Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 31 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 31

There are 11 regulatory influences for Module 31

Regulator Table (11)
Regulator Name Type
RSP_3464 tf
RSP_3339 tf
RSP_1077 tf
RSP_2867 tf
RSP_3694 tf
RSP_1867 tf
RSP_1231 tf
RSP_3616 tf
RSP_1660 tf
RSP_3400 tf
RSP_1518 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
7782 2.30e-14 CgccatCCcGaTcAtcatgaC
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7783 4.50e-11 GACCcGgCCGCCccCGGcCGGgc
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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 31 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Environmental Information Processing kegg category 3.50e-03 1.33e-02 6/26
Signal Transduction kegg subcategory 3.20e-05 4.71e-04 5/26
Two-component system kegg pathway 3.20e-05 4.71e-04 5/26
Cellular Processes kegg category 0.00e+00 0.00e+00 9/26
Cell Motility kegg subcategory 0.00e+00 0.00e+00 9/26
Bacterial chemotaxis kegg pathway 0.00e+00 0.00e+00 8/26

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cellular processes and signaling cog category 5.07e-04 9.81e-04 10/26
Signal transduction mechanisms cog subcategory 6.40e-05 1.64e-04 6/26
Cell motility cog subcategory 0.00e+00 0.00e+00 7/26
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 31

There are 26 genes in Module 31

Gene Member Table (26)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0514 RSP_0514 CDS None chromosome 1 2250807 2251820 - dTDP-glucose 4,6-dehydratase protein (NCBI) False
RSP_1302 motB CDS None chromosome 1 3073609 3074445 + putative chemotaxis MotB protein (NCBI) False
RSP_1307 flgI CDS None chromosome 1 3078397 3079488 + putative flagellar P-ring protein (NCBI) False
RSP_1393 thiQ CDS None chromosome 1 3171489 3172184 + ABC thiamine transporter, ATPase subunit (NCBI) False
RSP_1456 RSP_1456 CDS None chromosome 1 40299 41243 + hypothetical protein (NCBI) False
RSP_1630 RSP_1630 CDS None chromosome 1 226147 226464 - hypothetical protein (NCBI) False
RSP_1635 RSP_1635 CDS None chromosome 1 228765 229655 - hypothetical protein (NCBI) False
RSP_1636 RSP_1636 CDS None chromosome 1 229655 234661 - phage-related protein, probable phage tail tape meausure protein, lambda family (NCBI) False
RSP_2054 RSP_2054 CDS None chromosome 1 648313 648630 - hypothetical protein (NCBI) False
RSP_2058 RSP_2058 CDS None chromosome 1 650933 651823 - hypothetical protein (NCBI) False
RSP_2059 RSP_2059 CDS None chromosome 1 651823 656844 - Potential phage tail tape measure protein (NCBI) False
RSP_2432 RSP_2432 CDS None chromosome 1 1066170 1066517 - hypothetical protein (NCBI) False
RSP_2434 cheR1 CDS None chromosome 1 1066878 1067795 - Putative MCP methyltransferase, CheR1 (NCBI) False
RSP_2435 cheW1 CDS None chromosome 1 1067792 1068250 - Putative chemotaxis scaffold protein, CheW1 (NCBI) False
RSP_2436 cheA1 CDS None chromosome 1 1068252 1070312 - Chemotaxis histidine protein kinase, CheA1 (NCBI) False
RSP_2437 cheY1 CDS None chromosome 1 1070320 1070688 - chemotaxis response regulator, CheY1 (NCBI) False
RSP_2438 cheX CDS None chromosome 1 1070679 1070963 - Putative CheX protein (NCBI) False
RSP_2439 cheD CDS None chromosome 1 1070960 1071559 - putative chemotaxis protein, CheD (NCBI) False
RSP_2440 mcpA CDS None chromosome 1 1071682 1073994 - Methyl accepting chemotaxis protein (NCBI) False
RSP_3516 RSP_3516 CDS None chromosome 2 595543 596532 + ABC polyamine/opine transporter, ATPase subunit (NCBI) False
RSP_3518 RSP_3518 CDS None chromosome 2 597387 598172 + ABC polyamine/opine transporter, inner membrane subunit (NCBI) False
RSP_3632 RSP_3632 CDS None chromosome 2 743300 743617 + hypothetical protein (NCBI) False
RSP_3656 RSP_3656 CDS None chromosome 2 764787 766313 - NAD-dependent aldehyde dehydrogenases (NCBI) False
RSP_3690 RSP_3690 CDS None chromosome 2 811358 812422 + resiniferatoxin-binding, phosphotriesterase-related protein (NCBI) False
RSP_3691 RSP_3691 CDS None chromosome 2 812445 813209 + putative cytoplasmic protein (NCBI) False
RSP_3767 RSP_3767 CDS None chromosome 2 891012 891329 - hypothetical protein (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 31

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.