Organism : Geobacter sulfurreducens | Module List:
Module 160 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 160

There are 11 regulatory influences for Module 160

Regulator Table (11)
Regulator Name Type
GSU2571 tf
GSU2670 tf
GSU2980 tf
GSU0770 tf
GSU3457 tf
GSU2033 tf
GSU0836 tf
GSU2753 tf
GSU0776 tf
GSU1495 tf
GSU2941 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
2480 2.90e+03 TCCcttCttCTttC
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2481 3.90e+03 ctcatT.tgcTAtAct..c..tTt
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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 160 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 6.79e-03 2.08e-02 10/32
Amino Acid Metabolism kegg subcategory 8.93e-03 2.47e-02 4/32
Arginine and proline metabolism kegg pathway 5.00e-05 1.01e-03 3/32
Global kegg category 2.97e-03 1.29e-02 10/32
Metabolism kegg subcategory 2.97e-03 1.29e-02 10/32
Metabolic pathways kegg pathway 2.29e-03 1.15e-02 10/32
Biosynthesis of secondary metabolites kegg pathway 7.61e-03 2.24e-02 5/32
Microbial metabolism in diverse environments kegg pathway 1.78e-02 3.89e-02 3/32

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 1.01e-03 1.97e-03 4/32
Unknown function tigr mainrole 7.68e-04 1.53e-03 4/32
General tigr sub1role 1.45e-03 2.71e-03 3/32
Amino acid biosynthesis tigr mainrole 1.67e-03 3.06e-03 3/32
Glutamate family tigr sub1role 2.00e-06 6.00e-06 3/32

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 160

There are 32 genes in Module 160

Gene Member Table (32)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
GSU0073 GSU0073 CDS None chromosome 87476 88078 - outer membrane protein, putative (VIMSS) False
GSU0074 elbB CDS None chromosome 88132 88785 - enhancing lycopene biosynthesis protein 2 (NCBI) False
GSU0135 hemB CDS None chromosome 149856 150833 - delta-aminolevulinic acid dehydratase (NCBI) False
GSU0153 argG CDS None chromosome 170807 172027 + argininosuccinate synthase (NCBI) False
GSU0155 GSU0155 CDS None chromosome 172648 173811 + hypothetical protein (VIMSS) False
GSU0451 tcrA CDS None chromosome 481052 481726 + DNA-binding response regulator (NCBI) False
GSU0452 GSU0452 CDS None chromosome 481730 483139 + sensor histidine kinase (VIMSS) False
GSU0453 pfs CDS None chromosome 483145 483876 + MTA/SAH nucleosidase (NCBI) False
GSU0454 GSU0454 CDS None chromosome 483876 484712 + conserved hypothetical protein (VIMSS) False
GSU0577 recO CDS None chromosome 606305 607036 + DNA repair protein RecO (NCBI) False
GSU0776 GSU0776 CDS None chromosome 833267 834664 - sigma-54 dependent DNA-binding response regulator (VIMSS) True
GSU0846 acnA CDS None chromosome 905137 907944 - aconitate hydratase 1 (NCBI) False
GSU1025 GSU1025 CDS None chromosome 1104518 1105120 - conserved domain protein (NCBI) False
GSU1026 GSU1026 CDS None chromosome 1105190 1105723 - conserved hypothetical protein (VIMSS) False
GSU1316 GSU1316 CDS None chromosome 1442251 1443225 - response regulator (VIMSS) False
GSU1938 GSU1938 CDS None chromosome 2120112 2120639 + hypothetical protein (VIMSS) False
GSU2458 GSU2458 CDS None chromosome 2696275 2697288 - penicillin-binding protein, putative (NCBI) False
GSU2489 GSU2489 CDS None chromosome 2733951 2735339 + deoxyribonuclease, TatD family (VIMSS) False
GSU2492 GSU2492 CDS None chromosome 2738467 2740959 + sensory box histidine kinase (VIMSS) False
GSU2859 tuf-1 CDS None chromosome 3129545 3130735 - translation elongation factor Tu (NCBI) False
GSU2871 tuf-2 CDS None chromosome 3145862 3147052 - translation elongation factor Tu (NCBI) False
GSU3049 GSU3049 CDS None chromosome 3352126 3352245 + hypothetical protein (VIMSS) False
GSU3112 GSU3112 CDS None chromosome 3414131 3416368 - cell division protein FtsK, putative (VIMSS) False
GSU3207 gpmA CDS None chromosome 3513216 3514757 - phosphoglycerate mutase, 2,3-bisphosphoglycerate-independent (NCBI) False
GSU3209 GSU3209 CDS None chromosome 3515275 3515670 - iojap-related protein (VIMSS) False
GSU3210 nadD CDS None chromosome 3515660 3516310 - nicotinate (nicotinamide) nucleotide adenylyltransferase (NCBI) False
GSU3211 proA CDS None chromosome 3516342 3517598 - gamma-glutamyl phosphate reductase (NCBI) False
GSU3212 proB CDS None chromosome 3517870 3518991 - glutamate 5-kinase (NCBI) False
GSU3336 GSU3336 CDS None chromosome 3663853 3664125 + hypothetical protein (NCBI) False
GSU3373 sun CDS None chromosome 3707306 3708652 + Sun protein (NCBI) False
GSU3374 rpe CDS None chromosome 3708688 3709353 + ribulose-phosphate 3-epimerase (NCBI) False
GSU3434 nuoI-2 CDS None chromosome 3779688 3780218 - NADH dehydrogenase I, I subunit (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 160

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.