Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 246 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 246

There are 5 regulatory influences for Module 246

Regulator Table (5)
Regulator Name Type
RSP_3684 tf
RSP_3464 tf
RSP_3700 tf
RSP_2867 tf
RSP_1231 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
8210 3.60e-01 cgcCatcacgTtcat
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8211 9.20e+03 ATcgAacTGttcgC
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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 246 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Carbohydrate Metabolism kegg subcategory 2.18e-02 4.52e-02 4/28
Inositol phosphate metabolism kegg pathway 0.00e+00 1.30e-05 3/28
Cellular Processes kegg category 3.90e-05 5.59e-04 5/28
Cell Motility kegg subcategory 3.90e-05 5.59e-04 5/28
Flagellar assembly kegg pathway 4.60e-05 6.32e-04 4/28

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cellular processes and signaling cog category 1.37e-02 2.18e-02 8/28
Cell motility cog subcategory 1.10e-05 4.00e-05 5/28
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 246

There are 28 genes in Module 246

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0028 RSP_0028 CDS None chromosome 1 1729383 1730381 + Putative short-chain dehydrogenase/reductase (NCBI) False
RSP_0522 RSP_0522 CDS None chromosome 1 2260602 2261627 + putative oxidoreductase (NCBI) False
RSP_0835 manB CDS None chromosome 1 2580781 2582157 + phosphomannomutase (NCBI) False
RSP_1115 RSP_1115 CDS None chromosome 1 2874093 2875880 + hypothetical protein (NCBI) False
RSP_1116 RSP_1116 CDS None chromosome 1 2875880 2877121 + glycosyltransferase (NCBI) False
RSP_1117 RSP_1117 CDS None chromosome 1 2877118 2879298 + hypothetical protein (NCBI) False
RSP_1118 RSP_1118 CDS None chromosome 1 2879295 2880572 + group 1 glycosyltransferase (NCBI) False
RSP_1119 RSP_1119 CDS None chromosome 1 2880565 2882286 + ABC protein exporter, fused ATPase and inner membrane subunits (NCBI) False
RSP_1120 RSP_1120 CDS None chromosome 1 2882283 2883584 + protein secretion protein, HlyD family, membrane fusion protein (NCBI) False
RSP_1302 motB CDS None chromosome 1 3073609 3074445 + putative chemotaxis MotB protein (NCBI) False
RSP_1303 flgE CDS None chromosome 1 3074540 3075937 + putative flagellar hook protein (NCBI) False
RSP_1304 RSP_1304 CDS None chromosome 1 3075950 3077395 + putative flagellar hook protein (NCBI) False
RSP_1305 RSP_1305 CDS None chromosome 1 3077396 3078397 + putative flagellar hook-associated protein (NCBI) False
RSP_1307 flgI CDS None chromosome 1 3078397 3079488 + putative flagellar P-ring protein (NCBI) False
RSP_1630 RSP_1630 CDS None chromosome 1 226147 226464 - hypothetical protein (NCBI) False
RSP_2757 RSP_2757 CDS None chromosome 1 1406572 1407225 + hypothetical protein (NCBI) False
RSP_2758 RSP_2758 CDS None chromosome 1 1407231 1407743 + hypothetical protein (NCBI) False
RSP_2759 RSP_2759 CDS None chromosome 1 1407736 1408137 + hypothetical protein (NCBI) False
RSP_2760 RSP_2760 CDS None chromosome 1 1408130 1408582 + hypothetical protein (NCBI) False
RSP_2761 RSP_2761 CDS None chromosome 1 1408579 1408812 + putative P2-like prophage tail protein X (NCBI) False
RSP_3108 RSP_3108 CDS None chromosome 2 153123 154811 - Putative methyl accepting chemotaxis protein (NCBI) False
RSP_3116 RSP_3116 CDS None chromosome 2 160781 161947 - Conserved hypothetical membrane/transport protein (NCBI) False
RSP_3284 iolD CDS None chromosome 2 340942 342786 + Acetolactate synthase (NCBI) False
RSP_3285 iolE CDS None chromosome 2 342796 343704 + possible sugar phosphate isomerases/epimerases, IolE (NCBI) False
RSP_3286 iolB CDS None chromosome 2 343813 344619 + Uncharacterized enzyme involved in inositol metabolism, IolB (NCBI) False
RSP_3630 RSP_3630 CDS None chromosome 2 742534 742836 + hypothetical protein (NCBI) False
RSP_3811 RSP_3811 CDS None chromosome 2 9093 9416 - hypothetical protein (NCBI) False
RSP_4345 RSP_4345 tRNA None chromosome 1 766852 766926 + tRNA-Glu (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 246

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.