Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 235 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 235

There are 11 regulatory influences for Module 235

Regulator Table (11)
Regulator Name Type
RSP_3684 tf
RSP_3064 tf
RSP_3464 tf
RSP_3238 tf
RSP_1077 tf
RSP_3418 tf
RSP_1660 tf
RSP_3179 tf
RSP_3676 tf
RSP_1607 tf
RSP_1231 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
8188 8.60e-02 agtatcTgCtTgaGctt
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8189 4.00e+02 GttcGcgCAcaAtctCGcGAcGA
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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 235 is enriched for following functions.

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Mobile and extrachromosomal element functions tigr mainrole 1.00e-06 3.00e-06 4/30
Prophage functions tigr sub1role 1.00e-06 2.00e-06 4/30

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 235

There are 30 genes in Module 235

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0206 RSP_0206 CDS None chromosome 1 1921201 1921707 - hypothetical protein (NCBI) False
RSP_0234 tlpL CDS None chromosome 1 1953030 1954142 - TlpL, putative cytoplasmic chemoreceptor (NCBI) False
RSP_1332 RSP_1332 CDS None chromosome 1 3100881 3102191 + H+-transporting two-sector ATPase, alpha/beta subunit (NCBI) False
RSP_1619 RSP_1619 CDS None chromosome 1 217086 217379 - hypothetical protein (NCBI) False
RSP_1620 RSP_1620 CDS None chromosome 1 217383 217676 + hypothetical protein (NCBI) False
RSP_1782 RSP_1782 CDS None chromosome 1 367170 367625 - hypothetical membrane protein (NCBI) False
RSP_1783 RSP_1783 CDS None chromosome 1 367772 368866 + Predicted membrane protein (NCBI) False
RSP_1957 RSP_1957 CDS None chromosome 1 552259 552570 - hypothetical protein (NCBI) False
RSP_1961 RSP_1961 CDS None chromosome 1 554166 554417 + hypothetical protein (NCBI) False
RSP_2034 RSP_2034 CDS None chromosome 1 630649 631383 + possible CAAX amino terminal protease family (NCBI) False
RSP_2040 RSP_2040 CDS None chromosome 1 635422 635619 + possible Transposase fragment (NCBI) False
RSP_2043 RSP_2043 CDS None chromosome 1 636721 636984 + hypothetical protein (NCBI) False
RSP_2068 RSP_2068 CDS None chromosome 1 661551 662390 - putative ClpP-like protease (NCBI) False
RSP_2466 RSP_2466 CDS None chromosome 1 1106432 1106836 + hypothetical protein (NCBI) False
RSP_2471 RSP_2471 CDS None chromosome 1 1110244 1111440 + Predicted phage phi-C31 gp36 major capsid-like protein (NCBI) False
RSP_2472 RSP_2472 CDS None chromosome 1 1111535 1112134 + hypothetical protein (NCBI) False
RSP_2478 RSP_2478 CDS None chromosome 1 1115999 1116439 + hypothetical protein (NCBI) False
RSP_2479 RSP_2479 CDS None chromosome 1 1116439 1120329 + putative phage host specificity protein (NCBI) False
RSP_2480 RSP_2480 CDS None chromosome 1 1120333 1120746 + hypothetical protein (NCBI) False
RSP_2871 aglG CDS None chromosome 1 1539474 1540595 - ABC alpha-glucoside transporter, inner membrane subunit AglG (NCBI) False
RSP_2930 RSP_2930 CDS None chromosome 1 1607702 1608325 - hypothetical protein (NCBI) False
RSP_2990 RSP_2990 CDS None chromosome 1 1680503 1683964 - hypothetical protein (NCBI) False
RSP_2996 RSP_2996 CDS None chromosome 1 1692961 1693485 - putative prohead protease (NCBI) False
RSP_2997 RSP_2997 CDS None chromosome 1 1693482 1694708 - putative head portal protein (NCBI) False
RSP_3064 RSP_3064 CDS None chromosome 2 104527 105309 + transcriptional regulator, DeoR family (NCBI) True
RSP_3201 RSP_3201 CDS None chromosome 2 254301 255320 - putative oxidoreductase (NCBI) False
RSP_3390 RSP_3390 CDS None chromosome 2 454987 455769 - ABC Fe3+-siderophores transporter, ATPase subunit (NCBI) False
RSP_3417 RSP_3417 CDS None chromosome 2 483781 485928 + TonB dependent outer membrane ferrichrome-iron receptor (NCBI) False
RSP_3624 RSP_3624 CDS None chromosome 2 737248 737964 - hypothetical protein (NCBI) False
RSP_3684 solR CDS None chromosome 2 805374 806054 + transcriptional regulator, LuxR family (NCBI) True

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 235

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.