Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 279 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 279

There are 14 regulatory influences for Module 279

Regulator Table (14)
Regulator Name Type
RSP_1231 tf
RSP_1163 tf
RSP_0489 tf
RSP_3616 tf
RSP_2850 tf
RSP_0395 tf
RSP_1191 tf
RSP_2324 tf
RSP_2730 tf
RSP_3022 tf
RSP_1922 tf
RSP_0511 tf
RSP_0443 tf
RSP_0527 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
8272 4.40e-07 CCTcTGcaaGgCGacttcTCaaG
Loader icon
8273 1.90e+00 AaAcAGGA.CG
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 279 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 6.41e-04 4.60e-03 13/28
Carbohydrate Metabolism kegg subcategory 2.18e-02 4.52e-02 4/28
Citrate cycle (TCA cycle) kegg pathway 2.60e-05 3.96e-04 3/28
Environmental Information Processing kegg category 5.49e-03 1.76e-02 6/28
Membrane Transport kegg subcategory 3.73e-03 1.38e-02 5/28
ABC transporters kegg pathway 1.99e-03 9.49e-03 5/28
Global kegg category 4.82e-04 3.76e-03 12/28
Metabolism kegg subcategory 4.82e-04 3.76e-03 12/28
Metabolic pathways kegg pathway 3.93e-03 1.43e-02 10/28
Biosynthesis of secondary metabolites kegg pathway 2.41e-03 1.06e-02 6/28
Microbial metabolism in diverse environments kegg pathway 3.73e-03 1.38e-02 5/28

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 3.17e-03 4.62e-03 4/28
TCA cycle tigr sub1role 4.00e-06 1.00e-05 3/28
Protein synthesis tigr mainrole 9.37e-04 1.58e-03 4/28

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Translation, ribosomal structure and biogenesis cog subcategory 2.83e-02 4.31e-02 3/28
Amino acid transport and metabolism cog subcategory 1.16e-02 1.86e-02 6/28
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 279

There are 28 genes in Module 279

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0446 RSP_0446 CDS None chromosome 1 2176388 2177602 + Isocitrate dehydrogenase (NCBI) False
RSP_0561 RSP_0561 CDS None chromosome 1 2299128 2299787 + Transaldolase (NCBI) False
RSP_0562 RSP_0562 CDS None chromosome 1 2299810 2300499 + hypothetical protein (NCBI) False
RSP_0584 RSP_0584 CDS None chromosome 1 2326302 2327882 + Lysyl-tRNA synthetase (NCBI) False
RSP_0756 ribH1 CDS None chromosome 1 2498532 2499068 - 6,7-dimethyl-8-ribityllumazine synthase beta chain (NCBI) False
RSP_0757 ribBA CDS None chromosome 1 2499072 2500175 - Bifunctional GTP cyclohydrolase II/3,4-dihydroxy-2butanone-4-phosphate synthase (NCBI) False
RSP_0873 RSP_0873 CDS None chromosome 1 2621209 2621700 + N-formylmethionyl tRNA deformylase (NCBI) False
RSP_0883 RSP_0883 CDS None chromosome 1 2633511 2633984 + SmpB protein (NCBI) False
RSP_1045 trmD CDS None chromosome 1 2805259 2806095 - tRNA (guanine-N1-)-methyltransferase (NCBI) False
RSP_1350 serB CDS None chromosome 1 3120103 3120978 - phosphoserine phosphatase (NCBI) False
RSP_1459 RSP_1459 CDS None chromosome 1 45667 46413 + hypothetical protein (NCBI) False
RSP_1461 kdtA CDS None chromosome 1 46812 47999 + Putative 3-deoxy-D-manno-octulosonic-acid transferase (NCBI) False
RSP_1806 RSP_1806 CDS None chromosome 1 389587 392331 - aconitate hydratase (RefSeq) False
RSP_1994 gltA CDS None chromosome 1 590962 592248 - Citrate synthase (NCBI) False
RSP_2306 RSP_2306 CDS None chromosome 1 928696 929589 - putative HAD superfamily protein (NCBI) False
RSP_2845 RSP_2845 CDS None chromosome 1 1460728 1463199 + putative penicillin acylase (penicillin amidase) (NCBI) False
RSP_2910 RSP_2910 CDS None chromosome 1 1588532 1589698 - Predicted Metal-dependent amidase/aminoacylase/carboxypeptidase (NCBI) False
RSP_2912 RSP_2912 CDS None chromosome 1 1589910 1590716 + Predicted pyrophosphatase (NCBI) False
RSP_3230 RSP_3230 CDS None chromosome 2 289081 289290 - hypothetical protein (NCBI) False
RSP_3231 RSP_3231 CDS None chromosome 2 289521 291119 + ABC peptide transporter, periplasmic binding protein (NCBI) False
RSP_3232 RSP_3232 CDS None chromosome 2 291187 292194 + ABC peptide transporter, inner membrane subunit (NCBI) False
RSP_3233 RSP_3233 CDS None chromosome 2 292202 293104 + ABC peptide transporter, inner membrane subunit (NCBI) False
RSP_3235 RSP_3235 CDS None chromosome 2 293109 293957 + ABC peptide transporter, ATPase subunit (NCBI) False
RSP_3236 RSP_3236 CDS None chromosome 2 293957 294805 + ABC peptide transporter, ATPase subunit (NCBI) False
RSP_3328 RSP_3328 CDS None chromosome 2 391400 392311 - hypothetical protein (NCBI) False
RSP_3716 selD CDS None chromosome 2 838858 839913 + selenide, water dikinase (selenophosphate synthetase) (NCBI) False
RSP_3749 ampC CDS None chromosome 2 874559 875701 + putative beta-lactamase precursor (NCBI) False
RSP_3822 RSP_3822 CDS None chromosome 2 17904 18932 + GTP1/OBG family 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 279

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.