Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 297 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 297

There are 4 regulatory influences for Module 297

Regulator Table (4)
Regulator Name Type
RSP_1274 tf
RSP_1739 tf
RSP_1163 tf
RSP_1164 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
8308 2.70e-01 AAAtTC
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8309 9.60e+00 aaAagGGTtTT
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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 297 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 1.57e-03 8.22e-03 11/24
Carbohydrate Metabolism kegg subcategory 0.00e+00 0.00e+00 11/24
Citrate cycle (TCA cycle) kegg pathway 0.00e+00 0.00e+00 11/24
Butanoate metabolism kegg pathway 4.00e-06 9.00e-05 4/24
Energy Metabolism kegg subcategory 0.00e+00 3.00e-06 9/24
Oxidative phosphorylation kegg pathway 4.90e-05 6.72e-04 4/24
Carbon fixation pathways in prokaryotes kegg pathway 0.00e+00 0.00e+00 8/24
Xenobiotics Biodegradation and Metabolism kegg subcategory 3.60e-05 5.27e-04 4/24
Toluene degradation kegg pathway 0.00e+00 0.00e+00 4/24
Membrane Transport kegg subcategory 9.10e-03 2.44e-02 4/24
ABC transporters kegg pathway 5.40e-03 1.74e-02 4/24
Global kegg category 3.39e-04 2.91e-03 11/24
Metabolism kegg subcategory 3.39e-04 2.91e-03 11/24
Metabolic pathways kegg pathway 1.83e-04 1.91e-03 11/24
Biosynthesis of secondary metabolites kegg pathway 0.00e+00 0.00e+00 11/24
Microbial metabolism in diverse environments kegg pathway 0.00e+00 0.00e+00 11/24

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 0.00e+00 0.00e+00 10/24
TCA cycle tigr sub1role 0.00e+00 0.00e+00 9/24

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 3.92e-03 6.58e-03 14/24
Posttranslational modification, protein turnover, chaperones cog subcategory 5.70e-05 1.51e-04 5/24
Energy production and conversion cog subcategory 0.00e+00 0.00e+00 11/24
Inorganic ion transport and metabolism cog subcategory 2.46e-02 3.78e-02 3/24
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 297

There are 24 genes in Module 297

Gene Member Table (24)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0353 RSP_0353 DUMMY None chromosome 1 0 0 + None False
RSP_0355 RSP_0355 CDS None chromosome 1 2084795 2086276 - possible serine protease (NCBI) False
RSP_0356 RSP_0356 CDS None chromosome 1 2086429 2087451 - Probable HflC protein (NCBI) False
RSP_0357 RSP_0357 CDS None chromosome 1 2087451 2088632 - Probable HflK protein (NCBI) False
RSP_0446 RSP_0446 CDS None chromosome 1 2176388 2177602 + Isocitrate dehydrogenase (NCBI) False
RSP_0964 sucB CDS None chromosome 1 2723312 2724844 - Dihydrolipoamide transsuccinylase (NCBI) False
RSP_0965 sucA CDS None chromosome 1 2724844 2727822 - 2-oxoglutarate dehydrogenase E1 component (RefSeq) False
RSP_0966 sucD CDS None chromosome 1 2727862 2728746 - Succinyl-CoA synthetase, alpha subunit (NCBI) False
RSP_0967 sucC CDS None chromosome 1 2728751 2729944 - Succinyl-CoA synthetase, beta subunit (NCBI) False
RSP_0974 RSP_0974 CDS None chromosome 1 2735026 2735409 + Succinate dehydrogenase cytochrome b-556 subunit (NCBI) False
RSP_0975 RSP_0975 CDS None chromosome 1 2735421 2735792 + putative succinate dehydrogenase, hydrophobic membrane anchor protein (NCBI) False
RSP_0976 sdhA CDS None chromosome 1 2735804 2737606 + Succinate dehydrogenase flavoprotein subunit (NCBI) False
RSP_0977 RSP_0977 CDS None chromosome 1 2737606 2737926 + hypothetical protein (NCBI) False
RSP_0978 RSP_0978 CDS None chromosome 1 2737930 2738208 + hypothetical protein (NCBI) False
RSP_0979 sdhB CDS None chromosome 1 2738227 2739006 + Succinate dehydrogenase iron-sulfur protein (NCBI) False
RSP_1172 dnaJ CDS None chromosome 1 2938529 2939677 - Chaperone, DnaJ (NCBI) False
RSP_1173 dnaK CDS None chromosome 1 2939750 2941660 - Heat shock protein (Hsp70, DnaK (NCBI) False
RSP_1680 pckA CDS None chromosome 1 270577 272175 - Phosphoenolpyruvate carboxykinase (NCBI) False
RSP_1806 RSP_1806 CDS None chromosome 1 389587 392331 - aconitate hydratase (RefSeq) False
RSP_3232 RSP_3232 CDS None chromosome 2 291187 292194 + ABC peptide transporter, inner membrane subunit (NCBI) False
RSP_3233 RSP_3233 CDS None chromosome 2 292202 293104 + ABC peptide transporter, inner membrane subunit (NCBI) False
RSP_3235 RSP_3235 CDS None chromosome 2 293109 293957 + ABC peptide transporter, ATPase subunit (NCBI) False
RSP_3236 RSP_3236 CDS None chromosome 2 293957 294805 + ABC peptide transporter, ATPase subunit (NCBI) False
RSP_3821 RSP_3821 CDS None chromosome 2 17201 17809 + Putative acetyltransferase (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.