Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 7 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 7

There are 16 regulatory influences for Module 7

Regulator Table (16)
Regulator Name Type
RSP_2838 tf
RSP_2950 tf
RSP_1590 tf
RSP_2850 tf
RSP_1272 tf
RSP_0591 tf
RSP_0623 tf
RSP_2236 tf
RSP_2965 tf
RSP_1606 tf
RSP_1014 tf
RSP_2171 tf
RSP_2840 tf
RSP_3203 tf
RSP_3680 tf
RSP_1225 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
7736 2.40e+01 TTCCAaGcGactGCCgACTTTa
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7737 4.30e+00 gCaTGgA.AAgcTcatcgC
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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 7 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Function unknown cog subcategory 2.08e-02 3.23e-02 5/29
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 7

There are 29 genes in Module 7

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0586 RSP_0586 CDS None chromosome 1 2329105 2329674 - probable nicotinate-nucleotide adenylyltransferase (NCBI) False
RSP_0650 RSP_0650 CDS None chromosome 1 2388918 2389370 - Probable transglycosylase (NCBI) False
RSP_0866 RSP_0866 CDS None chromosome 1 2616742 2617209 + hypothetical protein (NCBI) False
RSP_0879 RSP_0879 CDS None chromosome 1 2628115 2628915 - hypothetical protein (NCBI) False
RSP_0895 RSP_0895 CDS None chromosome 1 2646151 2646921 + phosphodiesterase-like (NCBI) False
RSP_0896 RSP_0896 CDS None chromosome 1 2646991 2648235 + hypothetical protein (NCBI) False
RSP_0949 ostB CDS None chromosome 1 2701825 2702607 - putative trehalose-6-phosphate phosphatase (NCBI) False
RSP_1005 gshA CDS None chromosome 1 2763433 2764797 - putative glutathione synthetase (NCBI) False
RSP_1006 RSP_1006 CDS None chromosome 1 2764850 2765416 - hypothetical protein (NCBI) False
RSP_1187 RSP_1187 CDS None chromosome 1 2959017 2961185 - hypothetical protein (NCBI) False
RSP_1219 grpE CDS None chromosome 1 2992502 2993071 - putative chaperone protein GrpE (heat shock protein) (NCBI) False
RSP_1223 tdcF CDS None chromosome 1 2995590 2995964 + Putative translation initiation inhibitor, yjgF family / putative Endoribonuclease L-PSP (NCBI) False
RSP_1337 aarF CDS None chromosome 1 3105782 3107263 - probable ubiquinone biosynthesis protein (NCBI) False
RSP_1380 RSP_1380 CDS None chromosome 1 3158690 3159505 + hypothetical protein (NCBI) False
RSP_1387 RSP_1387 CDS None chromosome 1 3164840 3166318 + AMP nucleosidase (NCBI) False
RSP_1468 RSP_1468 CDS None chromosome 1 54227 55345 - Site-specific DNA-methyltransferase (NCBI) False
RSP_1570 purK CDS None chromosome 1 163084 164166 - Phosphoribosylaminoimidazole carboxylase, ATPase subunit (NCBI) False
RSP_1775 RSP_1775 CDS None chromosome 1 359087 360046 - hypothetical protein (NCBI) False
RSP_2104 RSP_2104 CDS None chromosome 1 705250 705720 + hypothetical protein (NCBI) False
RSP_2544 RSP_2544 CDS None chromosome 1 1188005 1188664 - Protein-L-isoaspartate O-methyltransferase (NCBI) False
RSP_2651 RSP_2651 CDS None chromosome 1 1294180 1295583 - hypothetical protein (NCBI) False
RSP_2652 RSP_2652 CDS None chromosome 1 1295580 1296032 - putative Acetyltransferase (NCBI) False
RSP_2715 RSP_2715 CDS None chromosome 1 1364718 1365539 + hypothetical protein (NCBI) False
RSP_2716 lpxB CDS None chromosome 1 1365536 1366675 + putative lipid-A-disaccharide synthase (NCBI) False
RSP_2917 RSP_2917 CDS None chromosome 1 1594847 1596040 - putative cystathionine gamma-synthase beta-lyase (NCBI) False
RSP_2950 RSP_2950 CDS None chromosome 1 1631639 1632532 + Transcriptional regulator, LysR family (NCBI) True
RSP_3209 cbiQ CDS None chromosome 2 263792 264502 + ABC cobalt transporter, inner membrane subunit, CbiQ (NCBI) False
RSP_3237 lguL CDS None chromosome 2 294958 295353 + Lactoylglutathione lyase (NCBI) False
RSP_3564 RSP_3564 CDS None chromosome 2 659453 660088 + Generic methyltransferase (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 7

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.