Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 207 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 207

There are 18 regulatory influences for Module 207

Regulator Table (18)
Regulator Name Type
RSP_1606 tf
RSP_0087 tf
RSP_3029 tf
RSP_2922 tf
RSP_1243 tf
RSP_2610 tf
RSP_2838 tf
RSP_1297 tf
RSP_1607 tf
RSP_0327 tf
RSP_1220 tf
RSP_1550 tf
RSP_1231 tf
RSP_3124 tf
RSP_2591 tf
RSP_3203 tf
RSP_0014 tf
RSP_3514 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
8134 5.00e+02 CAgGgggaAG
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8135 7.00e+00 GAAAgGc.accggcGccg
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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 207 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 1.00e-03 6.22e-03 13/29
Amino Acid Metabolism kegg subcategory 1.26e-03 7.15e-03 6/29
Phenylalanine tyrosine and tryptophan biosynthesis kegg pathway 1.70e-05 2.84e-04 3/29
Metabolism of Cofactors and Vitamins kegg subcategory 6.48e-04 4.62e-03 5/29
Pantothenate and CoA biosynthesis kegg pathway 1.40e-05 2.42e-04 3/29
Global kegg category 1.74e-04 1.83e-03 13/29
Metabolism kegg subcategory 1.74e-04 1.83e-03 13/29
Metabolic pathways kegg pathway 8.60e-05 1.06e-03 13/29
Biosynthesis of secondary metabolites kegg pathway 9.60e-05 1.16e-03 8/29

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 8.30e-05 1.70e-04 5/29

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 1.78e-03 3.11e-03 17/29
Posttranslational modification, protein turnover, chaperones cog subcategory 1.04e-02 1.69e-02 3/29
Amino acid transport and metabolism cog subcategory 8.32e-04 1.54e-03 8/29
Coenzyme transport and metabolism cog subcategory 9.00e-06 3.20e-05 7/29
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 207

There are 29 genes in Module 207

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0024 rfbC CDS None chromosome 1 1724906 1725439 + Putative dTDP-4-dehydrorhamnose 3,5-epimerase (dTDP-L-rhamnose synthetase) (NCBI) False
RSP_0412 RSP_0412 CDS None chromosome 1 2147002 2147694 - putative phosphatase (NCBI) False
RSP_0758 RSP_0758 CDS None chromosome 1 2501050 2501646 - Lumazine-binding protein (NCBI) False
RSP_0809 RSP_0809 CDS None chromosome 1 2552780 2553358 + hypothetical protein (NCBI) False
RSP_0810 RSP_0810 CDS None chromosome 1 2553355 2554047 + conserved hypothetical membrane protein (NCBI) False
RSP_0811 RSP_0811 CDS None chromosome 1 2554062 2554343 - hypothetical protein (NCBI) False
RSP_0871 patB CDS None chromosome 1 2619363 2620535 - putative aminotransferase (NCBI) False
RSP_0886 TyrB CDS None chromosome 1 2635130 2636314 + Aminotransferase (NCBI) False
RSP_1260 RSP_1260 CDS None chromosome 1 3028529 3028990 + hypothetical protein (NCBI) False
RSP_1367 RSP_1367 CDS None chromosome 1 3144801 3146093 - Nicotinate phosphoribosyltransferase (NCBI) False
RSP_1401 RSP_1401 CDS None chromosome 1 3179229 3180110 + Band 7 protein (NCBI) False
RSP_1594 cdd CDS None chromosome 1 189311 189715 + Cytidine deaminase (NCBI) False
RSP_1756 panB CDS None chromosome 1 339118 339951 + probable 3-methyl-2-oxobutanoate hydroxymethyltransferase (NCBI) False
RSP_1757 panC CDS None chromosome 1 339951 340790 + Probable pantoate--beta-alanine ligase (NCBI) False
RSP_2000 RSP_2000 CDS None chromosome 1 597938 598417 - molybdenum cofactor biosynthesis protein C (NCBI) False
RSP_2001 trpD CDS None chromosome 1 599260 600276 - Anthranilate phosphoribosyltransferase (NCBI) False
RSP_2002 trpG CDS None chromosome 1 600273 600860 - Anthranilate synthase component II (NCBI) False
RSP_2091 RSP_2091 CDS None chromosome 1 690398 691543 - Putative benzoate transporter, BenE (NCBI) False
RSP_2106 ftsW CDS None chromosome 1 706721 707887 + cell division protein FtsW (NCBI) False
RSP_2216 ilvE CDS None chromosome 1 828137 829000 - Aminotransferase, class IV (NCBI) False
RSP_2643 glnE CDS None chromosome 1 1283622 1286471 + Glutamate-ammonia-ligase adenylyltransferase (NCBI) False
RSP_2644 RSP_2644 CDS None chromosome 1 1286458 1286727 + hypothetical protein (NCBI) False
RSP_2695 RSP_2695 CDS None chromosome 1 1340171 1341493 + Possible peptidoglycan binding protein (NCBI) False
RSP_2846 RSP_2846 CDS None chromosome 1 1459785 1460675 - putative 3-hydroxyisobutyrate dehydrogenase (NCBI) False
RSP_2862 RSP_2862 CDS None chromosome 1 1437761 1438945 - Glycine/D-amino acid oxidases (deaminating) (NCBI) False
RSP_2969 RSP_2969 CDS None chromosome 1 1653920 1654495 - hypothetical protein (NCBI) False
RSP_3069 RSP_3069 CDS None chromosome 2 109061 109618 - NADPH-dependent FMN reductase (NCBI) False
RSP_3563 RSP_3563 CDS None chromosome 2 658350 659456 + putative FAD-dependent glycerol-3-phosphate dehydrogenase protein (NCBI) False
RSP_3730 RSP_3730 CDS None chromosome 2 855887 856768 + putative glutathione S-transferase (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.