Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 71 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 71

There are 17 regulatory influences for Module 71

Regulator Table (17)
Regulator Name Type
RSP_0958 tf
RSP_1272 tf
RSP_0402 tf
RSP_0728 tf
RSP_1163 tf
RSP_2236 tf
RSP_3528 tf
RSP_1274 tf
RSP_1231 tf
RSP_3238 tf
RSP_2801 tf
RSP_1925 tf
RSP_2922 tf
RSP_2610 tf
RSP_1890 tf
RSP_1077 tf
RSP_2130 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
7862 1.80e+00 aAGGGctaagtCaAtTTgGAgcAt
Loader icon
7863 4.80e+03 CctTtgCCaGa
Loader icon
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 71 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 8.90e-05 1.10e-03 7/26
Cysteine and methionine metabolism kegg pathway 1.00e-06 1.80e-05 4/26
Metabolism of Cofactors and Vitamins kegg subcategory 2.63e-03 1.12e-02 4/26
One carbon pool by folate kegg pathway 4.00e-06 7.70e-05 3/26

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Posttranslational modification, protein turnover, chaperones cog subcategory 7.05e-03 1.16e-02 3/26
Amino acid transport and metabolism cog subcategory 2.79e-02 4.26e-02 5/26
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 71

There are 26 genes in Module 71

Gene Member Table (26)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0549 RSP_0549 CDS None chromosome 1 2286494 2287276 + hypothetical protein (NCBI) False
RSP_0769 RSP_0769 CDS None chromosome 1 2511204 2511863 + Glutathione S-transferase (NCBI) False
RSP_0823 SHMT CDS None chromosome 1 2568235 2569530 - serine hydroxymethyltransferase protein (NCBI) False
RSP_0885 SseA CDS None chromosome 1 2634274 2635122 + Thiosulfate sulfurtransferase, Rhodanese-like (NCBI) False
RSP_0924 cinA CDS None chromosome 1 2673533 2674264 + Predicted nucleotide-utilizing enzyme/competence-damage associated protein (NCBI) False
RSP_1008 RSP_1008 CDS None chromosome 1 2766198 2767199 + 4-hydroxybenzoate octaprenyltransferase (NCBI) False
RSP_1009 RSP_1009 CDS None chromosome 1 2767269 2769227 + possible outer membrane protein, OmpA family (NCBI) False
RSP_1033 RSP_1033 CDS None chromosome 1 2796976 2797662 + OmpA family protein (NCBI) False
RSP_1460 RSP_1460 CDS None chromosome 1 46555 46800 + hypothetical protein (NCBI) False
RSP_1489 RSP_1489 CDS None chromosome 1 74424 75338 + Protein containing thioredoxin domain (NCBI) False
RSP_1760 RSP_1760 CDS None chromosome 1 342569 343225 + hypothetical protein (NCBI) False
RSP_1808 trpS CDS None chromosome 1 394430 395503 - tryptophanyl-tRNA synthetase (NCBI) False
RSP_1843 ftsY CDS None chromosome 1 433992 435173 - Signal recognition particle-docking protein FtsY (NCBI) False
RSP_1851 metZ CDS None chromosome 1 445037 446251 + O-succinylhomoserine sulfhydrylase (NCBI) False
RSP_2007 RSP_2007 CDS None chromosome 1 608386 609009 - conservd hypothetical protein (NCBI) False
RSP_2147 cysK CDS None chromosome 1 749066 750100 + O-acetylserine (Thiol)-lyase, cysteine synthase (NCBI) False
RSP_2193 gcvT CDS None chromosome 1 804825 805958 + predicted aminomethyltransferase, tetrahydrofolate dependent (NCBI) False
RSP_2336 RSP_2336 CDS None chromosome 1 963757 964488 + hypothetical protein (NCBI) False
RSP_2387 RSP_2387 CDS None chromosome 1 1016860 1017294 - hypothetical protein (NCBI) False
RSP_2408 RSP_2408 CDS None chromosome 1 1037772 1038017 - hypothetical protein (NCBI) False
RSP_2453 RSP_2453 CDS None chromosome 1 1094553 1095218 - putative oxidoreductase (NAD/NADP dependent) (NCBI) False
RSP_2768 RSP_2768 CDS None chromosome 1 1415997 1416971 - 5-methyltetrahydrofolate S-homocysteine methyltransferase (NCBI) False
RSP_2975 RSP_2975 CDS None chromosome 1 1662744 1663262 + hypothetical protein (NCBI) False
RSP_2985 RSP_2985 CDS None chromosome 1 1676110 1676679 - hypothetical protein (NCBI) False
RSP_2986 RSP_2986 CDS None chromosome 1 1676870 1678282 + ArgE/DapE/Acy1 family protein (NCBI) False
RSP_2987 RSP_2987 CDS None chromosome 1 1678279 1678722 + probable 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 71

Please add your comments for this module by using the form below. Your comments will be publicly available.

comments powered by Disqus
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.