS CDS None chromosome 1927964 1928857 - geranyltranstransferase (NCBI) False
GSU1937 GSU1937 CDS None chromosome 2118805 2120115 + GGDEF domain/HAMP domain protein (NCBI) False
GSU2082 GSU2082 CDS None chromosome 2288634 2289122 - conserved hypothetical protein (VIMSS) False
GSU2100 katG CDS None chromosome 2308644 2310827 + catalase/peroxidase (NCBI) False
GSU2184 GSU2184 CDS None chromosome 2393737 2395029 - polyA polymerase family protein (NCBI) False
GSU2185 GSU2185 CDS None chromosome 2395116 2395424 - flgM family protein (VIMSS) True
GSU2190 GSU2190 CDS None chromosome 2401250 2402416 - class II Aldolase and Adducin N-terminal domain protein (NCBI) False
GSU2196 GSU2196 CDS None chromosome 2408911 2409975 - hydrolase, putative (VIMSS) False
GSU2198 miaB CDS None chromosome 2410541 2411881 - tRNA-i(6)A37 modification enzyme MiaB (NCBI) False
GSU2218 cheW-6 CDS None chromosome 2434005 2434481 - chemotaxis protein CheW (NCBI) False
GSU2290 pncA CDS None chromosome 2508305 2508910 + pyrazinamidase/nicotinamidase, putative (NCBI) False
GSU2394 GSU2394 CDS None chromosome 2627199 2627315 - hypothetical protein (VIMSS) False
GSU2920 GSU2920 CDS None chromosome 3219402 3219512 + hypothetical protein (VIMSS) False
GSU2930 GSU2930 CDS None chromosome 3227678 3228295 - cytochrome c family protein (VIMSS) False
GSU3111 GSU3111 CDS None chromosome 3413770 3414057 - hypothetical protein (VIMSS) False
GSU3211 proA CDS None chromosome 3516342 3517598 - gamma-glutamyl phosphate reductase (NCBI) False
GSU3295 GSU3295 CDS None chromosome 3614102 3615421 + conserved hypothetical protein (VIMSS) False
GSU3296 GSU3296 CDS None chromosome 3615489 3616868 + glycolate oxidase subunit GlcD, putative (VIMSS) False
GSU3297 GSU3297 CDS None chromosome 3616956 3618221 + iron-sulfur cluster-binding protein (NCBI) False
GSU3348 hslO CDS None chromosome 3679517 3680422 + chaperonin, 33 kDa family (NCBI) 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 321

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.