Organism : Geobacter sulfurreducens | Module List:
Module 214 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 214

There are 11 regulatory influences for Module 214

Regulator Table (11)
Regulator Name Type
GSU1692 tf
GSU2202 tf
GSU0770 tf
GSU2571 tf
GSU1382 tf
GSU2980 tf
GSU0013 tf
GSU2262 tf
GSU0551 tf
GSU0514 tf
GSU1270 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
2588 7.60e+00 tGCAag.acAAa.aggagAagA
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2589 9.30e+01 CcctttC.ca.CcgtTgAaCAca
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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 214 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 1.23e-02 3.08e-02 9/30
Energy Metabolism kegg subcategory 5.26e-03 1.78e-02 4/30
Methane metabolism kegg pathway 5.40e-05 1.05e-03 3/30
Global kegg category 5.85e-03 1.87e-02 9/30
Metabolism kegg subcategory 5.85e-03 1.87e-02 9/30
Metabolic pathways kegg pathway 4.64e-03 1.67e-02 9/30
Biosynthesis of secondary metabolites kegg pathway 2.37e-02 4.77e-02 4/30
Microbial metabolism in diverse environments kegg pathway 3.10e-05 7.40e-04 6/30

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 6.01e-03 9.23e-03 3/30

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cell wall/membrane/envelope biogenesis cog subcategory 1.72e-02 2.96e-02 4/30
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 214

There are 30 genes in Module 214

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
GSU0023 GSU0023 CDS None chromosome 33645 34481 - TPR domain protein (NCBI) False
GSU0087 GSU0087 CDS None chromosome 98008 99012 - heterodisulfide reductase, iron-sulfur binding subunit, putative (VIMSS) False
GSU0088 GSU0088 CDS None chromosome 99056 99985 - heterodisulfide reductase subunit (VIMSS) False
GSU0090 GSU0090 CDS None chromosome 100519 102516 - heterodisulfide reductase subunit (VIMSS) False
GSU0091 GSU0091 CDS None chromosome 102517 103407 - heterodisulfide reductase subunit (VIMSS) False
GSU0092 GSU0092 CDS None chromosome 103404 103952 - heterodisulfide reductase subunit (NCBI) False
GSU0159 dapA CDS None chromosome 177446 178318 + dihydrodipicolinate synthase (NCBI) False
GSU0674 hcP-1 CDS None chromosome 707626 709272 - hydroxylamine reductase (RefSeq) False
GSU0792 GSU0792 CDS None chromosome 850642 851412 - conserved hypothetical protein (VIMSS) False
GSU0864 GSU0864 CDS None chromosome 922321 922644 - conserved hypothetical protein TIGR00251 (VIMSS) False
GSU0865 GSU0865 CDS None chromosome 922631 923080 - cell division protein DivIVA, putative (VIMSS) False
GSU1177 frdA CDS None chromosome 1282525 1284438 + fumarate reductase, flavoprotein subunit (NCBI) False
GSU1322 ccdA CDS None chromosome 1447999 1448727 + cytochrome c biogenesis protein CcdA (NCBI) False
GSU1334 GSU1334 CDS None chromosome 1461505 1462944 - cytochrome c family protein (NCBI) False
GSU1555 GSU1555 CDS None chromosome 1706780 1710118 - sensory box histidine kinase/response regulator (VIMSS) False
GSU1628 GSU1628 CDS None chromosome 1782373 1784337 - phosphoglycerate kinase/triosephosphate isomerase (VIMSS) False
GSU1761 GSU1761 CDS None chromosome 1922825 1924360 + cytochrome c family protein (VIMSS) False
GSU2049 argJ CDS None chromosome 2248053 2249234 - glutamate N-acetyltransferase/amino-acid acetyltransferase (NCBI) False
GSU2255 GSU2255 CDS None chromosome 2470409 2471341 - conserved hypothetical protein (VIMSS) False
GSU2260 GSU2260 CDS None chromosome 2475035 2476750 - ABC transporter, ATP-binding protein, MsbA family (VIMSS) False
GSU2261 lpxB CDS None chromosome 2476750 2477904 - lipid A disaccharide synthase (lpxB) (NCBI) False
GSU2262 degT CDS None chromosome 2477971 2479062 - pleiotropic regulatory protein (NCBI) True
GSU2268 GSU2268 CDS None chromosome 2483006 2485303 - outer membrane protein, putative (VIMSS) False
GSU2269 GSU2269 CDS None chromosome 2485370 2486044 - ABC transporter, ATP-binding protein (VIMSS) False
GSU2731 ferA CDS None chromosome 3007851 3010157 - polyheme membrane-associated cytochrome c (NCBI) False
GSU2732 GSU2732 CDS None chromosome 3010192 3010887 - cytochrome c family protein (NCBI) False
GSU2733 GSU2733 CDS None chromosome 3010903 3012114 - hypothetical protein (VIMSS) False
GSU2737 GSU2737 CDS None chromosome 3013390 3015624 - polyheme membrane-associated cytochrome c (VIMSS) False
GSU2739 GSU2739 CDS None chromosome 3016370 3017581 - hypothetical protein (VIMSS) False
GSU3210 nadD CDS None chromosome 3515660 3516310 - nicotinate (nicotinamide) nucleotide adenylyltransferase (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 214

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.