Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 366 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 366

There are 3 regulatory influences for Module 366

Regulator Table (3)
Regulator Name Type
RSP_2130 tf
RSP_2410 tf
RSP_2200 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
8430 2.30e-03 ATaTAGGa
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8431 5.20e+01 AGACGttcGatAgAGGAGACA
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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 366 is enriched for following functions.

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Protein fate tigr mainrole 2.77e-03 4.12e-03 3/33
Amino acid biosynthesis tigr mainrole 1.47e-03 2.35e-03 3/33

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cellular processes and signaling cog category 1.48e-02 2.34e-02 9/33
Poorly characterized cog category 5.68e-04 1.09e-03 13/33
Posttranslational modification, protein turnover, chaperones cog subcategory 4.20e-05 1.23e-04 6/33
General function prediction only cog subcategory 3.21e-02 4.86e-02 6/33
Function unknown cog subcategory 2.84e-03 4.83e-03 7/33
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 366

There are 33 genes in Module 366

Gene Member Table (33)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0011 RSP_0011 CDS None chromosome 1 1713674 1714627 + Predicted hydrolases or acyltransferases (alpha/beta hydrolase) (NCBI) False
RSP_0554 htpx CDS None chromosome 1 2291924 2292826 - heat shock protein--probable protease (NCBI) False
RSP_0569 RSP_0569 CDS None chromosome 1 2307782 2308837 - hypothetical protein (NCBI) False
RSP_0570 RSP_0570 CDS None chromosome 1 2308938 2310368 - hypothetical protein (NCBI) False
RSP_1076 sohB CDS None chromosome 1 2832130 2832927 - Peptidase family S49 (NCBI) False
RSP_1193 RSP_1193 DUMMY None chromosome 1 0 0 + None False
RSP_1194 grxC CDS None chromosome 1 2966047 2966304 - Glutaredoxin (NCBI) False
RSP_1207 hslO CDS None chromosome 1 2978214 2979203 - putative Hsp33 protein (NCBI) False
RSP_1237 secB CDS None chromosome 1 3007974 3008501 - Preprotein translocase subunit SecB (NCBI) False
RSP_1238 fxsA CDS None chromosome 1 3008535 3009011 - putative FxsA cytoplasmic membrane protein (NCBI) False
RSP_1239 RSP_1239 CDS None chromosome 1 3009155 3009814 + hypothetical protein (NCBI) False
RSP_1240 RSP_1240 CDS None chromosome 1 3009814 3010839 + putative membrane-bound lytic murein transglycosylase A transmembrane protein (NCBI) False
RSP_1241 RSP_1241 CDS None chromosome 1 3010839 3011435 + putative Smr protein/MutS2 (NCBI) False
RSP_1421 RSP_1421 CDS None chromosome 2 937519 937716 - hypothetical protein (NCBI) False
RSP_1532 RSP_1532 CDS None chromosome 1 119865 121166 + Heat shock protein HslVU, ATPase subunit (NCBI) False
RSP_1549 RSP_1549 CDS None chromosome 1 140534 141217 + hypothetical protein (NCBI) False
RSP_1563 RSP_1563 CDS None chromosome 1 152758 153765 - putative oxidoreductase (NCBI) False
RSP_1564 RSP_1564 CDS None chromosome 1 153818 155038 - Putative transmembrane transport protein (NCBI) False
RSP_1576 trxB CDS None chromosome 1 168853 169806 - Thioredoxin reductase (NCBI) False
RSP_1671 RSP_1671 CDS None chromosome 1 262693 263349 + hypothetical protein (NCBI) False
RSP_1840 RSP_1840 CDS None chromosome 1 431545 432309 + hypothetical protein (NCBI) False
RSP_1889 RSP_1889 CDS None chromosome 1 485753 486493 - conserved hypothetical membrane protein (NCBI) False
RSP_2121 RSP_2121 CDS None chromosome 1 722305 722934 - hypothetical protein (NCBI) False
RSP_2125 RSP_2125 CDS None chromosome 1 726399 726719 - hypothetical protein (NCBI) False
RSP_2130 RSP_2130 CDS None chromosome 1 730629 731957 + two component, sigma54 specific transcriptional regulator, fis family (NCBI) True
RSP_2172 metF CDS None chromosome 1 776298 777164 + 5,10-methylenetetrahydrofolate reductase (NCBI) False
RSP_2264 telA CDS None chromosome 1 881271 882461 - Tellurite resistance protein (NCBI) False
RSP_2265 RSP_2265 CDS None chromosome 1 882610 883488 - hypothetical protein (NCBI) False
RSP_2375 RSP_2375 CDS None chromosome 1 1002024 1003469 + hypothetical protein (NCBI) False
RSP_2636 ilvH CDS None chromosome 1 1276339 1276899 - Acetolactate synthase, small (regulatory) subunit (NCBI) False
RSP_2637 RSP_2637 CDS None chromosome 1 1276982 1278748 - Acetolactate synthase, large subunit, biosynthetic type (NCBI) False
RSP_2897 RSP_2897 CDS None chromosome 1 1572868 1573443 + hypothetical protein (NCBI) False
RSP_3552 RSP_3552 CDS None chromosome 2 642665 642865 + hypothetical protein (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 366

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.