Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 17 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 17

There are 15 regulatory influences for Module 17

Regulator Table (15)
Regulator Name Type
RSP_0068 tf
RSP_0616 tf
RSP_1139 tf
RSP_0547 tf
RSP_2236 tf
RSP_3621 tf
RSP_2346 tf
RSP_2800 tf
RSP_0907 tf
RSP_0760 tf
RSP_2850 tf
RSP_3665 tf
RSP_2200 tf
RSP_1077 tf
RSP_3341 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
7754 2.10e+02 GcgGctGgaCag.g.c.aga
Loader icon
7755 1.30e+03 ATGatTGTGC
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 17 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Environmental Information Processing kegg category 1.00e-06 3.00e-05 10/25
Membrane Transport kegg subcategory 0.00e+00 1.00e-06 10/25
ABC transporters kegg pathway 0.00e+00 0.00e+00 10/25

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 1.13e-04 2.69e-04 17/25
Amino acid transport and metabolism cog subcategory 0.00e+00 0.00e+00 13/25
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 17

There are 25 genes in Module 17

Gene Member Table (25)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0634 RSP_0634 CDS None chromosome 1 2371214 2372521 - TRAP-T family transporter, DctM (12 TMs) subunit (NCBI) False
RSP_0635 RSP_0635 CDS None chromosome 1 2372531 2373049 - TRAP-T family transporter, DctQ (4 TMs) subunit (NCBI) False
RSP_0636 RSP_0636 CDS None chromosome 1 2373108 2374232 - TRAP-T family transporter, DctP (periplasmic binding) subunit (NCBI) False
RSP_0760 mucS CDS None chromosome 1 2503434 2503943 - transcriptional regulator, MarR family (NCBI) True
RSP_1094 RSP_1094 CDS None chromosome 1 2850855 2851991 - hypothetical protein (NCBI) False
RSP_1451 RSP_1451 CDS None chromosome 1 33636 35210 + ABC peptide/nickel/opine transporter, periplasmic substrate-binding protein (NCBI) False
RSP_1452 RSP_1452 CDS None chromosome 1 35289 36269 + ABC peptide/nickel/opine transporter, inner membrane subunit (NCBI) False
RSP_1453 RSP_1453 CDS None chromosome 1 36269 37180 + ABC peptide/nickel/opine transporter, inner membrane subunit (NCBI) False
RSP_1454 RSP_1454 CDS None chromosome 1 37182 39035 + ABC peptide/nickel/opine transporter, fused ATPase subunits (NCBI) False
RSP_1455 RSP_1455 CDS None chromosome 1 39028 40302 + putative N-carbamoyl-beta-alanine amidohydrolase (NCBI) False
RSP_1457 RSP_1457 CDS None chromosome 1 41240 42184 + putative choline kinase (NCBI) False
RSP_2154 RSP_2154 CDS None chromosome 1 756778 758079 - hypothetical protein (NCBI) False
RSP_2155 hisD CDS None chromosome 1 758081 759406 - Histidinol dehydrogenase (NCBI) False
RSP_2532 birA CDS None chromosome 1 1174540 1175268 + putative biotin protein ligase (NCBI) False
RSP_2539 RSP_2539 CDS None chromosome 1 1182882 1184018 + ABC transporter, ATPase subunit (NCBI) False
RSP_3292 RSP_3292 CDS None chromosome 2 350977 352578 - Glucose-methanol-choline oxidoreductase (NCBI) False
RSP_3293 RSP_3293 CDS None chromosome 2 352580 353578 - ABC branched-chain amino acid transporter, inner membrane subunit (NCBI) False
RSP_3294 RSP_3294 CDS None chromosome 2 353580 354467 - ABC branched-chain amino acid transporter, inner membrane subunit (NCBI) False
RSP_3295 RSP_3295 CDS None chromosome 2 354469 355167 - ABC branched-chain amino acid transporter, ATPase subunit (NCBI) False
RSP_3296 RSP_3296 CDS None chromosome 2 355164 355937 - ABC branched-chain amino acid transporter, ATPase subunit (NCBI) False
RSP_3297 RSP_3297 CDS None chromosome 2 355940 357142 - ABC branched-chain amino acid transporter, periplasmic binding protein (NCBI) False
RSP_3401 RSP_3401 CDS None chromosome 2 466134 466535 + diguanylate cyclase (NCBI) False
RSP_3402 RSP_3402 CDS None chromosome 2 466542 469187 + multisensor diguanylate cyclase/phosphodiesterase (NCBI) False
RSP_3717 RSP_3717 CDS None chromosome 2 839985 840422 - hypothetical protein (NCBI) False
RSP_3718 RSP_3718 CDS None chromosome 2 840434 841885 - 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 17

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.