Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 10 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 10

There are 11 regulatory influences for Module 10

Regulator Table (11)
Regulator Name Type
RSP_3238 tf
RSP_0122 tf
RSP_1739 tf
RSP_0327 tf
RSP_1220 tf
RSP_1550 tf
RSP_0999 tf
RSP_3606 tf
RSP_1139 tf
RSP_0316 tf
RSP_1871 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
7740 3.00e-03 atgtttc.aTttcCTGcaaagCTg
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7741 9.60e+01 AAtccgctGCaaAt.tta.cG
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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 10 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism of Cofactors and Vitamins kegg subcategory 2.06e-02 4.32e-02 3/28

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Poorly characterized cog category 1.43e-02 2.27e-02 9/28
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 10

There are 28 genes in Module 10

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0419 RSP_0419 CDS None chromosome 1 2152500 2153177 + hypothetical protein (NCBI) False
RSP_0674 RSP_0674 CDS None chromosome 1 2415483 2416595 + Putative HolB DNA polymerase III delta prime subunit (NCBI) False
RSP_0715 RSP_0715 CDS None chromosome 1 2461281 2461901 + Ribonuclease T2 (NCBI) False
RSP_0765 RSP_0765 CDS None chromosome 1 2507492 2508133 - SAM-dependent methyltransferase (NCBI) False
RSP_0766 RSP_0766 CDS None chromosome 1 2508130 2509140 - hypothetical protein (NCBI) False
RSP_0825 ppnk CDS None chromosome 1 2569697 2570461 + probable inorganic polyphosphate/ATP-NAD kinase (NCBI) False
RSP_0845 RSP_0845 CDS None chromosome 1 2595826 2596320 - hypothetical protein (NCBI) False
RSP_0846 ribA CDS None chromosome 1 2596317 2597405 - GTP cyclohydrolase II (NCBI) False
RSP_0847 RSP_0847 CDS None chromosome 1 2597558 2598244 + two component transcriptional regulator, winged helix family (NCBI) False
RSP_0897 RSP_0897 CDS None chromosome 1 2648232 2648864 + Glutathione S-transferase (NCBI) False
RSP_1006 RSP_1006 CDS None chromosome 1 2764850 2765416 - hypothetical protein (NCBI) False
RSP_1007 RSP_1007 CDS None chromosome 1 2765413 2766186 - hypothetical protein (NCBI) False
RSP_1220 hrcA CDS None chromosome 1 2993068 2994138 - heat-inducible transcription repressor HrcA (NCBI) True
RSP_1384 RSP_1384 CDS None chromosome 1 3162861 3163850 + hypothetical protein (NCBI) False
RSP_1794 RSP_1794 CDS None chromosome 1 380074 380688 + putative lytic transglycosylase (NCBI) False
RSP_1834 RSP_1834 CDS None chromosome 1 426069 426875 + hypothetical protein (NCBI) False
RSP_1868 RSP_1868 CDS None chromosome 1 465545 466672 + serine-pyruvate aminotransferase (NCBI) False
RSP_1891 RSP_1891 CDS None chromosome 1 487915 488874 - Zinc-binding dehydrogenase (NCBI) False
RSP_2119 RSP_2119 CDS None chromosome 1 720407 720799 - hypothetical protein (NCBI) False
RSP_2120 RSP_2120 CDS None chromosome 1 720796 722169 - putative D-lactate dehydrogenase (cytochrome), FAD/FMN-containing oxidoreductase (NCBI) False
RSP_2142 RSP_2142 CDS None chromosome 1 743132 744370 + NifS-related protein (NCBI) False
RSP_2282 chrA CDS None chromosome 1 903198 904376 - Chromate efflux pump, ChrA (NCBI) False
RSP_2505 creA CDS None chromosome 1 1150144 1150704 - possible CreA protein (NCBI) False
RSP_2551 exoO CDS None chromosome 1 1194718 1196148 + Glycosyl transferase, family 2 (NCBI) False
RSP_2618 RSP_2618 CDS None chromosome 1 1257131 1257883 + Putative hemolysin (NCBI) False
RSP_2825 cobK CDS None chromosome 1 1488692 1489435 - Putative precorrin-6x reductase (NCBI) False
RSP_3606 RSP_3606 CDS None chromosome 2 701300 702598 + Sigma54-2 (RNA polymerase sigma-54 factor) (NCBI) True
RSP_3836 RSP_3836 CDS None chromosome 2 31518 33170 + Putative metal-dependent hydrolase (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.