Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 291 Profile

GeneModule member RegulatorRegulator MotifMotif
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 291

There are 12 regulatory influences for Module 291

Regulator Table (12)
Regulator Name Type
RSP_2591 tf
RSP_2130 tf
RSP_1231 tf
RSP_1139 tf
RSP_0402 tf
RSP_3202 tf
RSP_2681 tf
RSP_0327 tf
RSP_0014 tf
RSP_0316 tf
RSP_1191 tf
RSP_2853 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
8296 9.20e-04 GCtTtGacgGcaccga.tTgTCgC
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8297 2.30e+02 aaGCCaCCCcaTGCGgcgtaa
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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 291 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Nucleotide Metabolism kegg subcategory 2.55e-03 1.10e-02 3/24
Purine metabolism kegg pathway 8.15e-04 5.40e-03 3/24
Microbial metabolism in diverse environments kegg pathway 9.10e-03 2.44e-02 4/24

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Poorly characterized cog category 1.41e-02 2.24e-02 8/24
General function prediction only cog subcategory 1.15e-03 2.07e-03 7/24
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 291

There are 24 genes in Module 291

Gene Member Table (24)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0097 smoM CDS None chromosome 1 1808034 1809131 + TRAP-T family sorbitol/mannitol transporter, periplasmic binding protein, SmoM (NCBI) False
RSP_0099 RSP_0099 CDS None chromosome 1 1811327 1811941 - TRAP-T family sorbitol/mannitol transporter, DctQ (4TMs) subunit (NCBI) False
RSP_0169 RSP_0169 CDS None chromosome 1 1884473 1887157 - Na+/solute symporter (NCBI) False
RSP_0170 RSP_0170 CDS None chromosome 1 1887157 1887447 - hypothetical protein (NCBI) False
RSP_0171 RSP_0171 CDS None chromosome 1 1887444 1887812 - Response regulator receiver protein (NCBI) False
RSP_0576 RSP_0576 CDS None chromosome 1 2316462 2318279 - Na+/solute symporter (NCBI) False
RSP_0577 RSP_0577 CDS None chromosome 1 2318295 2318555 - hypothetical protein (NCBI) False
RSP_1613 RSP_1613 CDS None chromosome 1 211252 212205 + TRAP-T family transporter, DctP subunit (NCBI) False
RSP_2397 RSP_2397 CDS None chromosome 1 1025030 1026049 - ABC putrescine transporter, periplasmic substrate-binding subunit (NCBI) False
RSP_2398 RSP_2398 CDS None chromosome 1 1026077 1026877 - ABC putrescine transporter, inner membrane subunit (NCBI) False
RSP_2399 RSP_2399 CDS None chromosome 1 1026870 1027763 - ABC putrescine transporter, inner membrane subunit (NCBI) False
RSP_2541 tatC CDS None chromosome 1 1184882 1185751 + twin-arginine translocation system protein, TatC (NCBI) False
RSP_3553 dnaE CDS None chromosome 2 643014 646505 - DNA polymerase III alpha chain (NCBI) False
RSP_3554 xdhA CDS None chromosome 2 646688 648145 + xanthine dehydrogenase, small subunit (NCBI) False
RSP_3555 xdhB CDS None chromosome 2 648142 650619 + xanthine dehydrogenase, large subunit (NCBI) False
RSP_3556 xdhC CDS None chromosome 2 650612 651553 + xanthine dehydrogenase chaperone/MPT insertion protein (NCBI) False
RSP_3557 RSP_3557 CDS None chromosome 2 651550 653073 + ABC transporter, fused ATPase domains (NCBI) False
RSP_3558 RSP_3558 CDS None chromosome 2 653092 654174 + ABC transporter, inner membrane subunit (NCBI) False
RSP_3559 RSP_3559 CDS None chromosome 2 654174 655106 + ABC transporter, inner membrane subunit (NCBI) False
RSP_3560 RSP_3560 CDS None chromosome 2 655153 656247 + Possible ABC transporter, periplasmic binding protein (NCBI) False
RSP_4049 pdhAb CDS None chromosome 1 1122984 1124375 - Pyruvate dehydrogenase E1 component, beta subunit (NCBI) False
RSP_4050 pdhB CDS None chromosome 1 1121645 1122973 - Dihydrolipoamide acetyltransferase component (E2) of pyruvate dehydrogenase complex (NCBI) False
RSP_6136 RSP_6136 CDS None chromosome 1 2582403 2584784 + hypothetical protein (NCBI) False
RSP_6192 RSP_6192 CDS None chromosome 2 730303 730713 + 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.

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.