Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 309 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 309

There are 10 regulatory influences for Module 309

Regulator Table (10)
Regulator Name Type
RSP_2410 tf
RSP_1704 tf
RSP_1890 tf
RSP_1274 tf
RSP_0395 tf
RSP_0489 tf
RSP_1231 tf
RSP_3324 tf
RSP_0443 tf
RSP_1163 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
8332 2.70e-08 AatggGgCGag.TTcCcCcTT
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8333 7.00e-03 tCCTgtTTcgCaGgA
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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 309 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Amino Acid Metabolism kegg subcategory 2.01e-02 4.24e-02 4/27
Metabolism of Cofactors and Vitamins kegg subcategory 3.12e-03 1.23e-02 4/27
Global kegg category 1.47e-02 3.38e-02 9/27
Metabolism kegg subcategory 1.47e-02 3.38e-02 9/27
Metabolic pathways kegg pathway 9.52e-03 2.51e-02 9/27
Biosynthesis of secondary metabolites kegg pathway 9.08e-03 2.44e-02 5/27

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Protein fate tigr mainrole 1.29e-03 2.10e-03 3/27
Protein and peptide secretion and trafficking tigr sub1role 2.20e-05 5.30e-05 3/27
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 4.96e-03 6.85e-03 3/27

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cellular processes and signaling cog category 3.20e-02 4.85e-02 7/27
Translation, ribosomal structure and biogenesis cog subcategory 2.50e-02 3.85e-02 3/27
Cell wall/membrane/envelope biogenesis cog subcategory 1.82e-02 2.85e-02 3/27
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 309

There are 27 genes in Module 309

Gene Member Table (27)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0123 cerI CDS None chromosome 1 1837350 1837982 + Autoinducer synthesis protein (NCBI) False
RSP_0124 RSP_0124 CDS None chromosome 1 1838097 1838369 + hypothetical protein (NCBI) False
RSP_0217 int CDS None chromosome 1 1930262 1931503 - possible phage-related integrase (NCBI) False
RSP_0890 RSP_0890 CDS None chromosome 1 2640924 2641547 - possible protein yrbC precursor (NCBI) False
RSP_0891 vacJ CDS None chromosome 1 2641537 2642325 - putative lipoprotein (NCBI) False
RSP_0892 RSP_0892 CDS None chromosome 1 2642535 2644271 + ABC protein toxin exporter, fused ATPase and inner membrane domain (NCBI) False
RSP_0893 RSP_0893 CDS None chromosome 1 2644268 2645569 + RTX secretion protein D, HlyD family (NCBI) False
RSP_0929 accD CDS None chromosome 1 2678351 2679304 + Acetyl-CoA carboxylase carboxyl transferase, beta subunit (NCBI) False
RSP_1843 ftsY CDS None chromosome 1 433992 435173 - Signal recognition particle-docking protein FtsY (NCBI) False
RSP_1864 RSP_1864 CDS None chromosome 1 463014 463232 + hypothetical protein (NCBI) False
RSP_1948 RSP_1948 CDS None chromosome 1 546042 546398 - Protein of unknown function, HesB/YadR/YfhF (NCBI) False
RSP_1949 RSP_1949 CDS None chromosome 1 546482 546844 - hypothetical protein (NCBI) False
RSP_1986 gatB CDS None chromosome 1 581296 582807 - Glutamyl-tRNA amidotransferase subunit B (NCBI) False
RSP_1991 RSP_1991 CDS None chromosome 1 587720 588865 + Putative Ornithine decarboxylase (NCBI) False
RSP_1994 gltA CDS None chromosome 1 590962 592248 - Citrate synthase (NCBI) False
RSP_2193 gcvT CDS None chromosome 1 804825 805958 + predicted aminomethyltransferase, tetrahydrofolate dependent (NCBI) False
RSP_2329 mreB CDS None chromosome 1 952681 953718 - Cell shape determining protein MreB/Mrl (NCBI) False
RSP_2646 RSP_2646 DUMMY None chromosome 1 0 0 + None False
RSP_2718 RSP_2718 CDS None chromosome 1 1368835 1369437 + possible outer membrane protein (NCBI) False
RSP_2783 lipA CDS None chromosome 1 1431034 1431996 + lipoic acid synthetase (NCBI) False
RSP_2914 RSP_2914 CDS None chromosome 1 1592216 1593157 + Nucleoside hydrolase (NCBI) False
RSP_2921 RSP_2921 CDS None chromosome 1 1599130 1600500 - phospho-2-dehydro-3-deoxyheptonate (NCBI) False
RSP_2922 RSP_2922 CDS None chromosome 1 1600645 1601658 + Transcriptional regulator, AraC family (NCBI) True
RSP_2975 RSP_2975 CDS None chromosome 1 1662744 1663262 + hypothetical protein (NCBI) False
RSP_3074 ilvD CDS None chromosome 2 115149 116987 - Dihydroxy-acid and 6-phosphogluconate dehydratase (NCBI) False
RSP_3820 rpmA CDS None chromosome 2 16838 17107 + Ribosomal protein L27 (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.

Comments for Module 309

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.