Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 91 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 91

There are 14 regulatory influences for Module 91

Regulator Table (14)
Regulator Name Type
RSP_2324 tf
RSP_1243 tf
RSP_1034 tf
RSP_0394 tf
RSP_0774 tf
RSP_3528 tf
RSP_2888 tf
RSP_2533 tf
RSP_1286 tf
RSP_0611 tf
RSP_2572 tf
RSP_0068 tf
RSP_2963 tf
RSP_0386 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
7902 6.60e+02 tcccGCccgcgcGcT
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7903 2.10e+03 ATCCGcGCCgatGtGcAATG
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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 91 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Microbial metabolism in diverse environments kegg pathway 5.35e-03 1.74e-02 5/30

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Poorly characterized cog category 8.33e-03 1.36e-02 10/30
Transcription cog subcategory 1.82e-02 2.85e-02 4/30
Cell wall/membrane/envelope biogenesis cog subcategory 2.60e-02 3.99e-02 3/30
Function unknown cog subcategory 2.43e-02 3.75e-02 5/30
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 91

There are 30 genes in Module 91

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0010 RSP_0010 CDS None chromosome 1 1712767 1713684 + homoserine O-succinyltransferase (NCBI) False
RSP_0011 RSP_0011 CDS None chromosome 1 1713674 1714627 + Predicted hydrolases or acyltransferases (alpha/beta hydrolase) (NCBI) False
RSP_0013 RSP_0013 CDS None chromosome 1 1714668 1715552 + hypothetical protein (NCBI) False
RSP_0014 RSP_0014 CDS None chromosome 1 1715549 1716166 + transcriptional regulator, TetR family (NCBI) True
RSP_0774 RSP_0774 CDS None chromosome 1 2515853 2518174 - RNA binding protein (NCBI) True
RSP_1018 RSP_1018 CDS None chromosome 1 2777825 2779126 - Glycolate oxidase iron-sulfur subunit (NCBI) False
RSP_1019 RSP_1019 CDS None chromosome 1 2779139 2780215 - putative glycolate oxidase subunit protein (NCBI) False
RSP_1034 pdhR CDS None chromosome 1 2797903 2798670 + Pyruvate dehydrogenase complex repressor (NCBI) True
RSP_1130 RSP_1130 CDS None chromosome 1 2893534 2894352 - hypothetical membrane protein (NCBI) False
RSP_1172 dnaJ CDS None chromosome 1 2938529 2939677 - Chaperone, DnaJ (NCBI) False
RSP_1292 RSP_1292 CDS None chromosome 1 3059735 3061219 - putative Aldehyde dehydrogenase (NCBI) False
RSP_1487 RSP_1487 CDS None chromosome 1 73200 73547 + hypothetical protein (NCBI) False
RSP_1488 RSP_1488 CDS None chromosome 1 73549 74292 + Possible glyoxalase (NCBI) False
RSP_1516 RSP_1516 CDS None chromosome 1 103428 104012 + putative S-adenosyl L-homocystein hydrolase (NCBI) False
RSP_1895 RSP_1895 CDS None chromosome 1 491614 493977 + Small-conductance mechanosensitive ion channel (NCBI) False
RSP_1899 RSP_1899 CDS None chromosome 1 497371 498681 - Predicted ATPase (NCBI) False
RSP_1900 RSP_1900 CDS None chromosome 1 498697 499200 - hypothetical protein (NCBI) False
RSP_1901 RSP_1901 CDS None chromosome 1 499203 500051 - Hypothetical protein with TPR repeat (NCBI) False
RSP_2263 RSP_2263 CDS None chromosome 1 880293 881258 - hypothetical protein (NCBI) False
RSP_2456 radA CDS None chromosome 1 1097519 1098877 - DNA Repair Protein (NCBI) False
RSP_2605 RSP_2605 CDS None chromosome 1 1247175 1247864 - hypothetical protein (NCBI) False
RSP_2606 RSP_2606 CDS None chromosome 1 1247875 1248258 - ArsR family Arsenical Resistance Operon Repressor (NCBI) True
RSP_2607 RSP_2607 CDS None chromosome 1 1248295 1248795 - nitrilotriacetate monooxygenase component B (NCBI) False
RSP_2608 corA CDS None chromosome 1 1249031 1250026 + magnesium/cobalt transport protein, MIT family (NCBI) False
RSP_2810 RSP_2810 CDS None chromosome 1 1504712 1505485 - ABC transporter, ATPase subunit (NCBI) False
RSP_3107 RSP_3107 CDS None chromosome 2 152398 152670 - hypothetical protein (NCBI) False
RSP_3384 RSP_3384 CDS None chromosome 2 447238 448401 - mandelate racemase/muconate lactonizing enzyme family protein (NCBI) False
RSP_3435 RSP_3435 CDS None chromosome 2 506295 506627 + possible DNA-binding protein (NCBI) False
RSP_3456 RSP_3456 CDS None chromosome 2 525796 526722 + Putative dihydrodipicolinate synthase (NCBI) False
RSP_3785 RSP_3785 CDS None chromosome 2 902636 903658 - putative bacteriophage-related 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 91

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.