Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 231 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 231

There are 19 regulatory influences for Module 231

Regulator Table (19)
Regulator Name Type
RSP_0601 tf
RSP_1274 tf
RSP_3324 tf
RSP_2026 tf
RSP_3667 tf
RSP_2850 tf
RSP_0641 tf
RSP_1776 tf
RSP_1518 tf
RSP_0071 tf
RSP_1915 tf
RSP_2719 tf
RSP_2965 tf
RSP_2840 tf
RSP_1191 tf
RSP_0014 tf
RSP_0755 tf
RSP_2324 tf
RSP_0395 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
8180 6.70e+00 gaaAggcCa.GgaGa
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8181 5.70e+03 GgA.gctcccgcaGCAGGAgGag
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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 231 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Poorly characterized cog category 7.00e-06 2.40e-05 14/27
General function prediction only cog subcategory 1.09e-02 1.76e-02 6/27
Function unknown cog subcategory 1.14e-04 2.72e-04 8/27
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 231

There are 27 genes in Module 231

Gene Member Table (27)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_1025 RSP_1025 CDS None chromosome 1 2789360 2789926 + hypothetical protein (NCBI) False
RSP_1026 RSP_1026 CDS None chromosome 1 2789923 2790147 + hypothetical protein (NCBI) False
RSP_1127 ElaA CDS None chromosome 1 2891670 2892086 - acetyltransferase, GNAT family (NCBI) False
RSP_1146 gltB CDS None chromosome 1 2906721 2911259 - Glutamine-pyruvate aminotransferase (NCBI) False
RSP_1147 RSP_1147 CDS None chromosome 1 2911263 2911700 - hypothetical protein (NCBI) False
RSP_1148 RSP_1148 CDS None chromosome 1 2911690 2912424 - hypothetical protein (NCBI) False
RSP_1258 RSP_1258 CDS None chromosome 1 3027250 3028188 + putative hydrolase (NCBI) False
RSP_1490 RSP_1490 CDS None chromosome 1 75342 76010 + Putative ATP-dependent protease La, LON (NCBI) False
RSP_1491 RSP_1491 CDS None chromosome 1 76007 76186 + hypothetical protein (NCBI) False
RSP_1591 RSP_1591 CDS None chromosome 1 181568 182569 + Predicted Glutathione S-transferase (NCBI) False
RSP_1692 pduO CDS None chromosome 1 281914 282492 - hypothetical protein (NCBI) False
RSP_1895 RSP_1895 CDS None chromosome 1 491614 493977 + Small-conductance mechanosensitive ion channel (NCBI) False
RSP_2128 purQ CDS None chromosome 1 728140 728808 + phosphoribosylformylglycinamidine synthase I (FGAM) synthase (NCBI) False
RSP_2268 RSP_2268 CDS None chromosome 1 885996 886688 - metallo Beta lactamase superfamily (NCBI) False
RSP_2312 RSP_2312 CDS None chromosome 1 934513 935088 - hypothetical protein (NCBI) False
RSP_2314 RSP_2314 CDS None chromosome 1 936536 937354 + oxidoreductase, Chromogranin/secretogranin (NCBI) False
RSP_2389 RSP_2389 CDS None chromosome 1 1018151 1018681 + putative glutathione peroxidase (NCBI) False
RSP_2645 eda CDS None chromosome 1 1286934 1287572 - KDPG/KHG bifunctional aldolase (NCBI) False
RSP_2970 RSP_2970 CDS None chromosome 1 1654702 1655958 - Transporter, Major facilitator superfamily (MFS) (NCBI) False
RSP_3075 RSP_3075 CDS None chromosome 2 117226 118473 + hypothetical protein (NCBI) False
RSP_3076 RSP_3076 CDS None chromosome 2 118473 119405 + hypothetical protein (NCBI) False
RSP_3089 RSP_3089 CDS None chromosome 2 134379 134771 - hypothetical protein (NCBI) False
RSP_3162 RSP_3162 CDS None chromosome 2 216393 216980 - hypothetical protein (NCBI) False
RSP_3163 RSP_3163 CDS None chromosome 2 216988 219123 - Probable oxidoreductase (NCBI) False
RSP_3164 RSP_3164 CDS None chromosome 2 219127 219585 - ferredoxin like protein (NCBI) False
RSP_3351 RSP_3351 CDS None chromosome 2 417495 417728 + hypothetical protein (NCBI) False
RSP_3537 RSP_3537 CDS None chromosome 2 620593 621621 + alcohol dehydrogenase, zinc-containing (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 231

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.