Organism : Geobacter sulfurreducens | Module List:
Module 262 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 262

There are 12 regulatory influences for Module 262

Regulator Table (12)
Regulator Name Type
GSU0013 tf
GSU0041 tf
GSU0534 tf
GSU2915 tf
GSU0284 tf
GSU0655 tf
GSU0266 tf
GSU0812 tf
GSU0514 tf
GSU0178 tf
GSU0018 tf
GSU1542 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
2684 1.90e+01 aTtTTacggTTtatA
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2685 3.40e+00 cgATtc.Atc.tcaTt.tcaA
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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 262 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
Genetic Information Processing kegg category 1.46e-02 3.44e-02 4/29

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Protein synthesis tigr mainrole 1.66e-02 2.17e-02 3/29

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Transcription cog subcategory 2.01e-02 3.39e-02 3/29
Cell wall/membrane/envelope biogenesis cog subcategory 1.50e-02 2.61e-02 4/29
General function prediction only cog subcategory 2.34e-02 3.89e-02 5/29
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 262

There are 29 genes in Module 262

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
GSU0017 mfd CDS None chromosome 25356 28829 - transcription-repair coupling factor (NCBI) False
GSU0534 GSU0534 CDS None chromosome 566814 567278 + RrF2 family protein (VIMSS) True
GSU0604 thiC-1 CDS None chromosome 637928 639238 - thiamine biosynthesis protein ThiC (NCBI) False
GSU0613 GSU0613 CDS None chromosome 648569 649933 + ResB-like family protein (NCBI) False
GSU0614 GSU0614 CDS None chromosome 649955 650806 + cytochrome c biogenesis protein, CcmF/CcyK/CcsA family (VIMSS) False
GSU0615 GSU0615 CDS None chromosome 650845 651933 + cytochrome c family protein (VIMSS) False
GSU0616 GSU0616 CDS None chromosome 651948 652940 + cytochrome c family protein (VIMSS) False
GSU0626 gmd CDS None chromosome 663160 664209 + GDP-mannose 4,6-dehydratase (NCBI) False
GSU0627 GSU0627 CDS None chromosome 664202 665146 + GDP-fucose synthetase (VIMSS) False
GSU1121 GSU1121 CDS None chromosome 1204912 1206513 + conserved hypothetical protein (VIMSS) False
GSU1543 GSU1543 CDS None chromosome 1696802 1697134 + hypothetical protein (VIMSS) False
GSU2023 GSU2023 CDS None chromosome 2215648 2216010 - conserved hypothetical protein (VIMSS) False
GSU2195 guaB CDS None chromosome 2407306 2408781 - inosine-5'-monophosphate dehydrogenase (NCBI) False
GSU2226 era CDS None chromosome 2442138 2443037 - GTP-binding protein Era (NCBI) False
GSU2227 GSU2227 CDS None chromosome 2443076 2444104 - radical SAM domain protein (NCBI) False
GSU2228 rnc CDS None chromosome 2444101 2444847 - ribonuclease III (NCBI) False
GSU2231 GSU2231 CDS None chromosome 2446660 2447697 + conserved hypothetical protein (VIMSS) False
GSU2232 metG CDS None chromosome 2447694 2449226 + methionyl-tRNA synthetase (NCBI) False
GSU2261 lpxB CDS None chromosome 2476750 2477904 - lipid A disaccharide synthase (lpxB) (NCBI) False
GSU2277 GSU2277 CDS None chromosome 2493555 2494358 - lipoprotein, NLP/P60 family, putative (VIMSS) False
GSU2281 cutE CDS None chromosome 2497042 2498475 - apolipoprotein N-acyltransferase (NCBI) False
GSU2282 GSU2282 CDS None chromosome 2498496 2499248 - CBS domain protein (NCBI) False
GSU2284 GSU2284 CDS None chromosome 2500183 2500527 - conserved hypothetical protein TIGR00043 (NCBI) False
GSU2370 accD CDS None chromosome 2597156 2597998 - acetyl-CoA carboxylase, carboxyl transferase, beta subunit (NCBI) False
GSU2527 GSU2527 CDS None chromosome 2784677 2785978 - nitrite/sulfite reductase domain protein (NCBI) False
GSU2603 rpsA CDS None chromosome 2870277 2872001 - ribosomal protein S1 (NCBI) False
GSU2715 GSU2715 CDS None chromosome 2991035 2993629 - fibronectin type III domain protein (VIMSS) False
GSU2863 rpoB CDS None chromosome 3138159 3142271 - DNA-directed RNA polymerase, beta subunit (NCBI) False
GSU3110 GSU3110 CDS None chromosome 3413447 3413755 - hypothetical protein (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 262

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.