Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 311 Profile

GeneModule member RegulatorRegulator MotifMotif
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 311

There are 16 regulatory influences for Module 311

Regulator Table (16)
Regulator Name Type
RSP_0443 tf
RSP_0623 tf
RSP_1231 tf
RSP_2850 tf
RSP_3433 tf
RSP_3238 tf
RSP_3664 tf
RSP_1712 tf
RSP_2801 tf
RSP_0386 tf
RSP_1163 tf
RSP_2494 tf
RSP_1741 tf
RSP_1739 tf
RSP_3665 tf
RSP_2533 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
8336 8.50e-01 CcTTCGCGCCCCGgTtTCacaGga
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8337 3.90e+01 AcTcAAC.GaA.CGGccttCCtgt
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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 311 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Nucleotide Metabolism kegg subcategory 2.98e-03 1.21e-02 3/25
Pyrimidine metabolism kegg pathway 2.06e-04 2.07e-03 3/25

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Protein synthesis tigr mainrole 4.73e-03 6.57e-03 3/25

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Information storage and processing cog category 2.65e-02 4.06e-02 6/25
Metabolism cog category 6.76e-03 1.11e-02 14/25
Translation, ribosomal structure and biogenesis cog subcategory 4.65e-04 9.15e-04 5/25
Nucleotide transport and metabolism cog subcategory 1.37e-03 2.44e-03 3/25
Inorganic ion transport and metabolism cog subcategory 1.11e-04 2.65e-04 6/25
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 311

There are 25 genes in Module 311

Gene Member Table (25)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0164 RSP_0164 CDS None chromosome 1 1881031 1881285 - hypothetical protein (NCBI) False
RSP_0248 RSP_0248 CDS None chromosome 1 1972274 1972837 - elongation factor EF-P (NCBI) False
RSP_0425 metG CDS None chromosome 1 2156707 2158425 + Methionyl-tRNA synthetase (NCBI) False
RSP_1197 HemH CDS None chromosome 1 2967945 2969078 + Ferrochelatase (NCBI) False
RSP_1404 RSP_1404 CDS None chromosome 1 3181030 3181797 - Orotidine 5'-phosphate decarboxylase (NCBI) False
RSP_1475 RSP_1475 CDS None chromosome 1 59750 60988 + saccharopine dehydrogenase family (NCBI) False
RSP_1926 RSP_1926 CDS None chromosome 1 523580 524521 + tRNA-Dihydrouridine synthase (NCBI) False
RSP_1929 pyrE CDS None chromosome 1 527494 528192 - Orotate phosphoribosyltransferase (NCBI) False
RSP_2144 cfaS CDS None chromosome 1 745971 747182 + Cyclopropane-fatty-acyl-phospholipid synthase CfaS (NCBI) False
RSP_2284 RSP_2284 CDS None chromosome 1 905665 906750 + Histidinol-phosphate aminotransferase (NCBI) False
RSP_2696 RSP_2696 CDS None chromosome 1 1341579 1343417 + ABC transporter, fused ATPase and inner membrane subunits (NCBI) False
RSP_2717 RSP_2717 CDS None chromosome 1 1366799 1368622 + putative UUP ATPase (NCBI) False
RSP_2977 prfB CDS None chromosome 1 1664604 1665731 - Peptide chain release factor 2 (NCBI) False
RSP_2980 aspAT CDS None chromosome 1 1669765 1670916 - Putative aspartate aminotransferase A (NCBI) False
RSP_2981 RSP_2981 CDS None chromosome 1 1671084 1671827 + Putative protein-disulfide isomerase (NCBI) False
RSP_3045 dorR CDS None chromosome 2 80695 81393 - DMSO/TMAO-two component transcriptional regulator, winged helix family (NCBI) False
RSP_3547 RSP_3547 CDS None chromosome 2 636449 638716 - Ribonucleotide reductase (NCBI) False
RSP_3600 miaB CDS None chromosome 2 692968 694278 - MiaB tRNA modification protein (Radical SAM) (NCBI) False
RSP_3710 RSP_3710 CDS None chromosome 2 832475 832921 - Monovalent cation/proton antiporter subunit/mnhG (NCBI) False
RSP_3711 RSP_3711 CDS None chromosome 2 832918 833199 - Multisubunit Na+/H+ antiporter MnhF subunit (NCBI) False
RSP_3712 RSP_3712 CDS None chromosome 2 833196 833684 - Multisubunit Na+/H+ antiporter MnhE subunit (NCBI) False
RSP_3713 RSP_3713 CDS None chromosome 2 833681 835303 - pH adaptation potassium efflux system, phaD subunit (NCBI) False
RSP_3714 RSP_3714 CDS None chromosome 2 835300 835644 - pH adaption potassium efflux system, phaC subunit (NCBI) False
RSP_3715 RSP_3715 CDS None chromosome 2 835644 838538 - pH adaption potassium efflux system, PhaB subunit (NCBI) False
RSP_3716 selD CDS None chromosome 2 838858 839913 + selenide, water dikinase (selenophosphate synthetase) (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.

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.